bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of global inhibitors of cellular glycosylation
Authors: Sørensen Daniel Madriz , Büll Christian , Madsen Thomas D. , Lira-Navarrete Erandi , Clausen Thomas Mandel , Clark Alex E. , Garretson Aaron F. , Karlsson Richard , Pijnenborg Johan F. A. , Yin Xin , Miller Rebecca L. , Chanda Sumit K. , Boltje Thomas J. , Schjoldager Katrine T. , Vakhrushev Sergey Y. , Halim Adnan , Esko Jeffrey D. , Carlin Aaron F. , Hurtado-Guerrero Ramon , Weigert Roberto , Clausen Henrik , Narimatsu Yoshiki
Published: February 2023

Small molecule inhibitors of glycosylation enzymes are valuable tools for dissecting glycan functions and potential drug candidates. Screening for inhibitors of glycosyltransferases are mainly performed by in vitro enzyme assays with difficulties moving candidates to cells and animals. Here, we circumvent this by employing a cell-based screening assay using glycoengineered cells expressing tailored reporter glycoproteins. We focused on GalNAc-type O-glycosylation and selected the GalNAc-T11 isoenzyme that selectively glycosylates endocytic low-density lipoprotein receptor (LDLR)-related proteins as targets. Our screen of a limited small molecule compound library did not identify selective inhibitors of GalNAc-T11, however, we identify two compounds that broadly inhibited Golgi-localized glycosylation processes. These compounds mediate the reversible fragmentation of the Golgi system without affecting secretion. We demonstrate how these inhibitors can be used to manipulate glycosylation in cells to induce expression of truncated O-glycans and augment binding of cancer-specific Tn-glycoprotein antibodies and to inhibit expression of heparan sulfate and binding and infection of SARS-CoV-2.
Quantum Rabi dynamics of trapped atoms far in the deep strong coupling regime
Authors: Koch Johannes , Hunanyan Geram R. , Ockenfels Till , Rico Enrique , Solano Enrique , Weitz Martin
Published: February 2023

The coupling of a two-level system with an electromagnetic field, whose fully quantized version is the quantum Rabi model, is among the central topics of quantum physics. When the coupling strength becomes large enough that the field mode frequency is reached, the deep strong coupling regime is approached, and excitations can be created from the vacuum. Here we demonstrate a periodic variant of the quantum Rabi model in which the two-level system is encoded in the Bloch band structure of cold rubidium atoms in optical potentials. With this method we achieve a Rabi coupling strength of 6.5 times the field mode frequency, which is far in the deep strong coupling regime, and observe a subcycle timescale raise in bosonic field mode excitations. In a measurement recorded in the basis of the coupling term of the quantum Rabi Hamiltonian, a freezing of dynamics is revealed for small frequency splittings of the two-level system, as expected when the coupling term dominates over all other energy scales, and a revival for larger splittings. Our work demonstrates a route to realize quantum-engineering applications in yet unexplored parameter regimes.
Accurate descriptions of molecule-surface interactions in electrocatalytic CO2 reduction on the copper surfaces
Authors: Chen Zheng , Liu Zhangyun , Xu Xin
Published: February 2023

Copper-based catalysts play a pivotal role in many industrial processes and hold a great promise for electrocatalytic CO2 reduction reaction into valuable chemicals and fuels. Towards the rational design of catalysts, the growing demand on theoretical study is seriously at odds with the low accuracy of the most widely used functionals of generalized gradient approximation. Here, we present results using a hybrid scheme that combines the doubly hybrid XYG3 functional and the periodic generalized gradient approximation, whose accuracy is validated against an experimental set on copper surfaces. A near chemical accuracy is established for this set, which, in turn, leads to a substantial improvement for the calculated equilibrium and onset potentials as against the experimental values for CO2 reduction to CO on Cu(111) and Cu(100) electrodes. We anticipate that the easy use of the hybrid scheme will boost the predictive power for accurate descriptions of molecule-surface interactions in heterogeneous catalysis.
Impact of host genetic polymorphisms on response to inactivated influenza vaccine in children
Authors: Tsang Tim K. , Wang Can , Tsang Nicole N. Y. , Fang Vicky J. , Perera Ranawaka A. P. M. , Malik Peiris J. S. , Leung Gabriel M. , Cowling Benjamin J. , Ip Dennis K. M.
Published: February 2023

In randomized controlled trials of influenza vaccination, 550 children received trivalent-inactivated influenza vaccine, permitting us to explore relationship between vaccine response and host single nucleotide polymorphisms (SNPs) in 23 candidate genes with adjustment of multiple testing. For host SNPs in TLR7–1817G/T (rs5741880), genotype GT was associated with lower odds (OR: 0.22, 95% CI: 0.09, 0.53) of have post-vaccination hemagglutination-inhibiting (HAI) titers ≥40, compared with genotype GG and TT combined under the over-dominant model. For host SNPs in TLR8–129G/C (rs3764879), genotype GT was associated with lower odds (OR: 0.47; 95% CI: 0.28, 0.80) of have post vaccination HAI titers ≥40 compared with genotype GG and AA combined under the over-dominant model. Our results could contribute to the development of better vaccines that may offer improved protection to all recipients.
The determinants of household water consumption: A review and assessment framework for research and practice
Authors: Cominola A. , Preiss L. , Thyer M. , Maier H. R. , Prevos P. , Stewart R. A. , Castelletti A.
Published: February 2023

Achieving a thorough understanding of the determinants of household water consumption is crucial to support demand management strategies. Yet, existing research on household water consumption determinants is often limited to specific case studies, with findings that are difficult to generalize and not conclusive. Here, we first contribute an updated framework for review, classification, and analysis of the literature on the determinants of household water consumption. Our framework allows trade-off analysis of different criteria that account for the representation of a potential water consumption determinant in the literature, its impact across heterogeneous case studies, and the effort required to collect information on it. We then review a comprehensive set of 48 publications with our proposed framework. The results of our trade-off analysis show that distinct groups of determinants exist, allowing for the formulation of recommendations for practitioners and researchers on which determinants to consider in practice and prioritize in future research.
Antarctic shelf ocean warming and sea ice melt affected by projected El Niño changes
Authors: Cai Wenju , Jia Fan , Li Shujun , Purich Ariaan , Wang Guojian , Wu Lixin , Gan Bolan , Santoso Agus , Geng Tao , Ng Benjamin , Yang Yun , Ferreira David , Meehl Gerald A. , McPhaden Michael J.
Published: February 2023

Antarctic shelf ocean warming affects melt of ice shelf/sheets and sea ice but projected changes vary vastly across climate models. A projected increase in El Niño variability has been found to slow future mid-latitude Southern Ocean warming but how this impacts the Antarctic shelf ocean is unknown. Here we show that a projected increase in El Niño variability accelerates Antarctic shelf ocean warming, hastening ice shelf/sheet melt but slowing sea ice reduction.
A meta-analysis of genetic effects associated with neurodevelopmental disorders and co-occurring conditions
Authors: Gidziela Agnieszka , Ahmadzadeh Yasmin I. , Michelini Giorgia , Allegrini Andrea G. , Agnew-Blais Jessica , Lau Lok Yan , Duret Megan , Procopio Francesca , Daly Emily , Ronald Angelica , Rimfeld Kaili , Malanchini Margherita
Published: February 2023

A systematic understanding of the aetiology of neurodevelopmental disorders (NDDs) and their co-occurrence with other conditions during childhood and adolescence remains incomplete. In the current meta-analysis, we synthesized the literature on (1) the contribution of genetic and environmental factors to NDDs, (2) the genetic and environmental overlap between different NDDs, and (3) the co-occurrence between NDDs and disruptive, impulse control and conduct disorders (DICCs). Searches were conducted across three platforms: Web of Science, Ovid Medline and Ovid Embase. Studies were included only if 75% or more of the sample consisted of children and/or adolescents and the studies had measured the aetiology of NDDs and DICCs using single-generation family designs or genomic methods. Studies that had selected participants on the basis of unrelated diagnoses or injuries were excluded. We performed multilevel, random-effects meta-analyses on 296 independent studies, including over four million (partly overlapping) individuals. We further explored developmental trajectories and the moderating roles of gender, measurement, geography and ancestry. We found all NDDs to be substantially heritable (family-based heritability, 0.66 (s.e. = 0.03); SNP heritability, 0.19 (s.e. = 0.03)). Meta-analytic genetic correlations between NDDs were moderate (grand family-based genetic correlation, 0.36 (s.e. = 0.12); grand SNP-based genetic correlation, 0.39 (s.e. = 0.19)) but differed substantially between pairs of disorders. The genetic overlap between NDDs and DICCs was strong (grand family-based genetic correlation, 0.62 (s.e. = 0.20)). While our work provides evidence to inform and potentially guide clinical and educational diagnostic procedures and practice, it also highlights the imbalance in the research effort that has characterized developmental genetics research.
A longitudinal microstructural MRI dataset in healthy C57Bl/6 mice at 9.4 Tesla
Authors: Rahman Naila , Xu Kathy , Budde Matthew D. , Brown Arthur , Baron Corey A.
Published: February 2023

Multimodal microstructural MRI has shown increased sensitivity and specificity to changes in various brain disease and injury models in the preclinical setting. Here, we present an in vivo longitudinal dataset, including a subset of ex vivo data, acquired as control data and to investigate microstructural changes in the healthy mouse brain. The dataset consists of structural T2-weighted imaging, magnetization transfer ratio and saturation imaging, and advanced quantitative diffusion MRI (dMRI) methods. The dMRI methods include oscillating gradient spin echo (OGSE) dMRI and microscopic anisotropy (μA) dMRI, which provide additional insight by increasing sensitivity to smaller spatial scales and disentangling fiber orientation dispersion from true microstructural changes, respectively. The technical skills required to analyze microstructural MRI data are complex and include MRI sequence development, acquisition, and computational neuroimaging expertise. Here, we share unprocessed and preprocessed data, and scalar maps of quantitative MRI metrics. We envision utility of this dataset in the microstructural MRI field to develop and test biophysical models, methods that model temporal brain dynamics, and registration and preprocessing pipelines.
Individual structure mapping over six million trees for New York City USA
Authors: Ma Qin , Lin Jian , Ju Yang , Li Wenkai , Liang Lu , Guo Qinghua
Published: February 2023

Individual tree structure mapping in cities is important for urban environmental studies. Despite mapping products for tree canopy cover and biomass are reported at multiple spatial scales using various approaches, spatially explicit mapping of individual trees and their three-dimensional structure is sparse. Here we produced an individual tree dataset including tree locations, height, crown area, crown volume, and biomass over the entire New York City, USA for 6,005,690 trees. Individual trees were detected and mapped from remotely sensed datasets along with their height and crown size information. Tree biomass in 296 field plots was measured and modelled using i-Tree Eco. Wall-to-wall tree biomass was mapped using relationships between field measurements and remotely sensed datasets and downscaled to individual trees. Validation using field-plot measurements indicated that our mapping products overestimated tree number, mean tree height and maximum tree height by 11.1%, 8.6%, and 5.3%, respectively. These overestimations were mainly due to the spatial and temporal mis-match between field measurements and remote sensing observations and uncertainties in tree segmentation algorithms. This dataset enables the evaluation of urban forest ecosystem services including regulating urban heat and promoting urban health, which can provide valuable insights for urban forest management and policy making.
Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa)
Authors: Xia Hui , Deng Honghong , Li Mingzhang , Xie Yue , Lin Lijin , Zhang Huifen , Luo Xian , Lv Xiulan , Wang Jin , Liang Dong
Published: February 2023

The most commercialized kiwifruit, Actinidia chinensis var. deliciosa (Acd), is an allohexaploid (2n = 6x = 174), making high-quality assemblage genome challenging. We previously discovered a rare naturally occurring diploid Acd plant. Here, chromosome-level de novo genome assembly for this diploid Acd was reported, reaching approximately 621.98 Mb in length with contig and scaffold N50 values of 10.08 and 21.09 Mb, respectively, 99.66% of the bases anchored to 29 pseudochromosomes, and 38,990 protein-coding genes and 42.29% repetitive elements annotated. The divergence time of A. chinensis cv. ‘Red5’ and ‘Hongyang’ (11.1–27.7 mya) was more recent compared with the divergence time of them and Acd (19.9–41.2 mya), with the divergence time of A. eriantha cv. ‘White’ being the earliest (22.9–45.7 mya) among that of the four Actinidia species. The 4DTv distance distribution highlighted three recent whole-genome duplication events in Acd. This is the first high-quality diploid Acd genome, which lays an important foundation for not only kiwifruit functional genomics studies but also further elucidating genome evolution of allohexaploid Acd.
The necessity of incorporating non-genetic risk factors into polygenic risk score models
Authors: van Dam Sipko , Folkertsma Pytrik , Castela Forte Jose , de Vries Dylan H. , Herrera Cunillera Camila , Gannamani Rahul , Wolffenbuttel Bruce H. R.
Published: February 2023

The growing public interest in genetic risk scores for various health conditions can be harnessed to inspire preventive health action. However, current commercially available genetic risk scores can be deceiving as they do not consider other, easily attainable risk factors, such as sex, BMI, age, smoking habits, parental disease status and physical activity. Recent scientific literature shows that adding these factors can improve PGS based predictions significantly. However, implementation of existing PGS based models that also consider these factors requires reference data based on a specific genotyping chip, which is not always available. In this paper, we offer a method naïve to the genotyping chip used. We train these models using the UK Biobank data and test these externally in the Lifelines cohort. We show improved performance at identifying the 10% most at-risk individuals for type 2 diabetes (T2D) and coronary artery disease (CAD) by including common risk factors. Incidence in the highest risk group increases from 3.0- and 4.0-fold to 5.8 for T2D, when comparing the genetics-based model, common risk factor-based model and combined model, respectively. Similarly, we observe an increase from 2.4- and 3.0-fold to 4.7-fold risk for CAD. As such, we conclude that it is paramount that these additional variables are considered when reporting risk, unlike current practice with current available genetic tests.
Circular active noise barrier using theoretical control filter considering interaction between speaker and barrier
Authors: Lee Sanghyeon , Park Youngjin
Published: February 2023

A circular active noise barrier using a theoretically calculated control filter without real-time adaptation was proposed for noise reduction in a specific outdoor space. A compact circular barrier is used for the movable system to cope with changes in the location of the workspace, and noise in a wide frequency band can be reduced by conducting active noise control through control speakers arranged around a barrier. However, there was a significant performance gap compared with the maximum performance achieved by using the experimental fixed filter due to an extremely simplified theoretical model which ignores the interaction between the control speakers and the barrier. Therefore, this study tried to minimize the performance degradation when applying the theoretically calculated control filter. Another theoretical model is introduced to improve the noise reduction performance by considering the interaction between the control speaker and the barrier. Through experiment, it is confirmed that noise reduction performance is improved by about 2.6 dB in the frequency of interest.
The association of ODF4 with AK1 and AK2 in mice is essential for fertility through its contribution to flagellar shape
Authors: Ito Chizuru , Makino Tsukasa , Mutoh Tohru , Kikkawa Masahide , Toshimori Kiyotaka
Published: February 2023

Normal sperm flagellar shape and movement are essential for fertilization. The integral protein outer dense fiber 4 (ODF4) localizes to ODFs, but its function remains unclear. Adenylate kinase (AK) is a phosphotransferase that catalyzes the interconversion and controls the concentration equilibrium of adenine nucleotides. AK shuttles ATP to energy-consuming sites. Here, we report on the relationship of flagellar shape and movement with ODF4, AK1 and AK2 by using Odf4-deletion (Odf4−/−) mice. Soluble ODF4 is coimmunoprecipitated with AK1 and AK2 in Odf4+/+ spermatozoa. ODF4, AK1 and AK2 localize to whole flagella (plasmalemma, mitochondria, ODFs, and residual cytoplasmic droplets (CDs)), principal pieces, and midpieces, respectively. Odf4−/− sperm flagella lose ODF4 and reduce AK1 and AK2 but produce ATP. The flagellum is bent (hairpin flagellum) with a large CD in the midpiece. There is no motility in the midpiece, but the principal piece is motile. Odf4−/− spermatozoa progress backward and fail to ascend in the uterus. Thus, Odf4−/− males are infertile owing to abnormal flagellar shape and movement caused mainly by the loss of ODF4 with AK1 and AK2. This study is supported by the rescue experiment; the abnormalities and male infertility caused by Odf4 deletion were reversed by Odf4 restoration.
Full-visibility 3D imaging of oxygenation and blood flow by simultaneous multispectral photoacoustic fluctuation imaging (MS-PAFI) and ultrasound Doppler
Authors: Godefroy Guillaume , Arnal Bastien , Bossy Emmanuel
Published: February 2023

We present a method and setup that provide complementary three-dimensional (3D) images of blood oxygenation (via quantitative photoacoustic imaging) and blood flow dynamics (via ultrasound Doppler). The proposed approach is label-free and exploits blood-induced fluctuations, and is implemented on a sparse array with only 256 elements, driven with a commercially available ultrasound electronics. We first implement 3D photoacoustic fluctuation imaging (PAFI) to image chicken embryo, and obtain full-visibility images of the vascular morphology. We obtain simultaneously 3D ultrasound power Doppler with a comparable image quality. We then introduce multispectral photoacoustic fluctuation imaging (MS-PAFI), and demonstrate that it can provide quantitative measurements of the absorbed optical energy density with full visibility and enhanced contrast, as compared to conventional delay-and-sum multispectral photoacoustic imaging. We finally showcase the synergy and complementarity between MS-PAFI, which provides 3D quantitative oxygenation (SO$$_2$$

2

) imaging, and 3D ultrasound Doppler, which provides quantitative information on blood flow dynamics. MS-PAFI represents a promising alternative to model-based inversions with the advantage of resolving all the visibility artefacts without prior and regularization, by use of a straightforward processing scheme.
Symplectic encoders for physics-constrained variational dynamics inference
Authors: Bacsa Kiran , Lai Zhilu , Liu Wei , Todd Michael , Chatzi Eleni
Published: February 2023

We propose a new variational autoencoder (VAE) with physical constraints capable of learning the dynamics of Multiple Degree of Freedom (MDOF) dynamic systems. Standard variational autoencoders place greater emphasis on compression than interpretability regarding the learned latent space. We propose a new type of encoder, based on the recently developed Hamiltonian Neural Networks, to impose symplectic constraints on the inferred a posteriori distribution. In addition to delivering robust trajectory predictions under noisy conditions, our model is capable of learning an energy-preserving latent representation of the system. This offers new perspectives for the application of physics-informed neural networks on engineering problems linked to dynamics.
In silico assessment on TdP risks of drug combinations under CiPA paradigm
Authors: Qauli Ali Ikhsanul , Marcellinus Aroli , Setiawan Muhammad Aldo , Zain Andi Faiz Naufal , Pinandito Azka Muhammad , Lim Ki Moo
Published: February 2023

Researchers have recently proposed the Comprehensive In-vitro Proarrhythmia Assay (CiPA) to analyze medicines’ TdP risks. Using the TdP metric known as qNet, numerous single-drug effects have been studied to classify the medications as low, intermediate, and high-risk. Furthermore, multiple medication therapies are recognized as a potential method for curing patients, mainly when limited drugs are available. This work expands the TdP risk assessment of drugs by introducing a CiPA-based in silico analysis of the TdP risk of combined drugs. The cardiac cell model was simulated using the population of models approach incorporating drug-drug interactions (DDIs) models on several ion channels for various drug pairs. Action potential duration (APD90), qNet, and calcium duration (CaD90) were computed and analyzed as biomarker features. The drug combination maps were also used to illustrate combined medicines' TdP risk. We found that the combined drugs alter cell responses in terms of biomarkers such as APD90, qNet, and CaD90 in a highly nonlinear manner. The results also revealed that combinations of high-risk with low-risk and intermediate-risk with low-risk drugs could result in compounds with varying TdP risks depending on the drug concentrations.
Identifying inhibitors of β-haematin formation with activity against chloroquine-resistant Plasmodium falciparum malaria parasites via virtual screening approaches
Authors: Amod Leah , Mohunlal Roxanne , Teixeira Nicole , Egan Timothy J. , Wicht Kathryn J.
Published: February 2023

The biomineral haemozoin, or its synthetic analogue β-haematin (βH), has been the focus of several target-based screens for activity against Plasmodium falciparum parasites. Together with the known βH crystal structure, the availability of this screening data makes the target amenable to both structure-based and ligand-based virtual screening. In this study, molecular docking and machine learning techniques, including Bayesian and support vector machine classifiers, were used in sequence to screen the in silico ChemDiv 300k Representative Compounds library for inhibitors of βH with retained activity against P. falciparum. We commercially obtained and tested a prioritised set of inhibitors and identified the coumarin and iminodipyridinopyrimidine chemotypes as potent in vitro inhibitors of βH and whole cell parasite growth.
Deep learning ensemble 2D CNN approach towards the detection of lung cancer
Authors: Shah Asghar Ali , Malik Hafiz Abid Mahmood , Muhammad AbdulHafeez , Alourani Abdullah , Butt Zaeem Arif
Published: February 2023

In recent times, deep learning has emerged as a great resource to help research in medical sciences. A lot of work has been done with the help of computer science to expose and predict different diseases in human beings. This research uses the Deep Learning algorithm Convolutional Neural Network (CNN) to detect a Lung Nodule, which can be cancerous, from different CT Scan images given to the model. For this work, an Ensemble approach has been developed to address the issue of Lung Nodule Detection. Instead of using only one Deep Learning model, we combined the performance of two or more CNNs so they could perform and predict the outcome with more accuracy. The LUNA 16 Grand challenge dataset has been utilized, which is available online on their website. The dataset consists of a CT scan with annotations that better understand the data and information about each CT scan. Deep Learning works the same way our brain neurons work; therefore, deep learning is based on Artificial Neural Networks. An extensive CT scan dataset is collected to train the deep learning model. CNNs are prepared using the data set to classify cancerous and non-cancerous images. A set of training, validation, and testing datasets is developed, which is used by our Deep Ensemble 2D CNN. Deep Ensemble 2D CNN consists of three different CNNs with different layers, kernels, and pooling techniques. Our Deep Ensemble 2D CNN gave us a great result with 95% combined accuracy, which is higher than the baseline method.
Network evolution of regional brain volumes in young children reflects neurocognitive scores and mother’s education
Authors: Zhou Yidong , Müller Hans-Georg , Zhu Changbo , Chen Yaqing , Wang Jane-Ling , O’Muircheartaigh Jonathan , Bruchhage Muriel , Deoni Sean ,   RESONANCE Consortium, Braun Joseph , Bruchhage Muriel , Carnell Susan , Deoni Sean , D’Sa Viren , Huentelman Matthew , Klepac-Ceraj Vanja , LeBourgeois Monique , Müller Hans-Georg , O’Muircheartaigh Jonathan , Wang Jane-Ling
Published: February 2023

The maturation of regional brain volumes from birth to preadolescence is a critical developmental process that underlies emerging brain structural connectivity and function. Regulated by genes and environment, the coordinated growth of different brain regions plays an important role in cognitive development. Current knowledge about structural network evolution is limited, partly due to the sparse and irregular nature of most longitudinal neuroimaging data. In particular, it is unknown how factors such as mother’s education or sex of the child impact the structural network evolution. To address this issue, we propose a method to construct evolving structural networks and study how the evolving connections among brain regions as reflected at the network level are related to maternal education and biological sex of the child and also how they are associated with cognitive development. Our methodology is based on applying local Fréchet regression to longitudinal neuroimaging data acquired from the RESONANCE cohort, a cohort of healthy children (245 females and 309 males) ranging in age from 9 weeks to 10 years. Our findings reveal that sustained highly coordinated volume growth across brain regions is associated with lower maternal education and lower cognitive development. This suggests that higher neurocognitive performance levels in children are associated with increased variability of regional growth patterns as children age.
Itinerant-localized dichotomy in magnetic anisotropic properties of U-based ferromagnets
Authors: Shick Alexander B. , Halevy Itzhak , Tchaplianka Maxim , Legut Dominik
Published: February 2023

The electronic structure, spin and orbital magnetic moments, and the magnetic anisotropy energy in selected U-based compounds are investigated making use of the correlated band theory. First, we demonstrate that the LSDA+U approach with exact atomic limit implemented as a combination of the relativistic density functional theory with the Anderson impurity model provides a good quantitative description for UGa$${}_2$$

2

. Further, the method is applied to UFe$$_{12}$$

12

and UFe$${}_{10}$$

10

Si$${}_2$$

2

ferromagnets. The calculated positive uniaxial magnetic anisotropy together with negative enthalpy of formation for UFe$${}_{10}$$

10

Si$${}_2$$

2

make it as a candidate for the magnetically hard materials. Our studies suggest a viable route for further development of the rare-earth-lean permanent magnets by replacing a part of U atoms by some rare-earth like Sm in UFe$${}_{10}$$

10

Si$${}_2$$

2

.
Computational investigation of IP3 diffusion
Authors: Ornelas-Guevara Roberto , Gil Diana , Voorsluijs Valérie , Dupont Geneviève
Published: February 2023

Inositol 1,4,5-trisphosphate (IP3) plays a key role in calcium signaling. After stimulation, it diffuses from the plasma membrane where it is produced to the endoplasmic reticulum where its receptors are localized. Based on in vitro measurements, IP3 was long thought to be a global messenger characterized by a diffusion coefficient of ~ 280 μm2s−1. However, in vivo observations revealed that this value does not match with the timing of localized Ca2+ increases induced by the confined release of a non-metabolizable IP3 analog. A theoretical analysis of these data concluded that in intact cells diffusion of IP3 is strongly hindered, leading to a 30-fold reduction of the diffusion coefficient. Here, we performed a new computational analysis of the same observations using a stochastic model of Ca2+ puffs. Our simulations concluded that the value of the effective IP3 diffusion coefficient is close to 100 μm2s−1. Such moderate reduction with respect to in vitro estimations quantitatively agrees with a buffering effect by non-fully bound inactive IP3 receptors. The model also reveals that IP3 spreading is not much affected by the endoplasmic reticulum, which represents an obstacle to the free displacement of molecules, but can be significantly increased in cells displaying elongated, 1-dimensional like geometries.
Controllable Hartman effect by vortex beam in a one dimensional photonic crystal doped by graphene quantum dots
Authors: Kevin Saeideh , Sahrai Mostafa , Asadpour Seyyed Hossein
Published: February 2023

The Hartman effect is studied in a one dimensional photonic crystal doped with graphene quantum dots. It is shown that the Hartman effect can be switched from negative to positive by increasing the Rabi-frequency of the controlling field and also by manipulating the relative phase of the applied fields. The effect of the vortex beam on the Hartman effect is also presented. We show that the orbital angular momentum (OAM) and the azimuthal phase of the vortex beam do not affect the probe filed transmission while they change the Hartman effect from positive to negative.
Risk factors for stroke among anthropometric indices and lipid profiles in the Korean population: a large-scale cross-sectional study
Authors: Yim Mi Hong , Jeon Young Ju , Lee Bum Ju
Published: February 2023

Stroke is strongly associated with death and disability. However, the associations between stroke and lipid profiles such as total cholesterol, triglycerides, high-density lipoprotein cholesterol (HDL-C), and red blood cells (RBCs) and anthropometric indices such as waist circumference and waist-to-height ratio (WHtR) remain unclear. The objective of this study was to investigate these relationships in a Korean population. This large-scale cross-sectional study included data from 38,190 subjects collected from 2010 to 2018 by the Korea National Health and Nutrition Examination Survey (KNHANES). Simple logistic regression models and multiple logistic regression models were used to evaluate the association of stroke with lipid profiles and anthropometric indices in the crude model, adjusted Model 1, and fully adjusted Model 2. In men, stroke was negatively associated with height, weight, and hematocrit level. Total cholesterol and triglycerides were strongly negatively associated with stroke in Model 2. Creatinine level and stroke were weakly associated. Additionally, height, weight, total cholesterol, triglycerides, and hematocrit and creatinine levels were associated with stroke both before and after adjustment. In women, in Model 2, stroke was positively associated with height, weight, and creatinine level. A strong negative association was found between total cholesterol and stroke. Stroke was negatively associated with hemoglobin level, hematocrit level, and RBCs. Additionally, total cholesterol, hemoglobin level, hematocrit level, creatinine level, and RBCs were associated with stroke both before and after adjustment. Weight and height were more closely associated with stroke than waist circumference and WHtR in Korean men. Our results suggested that the association of stroke with triglycerides, height, and weight differed according to sex and that HDL-C was not associated with stroke in people of either sex.
Optimizing the operation strategy of a combined cooling, heating and power system based on energy storage technology
Authors: Zhang Yu , Deng Yan , Zheng Zimin , Yao Yao , Liu Yicai
Published: February 2023

Energy storage technology is the key to achieving a carbon emission policy. The purpose of the paper is to improve the overall performance of the combined cooling, heating and power-ground source heat pump (CCHP-GSHP) system by the battery. A new operation strategy (the two-point operation) is proposed by controlling the power generation unit work. The power generation unit has two operation modes of non-operation and rated efficiency operation by the storage electricity battery. The new operation strategy is compared with the traditional CCHP-GSHP that without a battery. The optimization goals include the primary energy saving ratio, the reduction ratio of carbon dioxide emissions, and the annual total cost saving ratio. The independent GSHP system is used as a reference system. Multipopulation genetic algorithms are selected to achieve the problem of optimization. A hotel building is selected for a case study. The optimal configuration of the coupling system is computed following the electric load strategy. Finally, the results show that the CCHP-GSHP system has a better performance under the new operation strategy compared with the traditional CCHP-GSHP (the primary energy saving ratio increases by 5.5%; the annual carbon dioxide emission reduction ratio increases by 1%; the annual total cost reduction ratio increases by 5.1%). This paper provides reference and suggestions for the integration and operation strategy of CCHP-GSHP in the future.
Isovists compactness and stairs as predictors of evacuation route choice
Authors: Snopková Dajana , De Cock Laure , Juřík Vojtěch , Kvarda Ondřej , Tancoš Martin , Herman Lukáš , Kubíček Petr
Published: February 2023

The building design is a crucial factor that can be actively adjusted and optimized to prevent human and property threats in emergency scenarios. Previous research suggests that specific building layouts may significantly influence human behaviour during evacuation. However, detailed empirical data about human behaviour in various types of buildings with different layouts are still missing and only marginal recommendations from this field are reflected in actual construction practice. In this study, desktop VR technologies were employed to study human decision-making in problematic T-intersections in the context of an emergency evacuation. More specifically, we studied fundamental attributes of buildings such as the width and length of the corridors and the presence of stairs to explore how they influence the choice of the evacuation route. The space-syntax isovist method was used to describe spatial parameters of corridors, which makes the results applicable to all buildings. Behavioural data from 208 respondents were analysed using multilevel regression models. Our results support previous claims concerning the importance of specific spatial layouts of evacuation corridors because respondents systematically chose wider and shorter corridors with visible staircases as the preferred evacuation route. The present findings further promote the ongoing discussion on the design of marked evacuation routes and building design that takes human factors into consideration.
Analysis of gaze patterns during facade inspection to understand inspector sense-making processes
Authors: Saleem Muhammad Rakeh , Mayne Robert , Napolitano Rebecca
Published: February 2023

This work seeks to capture how an expert interacts with a structure during a facade inspection so that more detailed and situationally-aware inspections can be done with autonomous robots in the future. Eye tracking maps where an inspector is looking during a structural inspection, and it recognizes implicit human attention. Experiments were performed on a facade during a damage assessment to analyze key, visually-based features that are important for understanding human-infrastructure interaction during the process. For data collection and analysis, experiments were conducted to assess an inspector’s behavioral changes while assessing a real structure. These eye tracking features provided the basis for the inspector’s intent prediction and were used to understand how humans interact with the structure during the inspection processes. This method will facilitate information-sharing and decision-making during the inspection processes for collaborative human-robot teams; thus, it will enable unmanned aerial vehicle (UAV) for future building inspection through artificial intelligence support.
A tool to enhance antimicrobial stewardship using similarity networks to identify antimicrobial resistance patterns across farms
Authors: Aguilar-Vega Cecilia , Scoglio Caterina , Clavijo María J. , Robbins Rebecca , Karriker Locke , Liu Xin , Martínez-López Beatriz
Published: February 2023

Antimicrobial resistance (AMR) is one of the major challenges of the century and should be addressed with a One Health approach. This study aimed to develop a tool that can provide a better understanding of AMR patterns and improve management practices in swine production systems to reduce its spread between farms. We generated similarity networks based on the phenotypic AMR pattern for each farm with information on important bacterial pathogens for swine farming based on the Euclidean distance. We included seven pathogens: Actinobacillus suis, Bordetella bronchiseptica, Escherichia coli, Glaesserella parasuis, Pasteurella multocida, Salmonella spp., and Streptococcus suis; and up to seventeen antibiotics from ten classes. A threshold criterion was developed to reduce the density of the networks and generate communities based on their AMR profiles. A total of 479 farms were included in the study although not all bacteria information was available on each farm. We observed significant differences in the morphology, number of nodes and characteristics of pathogen networks, as well as in the number of communities and susceptibility profiles of the pathogens to different antimicrobial drugs. The methodology presented here could be a useful tool to improve health management, biosecurity measures and prioritize interventions to reduce AMR spread in swine farming.
Presaccadic attention sharpens visual acuity
Authors: Kwak Yuna , Hanning Nina M. , Carrasco Marisa
Published: February 2023

Visual perception is limited by spatial resolution, the ability to discriminate fine details. Spatial resolution not only declines with eccentricity but also differs for polar angle locations around the visual field, also known as ‘performance fields'. To compensate for poor peripheral resolution, we make rapid eye movements—saccades—to bring peripheral objects into high-acuity foveal vision. Already before saccade onset, visual attention shifts to the saccade target location and prioritizes visual processing. Thispresaccadic shift of attentionimproves performance in many visual tasks, but whether it changes resolution is unknown. Here, we investigated whether presaccadic attention sharpens peripheral spatial resolution; and if so, whether such effect interacts with performance fields asymmetries. We measured acuity thresholds in an orientation discrimination task during fixation and saccade preparation around the visual field. The results revealed that presaccadic attention sharpens acuity, which can facilitate a smooth transition from peripheral to foveal representation. This acuity enhancement is similar across the four cardinal locations; thus, the typically robust effect of presaccadic attention does not change polar angle differences in resolution.
Diversification of the shell shape and size in Baikal Candonidae ostracods inferred from molecular phylogeny
Authors: Karanovic Ivana , Pham Huyen T. M. , Sitnikova Tatiana
Published: February 2023

Ostracod shells are used extensively in paleontology, but we know little about their evolution, especially in ancient lakes. Lake Baikal (LB) is the world’s most important stronghold of Candonidae diversity. These crustaceans radiated here rapidly (12–5 Ma) and with an unprecedented morphological diversity. We reconstruct their molecular phylogeny with 46 species and two markers (18S and 16S rRNA), and use it to estimate the evolution of the shell shape and size with landmark-based geometric morphometrics (LBGM). High posterior probabilities support four major clades, which differ in node depth and morphospace clustering. After removing a significant allometry, the first three principal components (PCs) describe about 88% of total variability, suggesting a strong integration. Reconstructed ancestral shapes are similar for all four clades, indicating that diversification happened after colonization. Major evolutionary changes occurred from trapezoidal to elongated shapes. Sister species are separated in morphospace, by centroid size, or both, as well as by vertical and horizontal distributions in LB. Ostracod shell is a strongly integrated structure that exhibits high evolvability, with some extreme shapes, although mostly along the first PC. This is the first study that combines molecular phylogeny and LBGM for ostracods and for any LB group.
Molecular mechanism of valine and its metabolite in improving triglyceride synthesis of porcine intestinal epithelial cells
Authors: Xu Mengmeng , Che Long , Niu Lizhu , Wang Liuzhen , Li Mengyun , Jiang Dongfeng , Deng Hongyu , Chen Wen , Jiang Zongyong
Published: February 2023

An insufficient energy supply to intestinal epithelial cells decreases production performance in weaned piglets. Triglycerides are the main energy source for intestinal epithelial cells in piglets. The present study aimed to investigate the effects and mechanisms of valine supplementation on triglyceride synthesis in porcine intestinal epithelial (IPEC-J2) cells. Valine supplementation in the medium significantly increased the content of triglycerides, fat droplets, and long-chain fatty acids (C17:0, C18:0, C20:0, C18:1, C20:1, and C22:1) (P < 0.05). Valine metabolite (3-hydroxyisobutyrate [3-HIB]) concentration increased significantly in the valine-supplemented group (P < 0.05). Silencing of the 3-HIB synthase enzyme 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) in IPEC-J2 cells significantly reduced the triglyceride concentration and lipid droplet synthesis. Further studies found that 3-HIB supplementation in the medium significantly increased the concentration of triglycerides, lipid droplets, and unsaturated fatty acids (C16:1, C18:1, C18:2, C18:3, C20:3, C20:4, and C20:5) (P < 0.05) by upregulating the expression of proteins involved in fatty acid transport (CD36) and fatty acid binding protein 3 (FABP3) or triglyceride synthesis (DGAT1) (P < 0.05), indicating that 3-HIB mediates valine-enhanced triglyceride synthesis in IPEC-J2 cells. In conclusion, our results demonstrated that valine enhanced triglyceride synthesis in IPEC-J2 cells via increasing the 3-HIB concentration, which may promote fatty acid transport via upregulation of proteins related to fatty acid transporter. These findings provide new insights into the mechanisms through which valine participates in lipid metabolism.
Insecticidal activity of essential oils from American native plants against Aedes aegypti (Diptera: Culicidae): an introduction to their possible mechanism of action
Authors: Duque Jonny E. , Urbina Diana L. , Vesga Luis C. , Ortiz-Rodríguez Luis A. , Vanegas Thomas S. , Stashenko Elena E. , Mendez-Sanchez Stelia C.
Published: February 2023

Searching for new bioactive molecules to design insecticides is a complex process since pesticides should be highly selective, active against the vector, and bio-safe for humans. Aiming to find natural compounds for mosquito control, we evaluated the insecticidal activity of essential oils (EOs) from 20 American native plants againstAedes aegyptilarvae using bioassay, biochemical, and in silico analyses. The highest larvicide activity was exhibited by EOs fromSteiractinia aspera(LC50 = 42.4 µg/mL),Turnera diffusa(LC50 = 70.9 µg/mL),Piper aduncum(LC50 = 55.8 µg/mL),Lippia origanoides(chemotype thymol/carvacrol) (LC50 = 61.9 µg/mL),L. origanoides(chemotype carvacrol/thymol) (LC50 = 59.8 µg/mL),Hyptis dilatata(LC50 = 61.1 µg/mL),Elaphandra quinquenervis(LC50 = 61.1 µg/mL), andCalycolpus moritzianus(LC50 = 73.29 µg/mL) after 24 h. This biological activity may be related to the disruption of the electron transport chain through the mitochondrial protein complexes. We hypothesized that the observed EOs' effect is due to their major components, where computational approaches such as homology modeling and molecular docking may suggest the possible binding pose of secondary metabolites that inhibit the mitochondrial enzymes and acetylcholinesterase activity (AChE). Our results provided insights into the possible mechanism of action of EOs and their major compounds for new insecticide designs targeting the mitochondria and AChE activity inA. aegyptifor effective and safe insecticide.
Long-term health-related quality of life after trauma with and without traumatic brain injury: a prospective cohort study
Authors: Kiwanuka Olivia , Lassarén Philipp , Thelin Eric P. , Hånell Anders , Sandblom Gabriel , Fagerdahl Ami , Boström Lennart
Published: February 2023

To purpose was to assess and compare the health-related quality of life (HRQoL) and risk of depression two years after trauma, between patients with and without traumatic brain injury (TBI) in a mixed Swedish trauma cohort. In this prospective cohort study, TBI and non-TBI trauma patients included in the Swedish Trauma registry 2019 at a level II trauma center in Stockholm, Sweden, were contacted two years after admission. HRQoL was assessed with RAND-36 and EQ-5D-3L, and depression with Montgomery Åsberg depression Rating Scale self-report (MADRS-S). Abbreviated Injury Score (AIS) head was used to grade TBI severity, and American Society of Anesthesiologists (ASA) score was used to assess comorbidities. Data were compared using Chi-squared test, Mann Whitney U test and ordered logistic regression, and Bonferroni correction was applied. A total of 170 of 737 eligible patients were included. TBI was associated with higher scores in 5/8 domains of RAND-36 and 3/5 domains of EQ-5D (p < 0.05). No significant difference in MADRS-S. An AIS (head) of three or higher was associated with lower scores in five domains of RAND-36 and two domains of EQ-5D but not for MADRS-S. An ASA-score of three was associated with lower scores in all domains of both RAND-36 (p < 0.05, except mental health) and EQ-5D (p < 0.001, except anxiety/depression), but not for MADRS-S. In conclusion, patients without TBI reported a lower HRQoL than TBI patients two years after trauma. TBI severity assessed according to AIS (head) was associated with HRQoL, and ASA-score was found to be a predictor of HRQoL, emphasizing the importance of considering pre-injury health status when assessing outcomes in TBI patients.