bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractAs 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

AbstractIce 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

AbstractMacrophages 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

AbstractAntiferromagnetic (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

AbstractAntimicrobial 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

AbstractPerivascular 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

AbstractElevated 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

AbstractOctopuses 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

AbstractThe 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

AbstractThe 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

AbstractWe 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

AbstractWe 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

AbstractTwo 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

AbstractGenomic 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

AbstractNonadherence 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

AbstractType 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.