bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transition from a polaronic condensate to a degenerate Fermi gas of heteronuclear molecules
Authors: Duda Marcel , Chen Xing-Yan , Schindewolf Andreas , Bause Roman , von Milczewski Jonas , Schmidt Richard , Bloch Immanuel , Luo Xin-Yu 
Published: February 2023

AbstractThe interplay of quantum statistics and interactions in atomic Bose–Fermi mixtures leads to a phase diagram markedly different from pure fermionic or bosonic systems. However, investigating this phase diagram remains challenging when bosons condense due to the resulting fast interspecies loss. Here we report observations consistent with a phase transition from a polaronic to a molecular phase in a density-matched degenerate Bose–Fermi mixture. The condensate fraction, representing the order parameter of the transition, is depleted by interactions, and the build-up of strong correlations results in the emergence of a molecular Fermi gas. The features of the underlying quantum phase transition represent a new phenomenon complementary to the paradigmatic Bose–Einstein condensate/Bardeen–Cooper–Schrieffer crossover observed in Fermi systems. By driving the system through the transition, we produce a sample of sodium–potassium molecules exhibiting a large molecule-frame dipole moment in the quantum-degenerate regime.
Structural basis of efficacy-driven ligand selectivity at GPCRs
Authors: Powers Alexander S. , Pham Vi , Burger Wessel A. C. , Thompson Geoff , Laloudakis Yianni , Barnes Nicholas W. , Sexton Patrick M. , Paul Steven M. , Christopoulos Arthur , Thal David M. , Felder Christian C. , Valant Celine , Dror Ron O. 
Published: February 2023

AbstractA drug’s selectivity for target receptors is essential to its therapeutic utility, but achieving selectivity between similar receptors is challenging. The serendipitous discovery of ligands that stimulate target receptors more strongly than closely related receptors, despite binding with similar affinities, suggests a solution. The molecular mechanism of such ‘efficacy-driven selectivity’ has remained unclear, however, hindering design of such ligands. Here, using atomic-level simulations, we reveal the structural basis for the efficacy-driven selectivity of a long-studied clinical drug candidate, xanomeline, between closely related muscarinic acetylcholine receptors (mAChRs). Xanomeline’s binding mode is similar across mAChRs in their inactive states but differs between mAChRs in their active states, with divergent effects on active-state stability. We validate this mechanism experimentally and use it to design ligands with altered efficacy-driven selectivity. Our results suggest strategies for the rational design of ligands that achieve efficacy-driven selectivity for many pharmaceutically important G-protein-coupled receptors.
Ki67 increase after core needle biopsy associated with worse disease outcome in HER2-negative breast cancer patients
Authors: Tong Yiwei , Dai Jiangfeng , Huang Jiahui , Fei Xiaochun , Shen Kunwei , Liu Qingmeng , Chen Xiaosong 
Published: February 2023

AbstractKi67 would change after core needle biopsy (CNB) in invasive breast cancer. However, whether Ki67 alteration (ΔKi67) influences disease outcomes remains unclear. Here we aim to evaluate the prognostic value of ΔKi67. Patients with paired CNB and open excision biopsy (OEB) samples between January 2009 and June 2016 were retrospectively analyzed. ΔKi67 was calculated as the absolute difference between Ki67 level in CNB and OEB samples, and the median value of 5% was adopted to category patients into high- and low ΔKi67 groups. Disease-free survival (DFS) and overall survival (OS) were compared between different ΔKi67 groups. Overall, 2173 invasive breast cancer patients were included. Median Ki67 was higher in OEB than CNB samples: 25.00% versus 20.00% (P < 0.001). Axillary nodal status, STI, histological grading, and molecular subtype were independently associated with ΔKi67 (P < 0.05). In the whole population, patients with low ΔKi67 showed superior 5-year DFS (89.6% vs 87.0%, P = 0.026), but similar OS (95.8% vs 94.3%, P = 0.118) compared to those with high ΔKi67. HER2 status at surgery was the only significant factor interacting with ΔKi67 on both DFS (P = 0.026) and OS (P = 0.007). For patients with HER2-negative disease, high ΔKi67 was associated with worse 5-year DFS (87.2% vs 91.2%, P = 0.004) as well as impaired 5-year OS (93.9% vs 96.8%, P = 0.010). ΔKi67 had no significant impact on survival of HER2-positive patients. Ki67 increase after CNB was significantly associated with worse disease outcomes in HER2-negative, but not in HER2-positive patients, which warrants further study.
Analysis of C-reactive protein from finger stick dried blood spot to predict high risk of cardiovascular disease
Authors: Schakelaar Michael Y. , Kemperman Hans , Schoneveld Arjan H. , Hoefer Imo E. , Tiel Groenestege Wouter M. 
Published: February 2023

AbstractC-reactive protein (CRP) is an acute-phase protein involved in inflammation. Furthermore, CRP is an important biomarker used in diagnostics to predict risk of cardiovascular disease (CVD) in addition to monitoring bacterial and viral infections. To measure plasma CRP, venipuncture is still necessitated and has to be performed by trained phlebotomists. As a solution, dried blood spots (DBS) are used for minimally invasive at-home sampling of blood and can be send to diagnostic laboratories by regular mail. In this study, we included 53 patients that presented to the outpatient clinic of the University Medical Center Utrecht. Capillary finger stick was used to spot blood on a filter paper card and allowed to dry. After extraction of DBS, CRP was analyzed on an automated high-throughput chemistry analyzer. Additional validation steps regarding stability, effect of hematocrit, precision, and limits of blank and quantitation were conducted according to corresponding Clinical and Laboratory Standards Institute standards. An excellent regression analysis of R2 (95% confidence interval) = 0.986 (0.982–0.989) was found. This enabled correct classification for high CVD risk of all 25 cases with sensitivity (95% CI) of 1.00 (1.00–1.00) and specificity (95% CI) of 0.96 (0.89–1.03) and correct diagnosis of inflammation of 12/13 cases with sensitivity (95% CI) of 0.92 (0.77–1.07) and specificity (95% CI) of 1.00 (1.00–1.00). Furthermore, CRP was found to be stable for 31 days and observed hematocrit variation amongst patients was clinically acceptable. CRP from DBS can be accurately measured on an automated high-throughput chemistry analyzer and used to diagnose inflammation and classify high CVD risk. This method enables individuals to engage in at-home sampling of blood on DBS for (tele)diagnostics, screening programs, patient follow-up, and medication management.
A validated LC–MS/MS method for clinical pharmacokinetics and presumptive phase II metabolic pathways following oral administration of Andrographis paniculata extract
Authors: Songvut Phanit , Pholphana Nanthanit , Suriyo Tawit , Rangkadilok Nuchanart , Panomvana Duangchit , Puranajoti Porranee , Satayavivad Jutamaad 
Published: February 2023

AbstractAndrographis paniculata, a medicinal plant in Thailand national list of essential medicines, has been proposed for treatment of patients with mild to moderate coronavirus disease 2019. This study aims to develop a highly selective and sensitive liquid chromatography triple quadrupole tandem mass spectrometry method for quantitative determination of major diterpenoids in plasma and urine with application in pharmacokinetics. Chromatographic separation was performed on C18 column using a gradient mobile phase of water and acetonitrile. Mass spectrometry was analyzed using multiple reaction monitoring with negative ionization mode. This validated analytical method was very sensitive, less time consuming in analysis, and allowed the reliability and reproducibility on its application. The clinical pharmacokinetics was evaluated after single oral administration of A. paniculata extract (calculated as 60 mg of andrographolide). The disposition kinetics demonstrated that major diterpenoids could enter into systemic circulation, but they are mostly biotransformed (phase II) into conjugated glucuronide and sulfate metabolites. These metabolites are predominantly found in plasma and then extremely eliminated, in part through urinary excretion. The successful application of this analytical method supports its suitable uses in further clinical benefits after oral administration of A. paniculata.
Role of periosteum in alveolar bone regeneration comparing with collagen membrane in a buccal dehiscence model of dogs
Authors: Ma Zhigui , Guo Ke , Chen Lu , Chen Xinwei , Zou Duohong , Yang Chi 
Published: February 2023

AbstractTo investigate the role of periosteum on the treatment of buccal dehiscence defects comparing with collagen membrane in canine model. Bilateral dehiscence-type defects at the buccal side on the distal root of the lower 3rd/4th premolars were created in six beagle dogs with a total of 24 defects and assigned into three groups: Group A: blood clot in an untreated defect; Group B: deproteinized bovine bone material (DBBM) covered with an absorbable membrane; Group C: DBBM covered with the periosteum. The structural parameters for trabecular architecture and vertical bone regeneration were evaluated. Histological and histomorphometric evaluation were carried out to observe new bone formation and mineralization in the graft site. Immunohistochemical analysis was performed to identify the expression of osteopontin (OPN) and osteocalcin (OCN) at postoperative 3 months. Group C achieved greater vertical alveolar bone gain than that of group A and group B. The periosteum-covered group showed significantly greater new bone formation and accelerated mineralization. The greater immunolabeling for OPN and OCN was observed in group C than in group A. Periosteal coverage has explicit advantages over collagen membranes for the quality and quantity of new bone regeneration in dehiscence defects repairing.
Persistent homology analysis distinguishes pathological bone microstructure in non-linear microscopy images
Authors: Pritchard Ysanne , Sharma Aikta , Clarkin Claire , Ogden Helen , Mahajan Sumeet , Sánchez-García Rubén J. 
Published: February 2023

AbstractWe present a topological method for the detection and quantification of bone microstructure from non-linear microscopy images. Specifically, we analyse second harmonic generation (SHG) and two photon excited autofluorescence (TPaF) images of bone tissue which capture the distribution of matrix (fibrillar collagen) structure and autofluorescent molecules, respectively. Using persistent homology statistics with a signed Euclidean distance transform filtration on binary patches of images, we are able to quantify the number, size, distribution, and crowding of holes within and across samples imaged at the microscale. We apply our methodology to a previously characterized murine model of skeletal pathology whereby vascular endothelial growth factor expression was deleted in osteocalcin-expressing cells (OcnVEGFKO) presenting increased cortical porosity, compared to wild type (WT) littermate controls. We show significant differences in topological statistics between the OcnVEGFKO and WT groups and, when classifying the males, or females respectively, into OcnVEGFKO or WT groups, we obtain high prediction accuracies of 98.7% (74.2%) and 77.8% (65.8%) respectively for SHG (TPaF) images. The persistence statistics that we use are fully interpretable, can highlight regions of abnormality within an image and identify features at different spatial scales.
The combination of polyphenols and phospholipids as an efficient platform for delivery of natural products
Authors: Hashemzadeh Hassan , Hanafi-Bojd Mohammad Yahya , Iranshahy Milad , Zarban Asghar , Raissi Heidar 
Published: February 2023

AbstractAlthough nature is a rich source of potential drugs and drug leads, the widespread application of natural products (NPs) is limited due to their poor absorption when administered orally. A strategy of using phytosome has emerged as a promising technique to increase the bioavailability of NPs. Here, a comprehensive computational investigation is performed to explore the nature of interactions in the formation of phytosomes between phosphatidylcholine (PC) and a series of polyphenols (PP), including epigallocatechin-3-gallate (Eg), luteolin (Lu), quercetin (Qu), and resveratrol (Re). Our quantum mechanical calculation revealed that the intermolecular hydrogen bonds (HBs) of phosphate and glycerol parts of PC with the polyphenol compounds are the main driving force in the formation of phytosomes. The strongest HB (with energy HB = − 108.718 kJ/mol) is formed between the Eg molecule and PC. This hydrogen bond results from the flexible structure of the drug which along with several van der Waals (vdW) interactions, makes Eg-PC the most stable complex (adsorption energy = − 164.93 kJ/mol). Energy decomposition analysis confirms that the electrostatic interactions (hydrogen bond and dipole-diploe interactions) have a major contribution to the stabilization of the studied complexes. The obtained results from the molecular dynamics simulation revealed that the formation of phytosomes varies depending on the type of polyphenol. It is found that the intermolecular hydrogen bonds between PP and PC are a key factor in the behavior of the PP-PC complex in the self-aggregation of phytosome. In Eg-PC, Lu-PC, and Qu-PC systems, the formation of strong hydrogen bonds (HBCP < 0 and ∇2ρBCP > 0) between PP and PC protects the PP-PC complexes from degradation. The steered molecular dynamics simulation results have a good agreement with experimental data and confirm that the phytosome platform facilitates the penetration of PP compounds into the membrane cells.
Antioxidant enzymes that target hydrogen peroxide are conserved across the animal kingdom, from sponges to mammals
Authors: Hewitt Olivia H. , Degnan Sandie M. 
Published: February 2023

AbstractOxygen is the sustenance of aerobic life and yet is highly toxic. In early life, antioxidants functioned solely to defend against toxic effects of reactive oxygen species (ROS). Later, as aerobic metabolisms evolved, ROS became essential for signalling. Thus, antioxidants are multifunctional and must detoxify, but also permit ROS signalling for vital cellular processes. Here we conduct metazoan-wide genomic assessments of three enzymatic antioxidant families that target the predominant ROS signaller, hydrogen peroxide: namely, monofunctional catalases (CAT), peroxiredoxins (PRX), and glutathione peroxidases (GPX). We reveal that the two most evolutionary ancient families, CAT and PRX, exhibit metazoan-wide conservation. In the basal animal lineage, sponges (phylum Porifera), we find all three antioxidant families, but with GPX least abundant. Poriferan CATs are distinct from bilaterian CATs, but the evolutionary divergence is small. Amongst PRXs, subfamily PRX6 is the most conserved, whilst subfamily AhpC-PRX1 is the largest; PRX4 is the only core member conserved from sponges to mammals and may represent the ancestral animal AhpC-PRX1. Conversely, for GPX, the most recent family to arise, only the cysteine-dependent subfamily GPX7 is conserved across metazoans, and common across Porifera. Our analyses illustrate that the fundamental functions of antioxidants have resulted in gene conservation throughout the animal kingdom.
A comparative study of effects of curcumin and its nanoparticles on the growth, immunity and heat stress resistance of Nile tilapia (Oreochromis niloticus)
Authors: Abdel-Ghany Heba M. , El-Sisy Doaa M. , Salem Mohamed El-S. 
Published: February 2023

AbstractThis study evaluated the effects of dietary supplementation with free- or nano-curcumin on the growth performance, immune status and heat stress resistance of Nile tilapia (Oreochromis niloticus). Seven isonitrogenous (28% protein) and isocaloric (445 kcal/100 g DM) diets were prepared. Six diets were supplemented with three levels of nano-curcumin (50 (CN50), 100 (CN100), 200 (CN200) mg kg−1diet) or free-curcumin (50 (C50), 100 (C100), 200 (C200) mg kg−1diet), and the control diet was left without an additive (CON). Fish (13.54 ± 0.32 g) (mean ± SD) fed the experimental diets for 65 days. Following the feeding trial, the fish were exposed to the acute heat stress by gradually raising the water temperature from 25 to 40 °C within 3 h. The fish were then exposed to 40 °C for 4 h. Results revealed the superiority of nano-curcumin over its free-form in enhancing the growth performance, with the highest results obtained at CN100, followed by CN200. Only heat stress, not the experimental diets, increased the platelets, mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), leukocytes and neutrophils count, while lymphocytes decreased. The CN50 and CN100 groups showed lower activity of liver enzymes (alanine aminotransferase (ALT) and aspartate aminotransferase (AST)) than the other treatments, while C200 gave the highest activity of these enzymes. The highest immunoglobulin (IgM) levels were detected in CN100, CN200, C100 and C200, followed by CN50. The C200 group showed higher levels of complement 3 and complement 4 (C3 and C4, respectively) than the other treatments. The C50 and CON groups gave the lowest values of IgM, C3 and C4. Cortisol levels were significantly lower in the CN50 and CN100 groups compared to the other groups. After the heat stress, ALT, AST, IgM, C3, C4, cortisol and glucose increased. Thus, nano-curcumin is more effective than its free-form in enhancing the resistance to heat stress, inducing innate immunity, lowering the stress indicators and promoting growth performance of Nile tilapia with the best concentration at 100 mg kg−1diet.
Isotherm and kinetic studies of cadmium biosorption and its adsorption behaviour in multi-metals solution using dead and immobilized archaeal cells
Authors: Hegazy Ghada E. , Soliman Nadia A. , Ossman Mona E. , Abdel-Fattah Yasser R. , Moawad Madelyn N. 
Published: February 2023

AbstractIt is crucial to identify more biological adsorbents that can efficiently uptake metals from wastewater. Dry haloalkaliphilic archaea Natronolimnobius innermongolicuswas evaluated for Cd ions biosorption. The optimal operating conditions (pH, biomass dose, initial metal concentration, contact time, and isotherms models) were tested. Biosorption process is influenced by the metal's solution pH with maximum removal of 83.36% being achieved at pH 8. Cadmium ions uptake reaches equilibrium in about 5 min of biosorption process. The Langmuir model was determined to better fit the Cd(II) biosorption by dry archaea. The maximal uptake capacity (qmax) of Cd(II) was 128.21 mg/g. The effect of multi-component system on biosorption behaviour of Pb, Ni, Cu, Fe, and Cd ions by immobilized dried archaeal cells, dried archaeal cells, and dried bryozoa was studied using Plackett–Burman experimental design. The investigated biosorbents were effective at removing metals from contaminated systems, particularly for Fe, Pb, and Cd ions. Moreover, the interaction behaviour of these metals was antagonistic, synergistic, or non-interactive in multi-metals system. SEM, EDX, and FTIR spectra revealed changes in surface morphology of the biomass through the biosorption process. Finally, continuous adsorption experiment was done to examine the ability of immobilized biomass to adsorb metals from wastewater.
A deep-learning approach for reconstructing 3D turbulent flows from 2D observation data
Authors: Yousif Mustafa Z. , Yu Linqi , Hoyas Sergio , Vinuesa Ricardo , Lim HeeChang 
Published: February 2023

AbstractTurbulence is a complex phenomenon that has a chaotic nature with multiple spatio-temporal scales, making predictions of turbulent flows a challenging topic. Nowadays, an abundance of high-fidelity databases can be generated by experimental measurements and numerical simulations, but obtaining such accurate data in full-scale applications is currently not possible. This motivates utilising deep learning on subsets of the available data to reduce the required cost of reconstructing the full flow in such full-scale applications. Here, we develop a generative-adversarial-network (GAN)-based model to reconstruct the three-dimensional velocity fields from flow data represented by a cross-plane of unpaired two-dimensional velocity observations. The model could successfully reconstruct the flow fields with accurate flow structures, statistics and spectra. The results indicate that our model can be successfully utilised for reconstructing three-dimensional flows from two-dimensional experimental measurements. Consequently, a remarkable reduction in the complexity of the experimental setup and the storage cost can be achieved.
The association between shift work and the incidence of reflux esophagitis in Korea: a cohort study
Authors: Nam Min-Woo , Lee Yesung , Mun Eunchan , Lee Woncheol 
Published: February 2023

AbstractShift work has adverse health effects such as diabetes, cardiovascular disease, sleep disturbance, depression, and breast cancer. Gastro-esophageal reflux disease (GERD) results in lesions such as reflux esophagitis (RE) and Barrett’s esophagus. This study investigated the association between shift work and RE. A cohort study was conducted with 140,553 participants who were followed up at least once from 2012 to 2018. Type of working and shift types were collected using standardized questionnaires. Esophagogastroduodenoscopy (EGD) was performed by experienced endoscopists who were blinded to the aims of this study. According to the Los Angeles classification, RE was categorized based on the extent of esophageal mucosal breaks. During the 469,217.2 person-years of follow-up, 35,185 participants developed incident cases of RE. The multivariable adjusted hazard ratio (95% confidence intervals) for incident cases comparing shift work to fixed day work was 1.09 (1.04–1.13). This association was more strongly observed in the younger age group (18–39 years old) and the female group. In conclusion, shift work was significantly associated with the incidence of RE. Particularly, the results were more significant in the younger and female groups.
Whole-genome sequencing-based analyses of drug-resistant Mycobacterium tuberculosis from Taiwan
Authors: Xiao Yu-Xin , Liu Kuang-Hung , Lin Wan-Hsuan , Chan Tai-Hua , Jou Ruwen 
Published: February 2023

AbstractDrug-resistant tuberculosis (DR-TB) posed challenges to global TB control. Whole-genome sequencing (WGS) is recommended for predicting drug resistance to guide DR-TB treatment and management. Nevertheless, data are lacking in Taiwan. Phenotypic drug susceptibility testing (DST) of 12 anti-TB drugs was performed for 200 Mycobacterium tuberculosis isolates. WGS was performed using the Illumina platform. Drug resistance profiles and lineages were predicted in silico using the Total Genotyping Solution for TB (TGS-TB). Using the phenotypic DST results as a reference, WGS-based prediction demonstrated high concordance rates of isoniazid (95.0%), rifampicin (RIF) (98.0%), pyrazinamide (98.5%) and fluoroquinolones (FQs) (99.5%) and 96.0% to 99.5% for second-line injectable drugs (SLIDs); whereas, lower concordance rates of ethambutol (87.5%), streptomycin (88.0%) and ethionamide (84.0%). Furthermore, minimum inhibitory concentrations confirmed that RIF rpoB S450L, FQs gyrA D94G and SLIDs rrs a1401g conferred high resistance levels. Besides, we identified lineage-associated mutations in lineage 1 (rpoB H445Y and fabG1 c-15t) and predominant lineage 2 (rpoB S450L and rpsL K43R). The WGS-based prediction of drug resistance is highly concordant with phenotypic DST results and can provide comprehensive genetic information to guide DR-TB precision therapies in Taiwan.