bluuebunny/crossref_metadata_2025 huggingface dataset:
Time-resolved β-lactam cleavage by L1 metallo-β-lactamase
Authors: Wilamowski M. , Sherrell D. A. , Kim Y. , Lavens A. , Henning R. W. , Lazarski K. , Shigemoto A. , Endres M. , Maltseva N. , Babnigg G. , Burdette S. C. , Srajer V. , Joachimiak A.
Published: November 2022

Serial x-ray crystallography can uncover binding events, and subsequent chemical conversions occurring during enzymatic reaction. Here, we reveal the structure, binding and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from Stenotrophomonas maltophilia. Using time-resolved serial synchrotron crystallography, we show the time course of β-lactam hydrolysis and determine ten snapshots (20, 40, 60, 80, 100, 150, 300, 500, 2000 and 4000 ms) at 2.20 Å resolution. The reaction is initiated by laser pulse releasing Zn2+ ions from a UV-labile photocage. Two metal ions bind to the active site, followed by binding of moxalactam and the intact β-lactam ring is observed for 100 ms after photolysis. Cleavage of β-lactam is detected at 150 ms and the ligand is significantly displaced. The reaction product adjusts its conformation reaching steady state at 2000 ms corresponding to the relaxed state of the enzyme. Only small changes are observed in the positions of Zn2+ ions and the active site residues. Mechanistic details captured here can be generalized to other MBLs.
Polymer nanoparticles pass the plant interface
Authors: Parkinson Sam J. , Tungsirisurp Sireethorn , Joshi Chitra , Richmond Bethany L. , Gifford Miriam L. , Sikder Amrita , Lynch Iseult , O’Reilly Rachel K. , Napier Richard M.
Published: November 2022

As agriculture strives to feed an ever-increasing number of people, it must also adapt to increasing exposure to minute plastic particles. To learn about the accumulation of nanoplastics by plants, we prepared well-defined block copolymer nanoparticles by aqueous dispersion polymerisation. A fluorophore was incorporated via hydrazone formation and uptake into roots and protoplasts of Arabidopsis thaliana was investigated using confocal microscopy. Here we show that uptake is inversely proportional to nanoparticle size. Positively charged particles accumulate around root surfaces and are not taken up by roots or protoplasts, whereas negatively charged nanoparticles accumulate slowly and become prominent over time in the xylem of intact roots. Neutral nanoparticles penetrate rapidly into intact cells at the surfaces of plant roots and into protoplasts, but xylem loading is lower than for negative nanoparticles. These behaviours differ from those of animal cells and our results show that despite the protection of rigid cell walls, plants are accessible to nanoplastics in soil and water.
The extreme yet transient nature of glacial erosion
Authors: Patton H. , Hubbard A. , Heyman J. , Alexandropoulou N. , Lasabuda A. P. E. , Stroeven A. P. , Hall A. M. , Winsborrow M. , Sugden D. E. , Kleman J. , Andreassen K.
Published: November 2022

Ice can sculpt extraordinary landscapes, yet the efficacy of, and controls governing, glacial erosion on geological timescales remain poorly understood and contended, particularly across Polar continental shields. Here, we assimilate geophysical data with modelling of the Eurasian Ice Sheet — the third largest Quaternary ice mass that spanned 49°N to 82°N — to decipher its erosional footprint during the entire last ~100 ka glacial cycle. Our results demonstrate extreme spatial and temporal heterogeneity in subglacial erosion, with rates ranging from 0 to 5 mm a−1 and a net volume equating to ~130,000 km3 of bedrock excavated to depths of ~190 m. A hierarchy of environmental controls ostensibly underpins this complex signature: lithology, topography and climate, though it is basal thermodynamics that ultimately regulates erosion, which can be variously protective, pervasive, or, highly selective. Our analysis highlights the remarkable yet fickle nature of glacial erosion — critically modulated by transient ice-sheet dynamics — with its capacity to impart a profound but piecemeal geological legacy across mid- and high latitudes.
Integrated proteomic and transcriptomic landscape of macrophages in mouse tissues
Authors: Qie Jingbo , Liu Yang , Wang Yunzhi , Zhang Fan , Qin Zhaoyu , Tian Sha , Liu Mingwei , Li Kai , Shi Wenhao , Song Lei , Sun Mingjun , Tong Yexin , Hu Ping , Gong Tao , Wang Xiaqiong , Huang Yi , Lin Bolong , Zheng Xuesen , Zhou Rongbin , Lv Jie , Du Changsheng , Wang Yi , Qin Jun , Yang Wenjun , He Fuchu , Ding Chen
Published: November 2022

Macrophages are involved in tissue homeostasis and are critical for innate immune responses, yet distinct macrophage populations in different tissues exhibit diverse gene expression patterns and biological processes. While tissue-specific macrophage epigenomic and transcriptomic profiles have been reported, proteomes of different macrophage populations remain poorly characterized. Here we use mass spectrometry and bulk RNA sequencing to assess the proteomic and transcriptomic patterns, respectively, of 10 primary macrophage populations from seven mouse tissues, bone marrow-derived macrophages and the cell line RAW264.7. The results show distinct proteomic landscape and protein copy numbers between tissue-resident and recruited macrophages. Construction of a hierarchical regulatory network finds cell-type-specific transcription factors of macrophages serving as hubs for denoting tissue and functional identity of individual macrophage subsets. Finally, Il18 is validated to be essential in distinguishing molecular signatures and cellular function features between tissue-resident and recruited macrophages in the lung and liver. In summary, these deposited datasets and our open proteome server (http://macrophage.mouseprotein.cn) integrating all information will provide a valuable resource for future functional and mechanistic studies of mouse macrophages.
Emergence of zero-field non-synthetic single and interchained antiferromagnetic skyrmions in thin films
Authors: Aldarawsheh Amal , Fernandes Imara Lima , Brinker Sascha , Sallermann Moritz , Abusaa Muayad , Blügel Stefan , Lounis Samir
Published: November 2022

Antiferromagnetic (AFM) skyrmions are envisioned as ideal localized topological magnetic bits in future information technologies. In contrast to ferromagnetic (FM) skyrmions, they are immune to the skyrmion Hall effect, might offer potential terahertz dynamics while being insensitive to external magnetic fields and dipolar interactions. Although observed in synthetic AFM structures and as complex meronic textures in intrinsic AFM bulk materials, their realization in non-synthetic AFM films, of crucial importance in racetrack concepts, has been elusive. Here, we unveil their presence in a row-wise AFM Cr film deposited on PdFe bilayer grown on fcc Ir(111) surface. Using first principles, we demonstrate the emergence of single and strikingly interpenetrating chains of AFM skyrmions, which can co-exist with the rich inhomogeneous exchange field, including that of FM skyrmions, hosted by PdFe. Besides the identification of an ideal platform of materials for intrinsic AFM skyrmions, we anticipate the uncovered knotted solitons to be promising building blocks in AFM spintronics.
A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China
Authors: Qiu Shaofu , Liu Kangkang , Yang Chaojie , Xiang Ying , Min Kaiyuan , Zhu Kunpeng , Liu Hongbo , Du Xinying , Yang Mingjuan , Wang Ligui , Sun Yong , Zhou Haijian , Mahe Muti , Zhao Jiayong , Li Shijun , Yu Deshan , Hawkey Jane , Holt Kathryn E. , Baker Stephen , Yang Juntao , Xu Xuebin , Song Hongbin
Published: November 2022

Antimicrobial resistance of Shigella sonnei has become a global concern. Here, we report a phylogenetic group of S. sonnei with extensive drug resistance, including a combination of multidrug resistance, coresistance to ceftriaxone and azithromycin (cefRaziR), reduced susceptibility to fluoroquinolones, and even colistin resistance (colR). This distinct clone caused six waterborne shigellosis outbreaks in China from 2015 to 2020. We collect 155 outbreak isolates and 152 sporadic isolates. The cefRaziR isolates, including outbreak strains, are mainly distributed in a distinct clade located in global Lineage III. The outbreak strains form a recently derived monophyletic group that may have emerged circa 2010. The cefRaziR and colR phenotypes are attributed to the acquisition of different plasmids, particularly the IncB/O/K/Z plasmid coharboring the blaCTX-M-14, mphA, aac(3)-IId, dfrA17, aadA5, and sul1 genes and the IncI2 plasmid with an mcr-1 gene. Genetic analyses identify 92 accessory genes and 60 single-nucleotide polymorphisms associated with the cefRaziR phenotype. Surveillance of this clone is required to determine its dissemination and threat to global public health.
Deciphering the heterogeneity of the Lyve1+ perivascular macrophages in the mouse brain
Authors: Siret C. , van Lessen M. , Bavais J. , Jeong H. W. , Reddy Samawar S. K. , Kapupara K. , Wang S. , Simic M. , de Fabritus L. , Tchoghandjian A. , Fallet M. , Huang H. , Sarrazin S. , Sieweke M. H. , Stumm R. , Sorokin L. , Adams R. H. , Schulte-Merker S. , Kiefer F. , van de Pavert S. A.
Published: November 2022

Perivascular macrophages (pvMs) are associated with cerebral vasculature and mediate brain drainage and immune regulation. Here, using reporter mouse models, whole brain and section immunofluorescence, flow cytometry, and single cell RNA sequencing, besides the Lyve1+F4/80+CD206+CX3CR1+ pvMs, we identify a CX3CR1– pvM population that shares phagocytic functions and location. Furthermore, the brain parenchyma vasculature mostly hosts Lyve1+MHCII– pvMs with low to intermediate CD45 expression. Using the double Cx3cr1GFP x Cx3cr1-Cre;RosatdT reporter mice for finer mapping of the lineages, we establish that CD45lowCX3CR1– pvMs are derived from CX3CR1+ precursors and require PU.1 during their ontogeny. In parallel, results from the Cxcr4-CreErt2;Rosa26tdT lineage tracing model support a bone marrow-independent replenishment of all Lyve1+ pvMs in the adult mouse brain. Lastly, flow cytometry and 3D immunofluorescence analysis uncover increased percentage of pvMs following photothrombotic induced stroke. Our results thus show that the parenchymal pvM population is more heterogenous than previously described, and includes a CD45low and CX3CR1– pvM population.
Whole-exome sequencing study identifies rare variants and genes associated with intraocular pressure and glaucoma
Authors: Gao Xiaoyi Raymond , Chiariglione Marion , Arch Alexander J.
Published: November 2022

Elevated intraocular pressure (IOP) is a major risk factor for glaucoma, the leading cause of irreversible blindness worldwide. IOP is also the only modifiable risk factor for glaucoma. Previous genome-wide association studies have established the contribution of common genetic variants to IOP. The role of rare variants for IOP was unknown. Using whole exome sequencing data from 110,260 participants in the UK Biobank (UKB), we conducted the largest exome-wide association study of IOP to date. In addition to confirming known IOP genes, we identified 40 novel rare-variant genes for IOP, such as BOD1L1, ACAD10 and HLA-B, demonstrating the power of including and aggregating rare variants in gene discovery. About half of these IOP genes are also associated with glaucoma phenotypes in UKB and the FinnGen cohort. Six of these genes, i.e. ADRB1, PTPRB, RPL26, RPL10A, EGLN2, and MTOR, are drug targets that are either established for clinical treatment or in clinical trials. Furthermore, we constructed a rare-variant polygenic risk score and showed its significant association with glaucoma in independent participants (n = 312,825). We demonstrated the value of rare variants to enhance our understanding of the biological mechanisms regulating IOP and uncovered potential therapeutic targets for glaucoma.
Cell type diversity in a developing octopus brain
Authors: Styfhals Ruth , Zolotarov Grygoriy , Hulselmans Gert , Spanier Katina I. , Poovathingal Suresh , Elagoz Ali M. , De Winter Seppe , Deryckere Astrid , Rajewsky Nikolaus , Ponte Giovanna , Fiorito Graziano , Aerts Stein , Seuntjens Eve
Published: November 2022

Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The brain cell types that control their sophisticated behavioral repertoire are still unknown. Here, we profile the cell diversity of the paralarval Octopus vulgaris brain to build a cell type atlas that comprises mostly neural cells, but also multiple glial subtypes, endothelial cells and fibroblasts. We spatially map cell types to the vertical, subesophageal and optic lobes. Investigation of cell type conservation reveals a shared gene signature between glial cells of mouse, fly and octopus. Genes related to learning and memory are enriched in vertical lobe cells, which show molecular similarities with Kenyon cells in Drosophila. We construct a cell type taxonomy revealing transcriptionally related cell types, which tend to appear in the same brain region. Together, our data sheds light on cell type diversity and evolution in the octopus brain.
Clostridioides difficile bile salt hydrolase activity has substrate specificity and affects biofilm formation
Authors: Aguirre Andrea Martinez , Adegbite Adegoke Oyeleye , Sorg Joseph A.
Published: November 2022

The Clostridioides difficile pathogen is responsible for nosocomial infections. Germination is an essential step for the establishment of C. difficile infection (CDI) because toxins that are secreted by vegetative cells are responsible for the symptoms of CDI. Germination can be stimulated by the combinatorial actions of certain amino acids and either conjugated or deconjugated cholic acid-derived bile salts. During synthesis in the liver, cholic acid- and chenodeoxycholic acid-class bile salts are conjugated with either taurine or glycine at the C24 carboxyl. During GI transit, these conjugated bile salts are deconjugated by microbes that express bile salt hydrolases (BSHs). Here, we surprisingly find that several C. difficile strains have BSH activity. We observed this activity in both C. difficile vegetative cells and in spores and that the observed BSH activity was specific to taurine-derived bile salts. Additionally, we find that this BSH activity can produce cholate for metabolic conversion to deoxycholate by C. scindens. The C. scindens-produced deoxycholate signals to C. difficile to initiate biofilm formation. Our results show that C. difficile BSH activity has the potential to influence the interactions between microbes, and this could extend to the GI setting.
A postmortem study suggests a revision of the dual-hit hypothesis of Parkinson’s disease
Authors: Borghammer Per , Just Mie Kristine , Horsager Jacob , Skjærbæk Casper , Raunio Anna , Kok Eloise H. , Savola Sara , Murayama Shigeo , Saito Yuko , Myllykangas Liisa , Van Den Berge Nathalie
Published: November 2022

The dual-hit hypothesis of Parkinson’s disease (PD) originally postulated that a neurotropic pathogen leads to formation of α-synuclein pathology in the olfactory bulb (OB) and dorsal motor nucleus of the vagus (DMV) and then invades the brain from these two entry points. Little work has been conducted to validate an important underlying premise for the dual-hit hypothesis, namely that the initial Lewy pathology does arise simultaneously in the OB and the enteric nervous system (ENS) plexuses and DMV at the earliest disease stage. We conducted a focused re-analysis of two postmortem datasets, which included large numbers of mild Lewy body disease (LBD) cases. We found that cases with α-synuclein pathology restricted to the peripheral autonomic nervous system and/or lower brainstem (early body-first LBD cases) very rarely had any OB pathology, suggesting that Lewy pathology commonly arises in the ENS without concomitant involvement of the OB. In contrast, cases with mild amygdala-predominant Lewy pathology (early brain-first LBD cases) nearly always showed OB pathology. This is compatible with the first pathology being triggered in the OB or amygdala followed by secondary spreading to connected structures, but without early involvement of the ENS or lower brainstem. These observations support that the pathologic process starts in either the olfactory bulb or the ENS, but rarely in the olfactory bulb and gut simultaneously. More studies on neuropathological datasets are warranted to reproduce these findings. The agreement between the revised single-hit hypothesis and the recently proposed brain-first vs. body-first model of LBD is discussed.
T-count and T-depth of any multi-qubit unitary
Authors: Gheorghiu Vlad , Mosca Michele , Mukhopadhyay Priyanka
Published: November 2022

We design an algorithm to determine the (minimum) T-count of any n-qubit (n ≥ 1) unitary W of size 2n × 2n, over the Clifford+T gate set. The space and time complexity of our algorithm are $$O\left({2}^{2n}\right)$$

O

2

2
n

and $$O\left({2}^{2n{{{{\mathcal{T}}}}}_{\epsilon }(W)+4n}\right)$$

O

2

2
n

T

ϵ

(

W

)

+
4
n

, respectively. $${{{{\mathcal{T}}}}}_{\epsilon }(W)$$

T

ϵ

(

W

)

(ϵ-T-count) is the (minimum) T-count of an exactly implementable unitary U ($${{{\mathcal{T}}}}(U)$$

T

(

U

)

), such that d(U,W) ≤ ϵ and $${{{\mathcal{T}}}}(U)\le {{{\mathcal{T}}}}({U}^{{\prime} })$$

T

(

U

)

≤
T

(

U

′

)

where $${U}^{{\prime} }$$

U

′

is any exactly implementable unitary with $$d({U}^{{\prime} },W)\le \epsilon$$

d

(

U

′

,
W

)

≤
ϵ

. d(. , .) is the global phase invariant distance. Our algorithm can also be used to determine the (minimum) T-depth as well as the minimum non-Clifford-gate count or depth required to implement any multi-qubit unitary with a finite universal gate set like Clifford+CS, Clifford+V, etc. For small enough ϵ, we can synthesize the optimal circuits.
Detection of molecular transitions with nitrogen-vacancy centers and electron-spin labels
Authors: Munuera-Javaloy C. , Puebla R. , D’Anjou B. , Plenio M. B. , Casanova J.
Published: November 2022

We present a protocol that detects molecular conformational changes with two nitroxide electron-spin labels and a nitrogen-vacancy (NV) center in diamond. More specifically, we demonstrate that the NV can detect energy shifts induced by the coupling between electron-spin labels. The protocol relies on the judicious application of microwave and radiofrequency pulses in a range of parameters that ensures stable nitroxide resonances. Furthermore, we demonstrate that our scheme is optimized by using nitroxides with distinct nitrogen isotopes. We develop a simple theoretical model that we combine with Bayesian inference techniques to demonstrate that our method enables the detection of conformational changes in ambient conditions including strong NV dephasing rates as a consequence of the diamond surface proximity and nitroxide thermalization mechanisms. Finally, we counter-intuitively show that with our method the small residual effect of random molecular tumbling becomes a resource that can be exploited to extract inter-label distances.
Superconductivity enhancement in polar metal regions of Sr0.95Ba0.05TiO3 and Sr0.985Ca0.015TiO3 revealed by systematic Nb doping
Authors: Tomioka Yasuhide , Shirakawa Naoki , Inoue Isao H.
Published: November 2022

Two different ferroelectric materials, Sr0.95Ba0.05TiO3 and Sr0.985Ca0.015TiO3, can be turned into polar metals with broken centrosymmetry via electron doping. Systematic substitution of Nb5+ for Ti4+ has revealed that these polar metals both commonly show a simple superconducting dome with a single convex shape. Interestingly, the superconducting transition temperature Tc is enhanced more strongly in these polar metals when compared with the nonpolar matrix Sr(Ti, Nb)O3. The maximum Tc reaches 0.75 K, which is the highest reported value among the SrTiO3-based families to date. However, the Tc enhancement is unexpectedly lower within the vicinity of the putative ferroelectric quantum critical point. The enhancement then becomes much more prominent at locations further inside the dilute carrier-density region, where the screening is less effective. These results suggest that centrosymmetry breaking, i.e., the ferroelectric nature, does not kill the superconductivity. Instead, it enhances the superconductivity directly, despite the absence of strong quantum fluctuations.
HeliantHOME, a public and centralized database of phenotypic sunflower data
Authors: Bercovich Natalia , Genze Nikita , Todesco Marco , Owens Gregory L. , Légaré Jean-Sébastien , Huang Kaichi , Rieseberg Loren H. , Grimm Dominik G.
Published: November 2022

Genomic studies often attempt to link natural genetic variation with important phenotypic variation. To succeed, robust and reliable phenotypic data, as well as curated genomic assemblies, are required. Wild sunflowers, originally from North America, are adapted to diverse and often extreme environments and have historically been a widely used model plant system for the study of population genomics, adaptation, and speciation. Moreover, cultivated sunflower, domesticated from a wild relative (Helianthus annuus) is a global oil crop, ranking fourth in production of vegetable oils worldwide. Public availability of data resources both for the plant research community and for the associated agricultural sector, are extremely valuable. We have created HeliantHOME (http://www.helianthome.org), a curated, public, and interactive database of phenotypes including developmental, structural and environmental ones, obtained from a large collection of both wild and cultivated sunflower individuals. Additionally, the database is enriched with external genomic data and results of genome-wide association studies. Finally, being a community open-source platform, HeliantHOME is expected to expand as new knowledge and resources become available.
Data on medication adherence in adults with neurological disorders: The NeuroGerAd study
Authors: Prell Tino , Schönenberg Aline , Mendorf Sarah , Mühlhammer Hannah M. , Grosskreutz Julian , Teschner Ulrike
Published: November 2022

Nonadherence to medication is a common issue that goes along with increased morbidity and mortality and immense health care costs. To improve medication adherence and outcome in ill people, their reasons of not taking their prescribed medication must be known. Here a dataset is presented based on the longitudinal observational NeuroGerAd study in adults with neurological disorders (N = 910). The dataset contains demographic background variables as well as measures of adherence, medication changes after hospital discharge, comprehensive geriatric assessments, personality, patient-physician relationship, and health-related quality of life. As such, the dataset offers unique opportunities to enable a plethora of analyses on personal, social, and institutional factors influencing medication adherence.
Comorbidity clusters associated with newly treated type 2 diabetes mellitus: a Bayesian nonparametric analysis
Authors: Martinez-De la Torre Adrian , Perez-Cruz Fernando , Weiler Stefan , Burden Andrea M.
Published: November 2022

Type 2 diabetes mellitus (T2DM) is associated with the development of chronic comorbidities, which can lead to high drug utilization and adverse events. We aimed to identify common comorbidity clusters and explore the progression over time in newly treated T2DM patients. The IQVIA Medical Research Data incorporating data from THIN, a Cegedim database of anonymized electronic health records, was used to identify all patients with a first-ever prescription for a non-insulin antidiabetic drug (NIAD) between January 2006 and December 2019. We selected 58 chronic comorbidities of interest and used Bayesian nonparametric models to identify disease clusters and model their progression over time. Among the 175,383 eligible T2DM patients, we identified the 20 most frequent comorbidity clusters, which were comprised of 14 latent features (LFs). Each LF was associated with a primary disease (e.g., 98% of patients in cluster 2, characterized by LF2, had congestive heart failure [CHF]). The presence of certain LFs increased the probability of having another LF active. For example, LF2 (CHF) frequently appeared with LFs related to chronic kidney disease (CKD). Over time, the clusters associated with cardiovascular diseases, such as CHF, progressed rapidly. Moreover, the onset of certain diseases led to further complications. Our models identified established T2DM complications and previously unknown connections, thus, highlighting the potential for Bayesian nonparametric models to characterize complex comorbidity patterns.
Prognostic value of the metabolic score obtained via [18F]FDG PET/CT and a new prognostic staging system for gastric cancer
Authors: Kim Sung Hoon , Song Bong-Il , Kim Hae Won , Won Kyoung Sook , Son Young-Gil , Ryu Seung Wan , Kang Yoo Na
Published: November 2022

We developed and validated a new staging system that includes metabolic information from pretreatment [18F]Fluorodeoxyglucose ([18F]FDG) positron emission tomography/computed tomography (PET/CT) for predicting disease-specific survival (DSS) in gastric cancer (GC) patients. Overall, 731 GC patients undergoing preoperative [18F]FDG PET/CT were enrolled and divided into the training (n = 543) and validation (n = 188) cohorts. A metabolic score (MS) was developed by combining the maximum standardized uptake value (SUVmax) of the primary tumor (T_SUVmax) and metastatic lymph node (N_SUVmax). A new staging system incorporating the MS and tumor-node-metastasis (TNM) stage was developed using conditional inference tree analysis. The MS was stratified as follows: score 1 (T_SUVmax ≤ 4.5 and N_SUVmax ≤ 1.9), score 2 (T_SUVmax > 4.5 and N_SUVmax ≤ 1.9), score 3 (T_SUVmax ≤ 4.5 and N_SUVmax > 1.9), and score 4 (T_SUVmax > 4.5 and N_SUVmax > 1.9) in the training cohort. The new staging system yielded five risk categories: category I (TNM I, II and MS 1), category II (TNM I, II and MS 2), category III (TNM I, II and MS ≥ 3), category IV (TNM III, IV and MS ≤ 3), and category V (TNM III, IV and MS 4) in the training cohort. DSS differed significantly between both staging systems; the new staging system showed better prognostic performance in both training and validation cohorts. The MS was an independent prognostic factor for DSS, and discriminatory power of the new staging system for DSS was better than that of the conventional TNM staging system alone.
Partial differential equations of entropy analysis on ternary hybridity nanofluid flow model via rotating disk with hall current and electromagnetic radiative influences
Authors: Al Oweidi Khalid Fanoukh , Shahzad Faisal , Jamshed Wasim , Usman  , Ibrahim Rabha W. , El Din El Sayed M. Tag , AlDerea Afrah M.
Published: November 2022

The flow of a fluid across a revolving disc has several technical and industrial uses. Examples of rotating disc flows include centrifugal pumps, viscometers, rotors, fans, turbines, and spinning discs. An important technology with implications for numerous treatments utilized in numerous sectors is the use of hybrid nanofluids (HNFs) to accelerate current advancements. Through investigation of ternary nanoparticle impacts on heat transfer (HT) and liquid movement, the thermal properties of tri-HNFs were to be ascertained in this study. Hall current, thermal radiation, and heat dissipation have all been studied in relation to the use of flow-describing equations. The ternary HNFs under research are composed of the nanomolecules aluminum oxide (Al2O3), copper oxide (CuO), silver (Ag), and water (H2O). For a number of significant physical characteristics, the physical situation is represented utilizing the boundary layer investigation, which produces partial differential equations (PDEs). The rheology of the movement is extended and computed in a revolving setting under the assumption that the movement is caused by a rotatingfloppy. Before the solution was found using the finite difference method, complicated generated PDEs were transformed into corresponding ODEs (Keller Box method). A rise in the implicated influencing factors has numerous notable physical impacts that have been seen and recorded. The Keller Box method (KBM) approach is also delivered for simulating the determination of nonlinear system problems faced in developing liquid and supplementary algebraic dynamics domains. The rate of entropy formation rises as the magnetic field parameter and radiation parameter increase. Entropy production rate decreases as the Brinkman number and Hall current parameter become more enriched. The thermal efficiency of ternary HNFs compared to conventional HNFs losses to a low of 4.8% and peaks to 5.2%.
Creating a kidney organoid-vasculature interaction model using a novel organ-on-chip system
Authors: Bas-Cristóbal Menéndez Amanda , Du Z. , van den Bosch T. P. P. , Othman A. , Gaio N. , Silvestri C. , Quirós W. , Lin H. , Korevaar S. , Merino A. , Mulder J. , Hoogduijn M. J.
Published: November 2022

Kidney organoids derived from human induced pluripotent stem cells (iPSCs) have proven to be a valuable tool to study kidney development and disease. However, the lack of vascularization of these organoids often leads to insufficient oxygen and nutrient supply. Vascularization has previously been achieved by implantation into animal models, however, the vasculature arises largely from animal host tissue. Our aim is to transition from an in vivo implantation model towards an in vitro model that fulfils the advantages of vascularization whilst being fully human-cell derived. Our chip system supported culturing of kidney organoids, which presented nephron structures. We also showed that organoids cultured on chip showed increased maturation of endothelial populations based on a colocalization analysis of endothelial markers. Moreover, we observed migration and proliferation of human umbilical vein endothelial cells (HUVECs) cultured in the channels of the chip inside the organoid tissue, where these HUVECs interconnected with endogenous endothelial cells and formed structures presenting an open lumen resembling vessels. Our results establish for the first-time vascularization of kidney organoids in HUVEC co-culture conditions using a microfluidic organ-on-chip. Our model therefore provides a useful insight into kidney organoid vascularization in vitro and presents a tool for further studies of kidney development and drug testing, both for research purposes and pre-clinical applications.
Development of eye phantom for mimicking the deformation of the human cornea accompanied by intraocular pressure alterations
Authors: Cho Han Saem , Jeoung Sae Chae , Yang Yun Sik
Published: November 2022

Comparative studies between artificial eyeball phantoms and in-vivo human subjects were carried out to better understanding the structural deformation of the cornea under varying intraocular pressure (IOP). The IOP-induced deformation and the tension of the cornea were measured by using an optical coherence tomography and noncontact tonometer readings, respectively. The dependence of the central cornea thickness (CCT) and corneal radius of curvature (CRC) on the IOP differed significantly between the full eyeball phantom (FEP) and cornea eyeball phantom (CEP) models. While the CCT changes were very similar between the two models, the relation between the CRC and the IOP was dependent on the type of eye phantom. For the CEP, the CRC drastically decreased as internal pressure increased. However, we found that the changes in the CRC of FEP was dependent on initial CCT under zero IOP (CCT0). When CCT0 was less than 460 μm, the CRC slightly decreased as IOP increased. Meanwhile, the CRC increased as IOP increased if CCT0 was 570 μm. A constitutive mechanical model was proposed to describe the response of the cornea accompanied by the changes in IOP. In vivo measurements on human subjects under both noninvasive and invasive conditions revealed that the relation between the CRC on the IOP is much closer to those observed from FEP. Considering the observed structural deformation of human cornea, we found that FEP mimics the human eye more accurately than the CEP. In addition, the tonometry readings of IOP show that the values from the CEP were overestimated, while those from the FEP were not. For these reasons, we expect that the FEP could be suitable for the estimation of true IOP and allow performance testing of tonometers for medical checkups and other clinical uses.
Comparing the extraction methods, chemical composition, phenolic contents and antioxidant activity of edible oils from Cannabis sativa and Silybum marianu seeds
Authors: Kalinowska Monika , Płońska Anna , Trusiak Magdalena , Gołębiewska Ewelina , Gorlewska-Pietluszenko Anna
Published: November 2022

In the study the cold-pressed, natural (unfiltered, unrefined) vegetable oils: hemp and milk thistle seed oils were tested for their chemical composition and antioxidant properties. The physico-chemical parameters, content of saturated and unsaturated fatty acids were determined. Solid phase extraction and simple extraction with the use of methanol, ethanol, 80% methanol, 80% ethanol were used to obtain the extracts for the analysis of antioxidant activity and phenolic compounds in oils. The composition of phenolic compounds was studied by means of high-performance liquid chromatography (HPLC–DAD) and spectrophotometric test with the Folin-Ciocalteu reagent. The antioxidant property of extracts was established by means of the following methods: with the DPPH•(2,2-diphenyl-1-picrylhydrazyl) radical, ABTS•+(2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) cation radical, FRAP (ferric ion reducing antioxidant parameter) and CUPRAC (cupric-reducing antioxidant capacity). Moreover the influence of chlorogenic acid on the inhibition of lipid peroxidation process in the hemp and milk thistle seed oils was also investigated. The tested oils showed different antioxidant properties which was related to the their different chemical composition. The main phenolic compounds present in hemp seed oil were vanillic, ferulic andp-coumaric acids, (-)epicatechin, catechin, kaempferol and procyanidin B2, whereas in milk thistle seed oil—catechins, procyanidin B2, procyanidin C1,p-coumaric acid, phloridzin, quercetin, protocatechuic acid, kaempferol, and syringic acid. The methanolic extracts of hemp and milk thistle seed oils showed the highest antiradical activity, whereas the ethanolic extracts revealed the best reducing properties. The obtained antioxidant parameters for hemp seed oil were: the IC50 = 3.433 ± 0.017 v/v (DPPH test), the percent of ABTS•+inhibition = 93.301 ± 1.099%, FRAP value = 1063.883 ± 39.225 µmol Fe2+, CUPRAC value = 420.471 ± 1.765 µmol of Trolox. Whereas the antioxidant parameters for milk thistle seed oil were: the IC50 = 5.280 ± 0.584 v/v (DPPH test), 79.59 ± 3.763% (ABTS test), 2891.08 ± 270.044 µmol Fe2+(FRAP test), 255.48 ± 26.169 µmol of Trolox (CUPRAC assay). Chlorogenic acid effectively inhibited the lipid peroxidation process in hemp and milk thistle seed oils.
Investigating longitudinal associations of hair cortisol and cortisone with cognitive functioning and dementia
Authors: Santoso Cornelia , Stuckler David , Ihle Andreas
Published: November 2022

We rigorously investigated potential longitudinal associations of hair cortisol and cortisone with verbal memory, time orientation, and dementia, adjusting for sociodemographic and health confounders. Data from the English Longitudinal Study of Ageing wave 6–9 (6-year follow-up, covering 4399 persons aged 50+) were analysed using linear random effects and cox regression models. In unadjusted models, hair cortisol was associated with worsened verbal memory (β 0.19; SE 0.08), but not with time orientation (β 0.02; SE 0.01), or dementia (β 0.07; SE 0.16). Hair cortisone was associated with worsened verbal memory (β 0.74; SE 0.14) and time orientation (β 0.06; SE 0.02), but not with dementia (β 0.47; SE 0.28). However, in the fully adjusted models, neither hair cortisol nor cortisone was associated with verbal memory, time orientation, or dementia. Consistent with prior studies, we found that more advanced age was associated with worsened verbal memory (β 0.15; SE 0.01), time orientation (β 0.01; SE 0.00), and dementia risk (β 0.11; SE 0.02). Our rigorous analyses did not detect robust associations of neither hair cortisol nor cortisone with cognitive functioning or dementia across 6 years. More detailed insights into potential mechanisms are discussed.
Enhancement of river flooding due to global warming
Authors: Alifu Haireti , Hirabayashi Yukiko , Imada Yukiko , Shiogama Hideo
Published: November 2022

Human-induced climate change has increased the frequency and intensity of heavy precipitation1. Due to the complexity of runoff generation and the streamflow process, the historical impact of human-induced climate change on river flooding remains uncertain. Here, we address the question of whether anthropogenic climate change has altered the probability of the extreme river flood events for the period 1951–2010 based on simulated river discharge derived from large ensemble climate experiments with and without human-induced climate change. The results indicate that human-induced climate change altered the probabilities of 20 of the 52 analyzed flood events. Fourteen of these 20 flood events, which occurred mainly in Asia and South America, were very likely to have been enhanced by human-induced climate change due to an increase in heavy precipitation. Conversely, two flood events in North/South America and two flood events in Asia and two flood events in Europe were suppressed by human-induced climate change, perhaps as a result of lower snowfall. Human-induced climate change has enhanced flooding more prominently in recent years, providing important insights into potential adaptation strategies for river flooding.
Rapid identification of Staphylococcus aureus based on a fluorescence imaging/detection platform that combines loop mediated isothermal amplification assay and the smartphone-based system
Authors: Cabrales-Arellano Patricia , Park Edward , Minor Martha , Delgado Efren , Valles-Rosales Delia , Taboada Heidi , Espiritu José , Su Jianzhong , Park Young Ho
Published: November 2022

Food associated diseases pose significant public health threat in the United States. Health risks associated with food-borne pathogens drive the need for constant monitoring of food products. An efficient method that can diagnose food-borne pathogens rapidly will be invaluable and in high demand. In this study, we showed the feasibility of a novel rapid detection platform based on fluorescence imaging/detection that combines a user-friendly, portable loop mediated isothermal amplification (LAMP) reaction device and a smartphone-based detection system. The proposed platform was used to detect Staphylococcus aureus which is one of the most important food-borne pathogen especially dairy products. The complete protocol is quicker; the reaction is performed under isothermal conditions and completed in 1 h or less. Experimental results show that LAMP assays were ten-fold more sensitive than PCR-based detection. The proposed smartphone detection system was able to detect and quantify LAMP assay samples containing three different concentrations of S. aureus from 109 CFU/mL down to 103 CFU/mL. The present proof-of-concept study demonstrated that this platform offers a portable, easy to use method for measuring target pathogens with LAMP amplification.
Moderation of marital status and living arrangements in the relationship between social participation and life satisfaction among older Indian adults
Authors: Nagargoje Varsha P. , James K. S. , Muhammad T.
Published: November 2022

Social participation is considered one of the central components of successful and healthy aging. This study aimed to examine the moderating role of marital status and living arrangement with social participation and its association with life satisfaction of older Indian adults. Samples of 31,464 individuals aged ≥ 60 years were extracted from the Longitudinal Ageing Study in India, wave-1. Descriptive statistics, bivariate analysis, and multivariable linear regression were performed for the analysis. The moderation effect of marital status and living arrangements on the relationship between social participation and level of life satisfaction among Indian older adults were also analyzed. Overall, life satisfaction among older men was relatively higher than older women in this study. Older adults’ involvement in social participation [β = 0.39, p < 0.05], being in marital union [β = 0.68, p < 0.001] and co-residing either with spouse [β = 1.73, p < 0.001] or with other family members [β = 2.18, p < 0.001] were positively related to their greater life satisfaction. Interaction of social participation with marital status showed that participating in social activities can boost life satisfaction only among married older people. Further, moderation effect of social participation with living arrangements showed that older adults who were not involved in social participation but living with a spouse or any other household members had higher life satisfaction, and again participation in social activities increased their life satisfaction to a greater level. The establishment of social clubs and advocating social policies oriented toward meaningful social connections are highly needed, especially for older Indians living alone or currently not in a marital union, which will help to enhance their overall life satisfaction.
Habitat types and megabenthos composition from three sponge-dominated high-Arctic seamounts
Authors: Stratmann Tanja , Simon-Lledó Erik , Morganti Teresa Maria , de Kluijver Anna , Vedenin Andrey , Purser Autun
Published: November 2022

Seamounts are isolated underwater mountains stretching > 1000 m above the seafloor. They are identified as biodiversity hotspots of marine life, and host benthic assemblages that may vary on regional (among seamounts) and local (within seamounts) scales. Here, we collected seafloor imagery of three seamounts at the Langseth Ridge in the central Arctic Ocean to assess habitats and megabenthos community composition at the Central Mount (CM), the Karasik Seamount (KS), and the Northern Mount (NM). The majority of seafloor across these seamounts comprised bare rock, covered with a mixed layer of sponge spicule mats intermixed with detrital debris composed of polychaete tubes, and sand, gravel, and/or rocks. The megabenthos assemblages consisted of in total 15 invertebrate epibenthos taxa and 4 fish taxa, contributing to mean megabenthos densities of 55,745 ind. ha−1at CM, 110,442 ind. ha−1at KS, and 65,849 ind. ha−1at NM. The faunal assemblages at all three seamounts were dominated by habitat-forming Tetractinellida sponges that contributed between 66% (KS) and 85% (CM) to all megabenthos. Interestingly, taxa richness did not differ at regional and local scale, whereas the megabenthos community composition did. Abiotic and biogenic factors shaping distinct habitat types played a major role in structuring of benthic communities in high-Arctic seamounts.
Increased aerosols can reverse Twomey effect in water clouds through radiative pathway
Authors: Khatri Pradeep , Hayasaka Tadahiro , Holben Brent N. , Singh Ramesh P. , Letu Husi , Tripathi Sachchida N.
Published: November 2022

Aerosols play important roles in modulations of cloud properties and hydrological cycle by decreasing the size of cloud droplets with the increase of aerosols under the condition of fixed liquid water path, which is known as the first aerosol indirect effect or Twomey-effect or microphysical effect. Using high-quality aerosol data from surface observations and statistically decoupling the influence of meteorological factors, we show that highly loaded aerosols can counter this microphysical effect through the radiative effect to result both the decrease and increase of cloud droplet size depending on liquid water path in water clouds. The radiative effect due to increased aerosols reduces the moisture content, but increases the atmospheric stability at higher altitudes, generating conditions favorable for cloud top entrainment and cloud droplet coalescence. Such radiatively driven cloud droplet coalescence process is relatively stronger in thicker clouds to counter relatively weaker microphysical effect, resulting the increase of cloud droplet size with the increase of aerosol loading; and vice-versa in thinner clouds. Overall, the study suggests the prevalence of both negative and positive relationships between cloud droplet size and aerosol loading in highly polluted regions.
Tandem repeats structure of gel-forming mucin domains could be revealed by SMRT sequencing data
Authors: Lang Tiange
Published: November 2022

Mucins are large glycoproteins that cover and protect epithelial surface of the body. Mucin domains of gel-forming mucins are rich in proline, threonine, and serine that are heavily glycosylated. These domains show great complexity with tandem repeats, thus make it difficult to study the sequences. With the coming of single molecule real-time (SMRT) sequencing technologies, we manage to present sequence structure of mucin domains via SMRT long reads for gel-forming mucins MUC2, MUC5AC, MUC5B and MUC6. Our study shows that for different individuals, single nucleotide polymorphisms could be found in mucin domains of MUC2, MUC5AC, MUC5B and MUC6, while different number of tandem repeats could be found in mucin domains of MUC2 and MUC6. Furthermore, we get the sequence of MUC2, MUC5AC, and MUC5B mucin domain in a Chinese individual for each nucleotide at accuracy of possibly 99.98–99.99%, 99.93–99.99%, and 99.76–99.99%, respectively. We report a new method to obtain DNA sequence of gel-forming mucin domains. This method will provided new insights on getting the sequence for Tandem Repeat parts which locate in coding region. With the sequences we obtained through this method, we can give more information for people to study the sequences of gel-forming mucin domains.
The relative role of the subsurface Southern Ocean in driving negative Antarctic Sea ice extent anomalies in 2016–2021
Authors: Zhang Liping , Delworth Thomas L. , Yang Xiaosong , Zeng Fanrong , Lu Feiyu , Morioka Yushi , Bushuk Mitchell
Published: November 2022

The low Antarctic sea ice extent following its dramatic decline in late 2016 has persisted over a multiyear period. However, it remains unclear to what extent this low sea ice extent can be attributed to changing ocean conditions. Here, we investigate the causes of this period of low Antarctic sea ice extent using a coupled climate model partially constrained by observations. We find that the subsurface Southern Ocean played a smaller role than the atmosphere in the extreme sea ice extent low in 2016, but was critical for the persistence of negative anomalies over 2016–2021. Prior to 2016, the subsurface Southern Ocean warmed in response to enhanced westerly winds. Decadal hindcasts show that subsurface warming has persisted and gradually destabilized the ocean from below, reducing sea ice extent over several years. The simultaneous variations in the atmosphere and ocean after 2016 have further amplified the decline in Antarctic sea ice extent.
Boosting cancer immunotherapy by biomineralized nanovaccine with ferroptosis-inducing and photothermal properties
Authors: Ma Siyu , Liang Xiao , Yang Ning , Yang Jie , Zhang Jun , Pan Xiuhua , Wei Yawen , Liu Zengyi , Shen Qi
Published: November 2022

The biomineralized nanovaccine with ferroptosis-inducing and photothermal properties boosted antitumor immunotherapy and exhibited satisfactory therapeutic effect for melanoma.
Ionic liquid-mediated hexagonally porous ZnO nanocrystal-supported Au catalysts: highly stable materials for aldehyde oxidative esterification
Authors: Zheng Yanxia , Yang Lixi , Chen Yao , Yang Yubo , Zuo Cuncun , An Jiutao , Wang Qian , Huang Haofei , Li Yuchao , Wang Ming
Published: November 2022

Ionic liquid-mediated hexagonally porous ZnO nanocrystal-supported Au catalysts: highly efficient and stable materials for oxidative esterification of methylacrolein.