bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscale reshaping of resonant dielectric microstructures by light-driven explosions
Authors: Shcherbakov Maxim R. , Sartorello Giovanni , Zhang Simin , Bocanegra Joshua , Bosch Melissa , Tripepi Michael , Talisa Noah , AlShafey Abdallah , Smith Joseph , Londo Stephen , Légaré François , Chowdhury Enam , Shvets Gennady 
Published: October 2023

AbstractFemtosecond-laser-assisted material restructuring employs extreme optical intensities to localize the ablation regions. To overcome the minimum feature size limit set by the wave nature of photons, there is a need for new approaches to tailored material processing at the nanoscale. Here, we report the formation of deeply-subwavelength features in silicon, enabled by localized laser-induced phase explosions in prefabricated silicon resonators. Using short trains of mid-infrared laser pulses, we demonstrate the controllable formation of high aspect ratio (>10:1) nanotrenches as narrow as $${\sim }{{{{{\boldsymbol{\lambda }}}}}}{{{{{\boldsymbol{/}}}}}}{{{{{\boldsymbol{80}}}}}}$$
~
λ
/
80
. The trench geometry is shown to be scalable with wavelength, and controlled by multiple parameters of the laser pulse train, such as the intensity and polarization of each laser pulse and their total number. Particle-in-cell simulations reveal localized heating of silicon beyond its boiling point and suggest its subsequent phase explosion on the nanoscale commensurate with the experimental data. The observed femtosecond-laser assisted nanostructuring of engineered microstructures (FLANEM) expands the nanofabrication toolbox and opens exciting opportunities for high-throughput optical methods of nanoscale structuring of solid materials.
Mass production of lumenogenic human embryoid bodies and functional cardiospheres using in-air-generated microcapsules
Authors: van Loo Bas , ten Den Simone A. , Araújo-Gomes Nuno , de Jong Vincent , Snabel Rebecca R. , Schot Maik , Rivera-Arbeláez José M. , Veenstra Gert Jan C. , Passier Robert , Kamperman Tom , Leijten Jeroen 
Published: October 2023

AbstractOrganoids are engineered 3D miniature tissues that are defined by their organ-like structures, which drive a fundamental understanding of human development. However, current organoid generation methods are associated with low production throughputs and poor control over size and function including due to organoid merging, which limits their clinical and industrial translation. Here, we present a microfluidic platform for the mass production of lumenogenic embryoid bodies and functional cardiospheres. Specifically, we apply triple-jet in-air microfluidics for the ultra-high-throughput generation of hollow, thin-shelled, hydrogel microcapsules that can act as spheroid-forming bioreactors in a cytocompatible, oil-free, surfactant-free, and size-controlled manner. Uniquely, we show that microcapsules generated by in-air microfluidics provide a lumenogenic microenvironment with near 100% efficient cavitation of spheroids. We demonstrate that upon chemical stimulation, human pluripotent stem cell-derived spheroids undergo cardiomyogenic differentiation, effectively resulting in the mass production of homogeneous and functional cardiospheres that are responsive to external electrical stimulation. These findings drive clinical and industrial adaption of stem cell technology in tissue engineering and drug testing.
Decline in Iran’s groundwater recharge
Authors: Noori Roohollah , Maghrebi Mohsen , Jessen Søren , Bateni Sayed M. , Heggy Essam , Javadi Saman , Noury Mojtaba , Pistre Severin , Abolfathi Soroush , AghaKouchak Amir 
Published: October 2023

AbstractGroundwater recharge feeds aquifers supplying fresh-water to a population over 80 million in Iran—a global hotspot for groundwater depletion. Using an extended database comprising abstractions from over one million groundwater wells, springs, and qanats, from 2002 to 2017, here we show a significant decline of around −3.8 mm/yr in the nationwide groundwater recharge. This decline is primarily attributed to unsustainable water and environmental resources management, exacerbated by decadal changes in climatic conditions. However, it is important to note that the former’s contribution outweighs the latter. Our results show the average annual amount of nationwide groundwater recharge (i.e., ~40 mm/yr) is more than the reported average annual runoff in Iran (i.e., ~32 mm/yr), suggesting the surface water is the main contributor to groundwater recharge. Such a decline in groundwater recharge could further exacerbate the already dire aquifer depletion situation in Iran, with devastating consequences for the country’s natural environment and socio-economic development.
Detecting the spin-polarization of edge states in graphene nanoribbons
Authors: Brede Jens , Merino-Díez Nestor , Berdonces-Layunta Alejandro , Sanz Sofía , Domínguez-Celorrio Amelia , Lobo-Checa Jorge , Vilas-Varela Manuel , Peña Diego , Frederiksen Thomas , Pascual José I. , de Oteyza Dimas G. , Serrate David 
Published: October 2023

AbstractLow dimensional carbon-based materials can show intrinsic magnetism associated to p-electrons in open-shell π-conjugated systems. Chemical design provides atomically precise control of the π-electron cloud, which makes them promising for nanoscale magnetic devices. However, direct verification of their spatially resolved spin-moment remains elusive. Here, we report the spin-polarization of chiral graphene nanoribbons (one-dimensional strips of graphene with alternating zig-zag and arm-chair boundaries), obtained by means of spin-polarized scanning tunnelling microscopy. We extract the energy-dependent spin-moment distribution of spatially extended edge states with π-orbital character, thus beyond localized magnetic moments at radical or defective carbon sites. Guided by mean-field Hubbard calculations, we demonstrate that electron correlations are responsible for the spin-splitting of the electronic structure. Our versatile platform utilizes a ferromagnetic substrate that stabilizes the organic magnetic moments against thermal and quantum fluctuations, while being fully compatible with on-surface synthesis of the rapidly growing class of nanographenes.
Soluble TREM2 ameliorates tau phosphorylation and cognitive deficits through activating transgelin-2 in Alzheimer’s disease
Authors: Zhang Xingyu , Tang Li , Yang Jiaolong , Meng Lanxia , Chen Jiehui , Zhou Lingyan , Wang Jiangyu , Xiong Min , Zhang Zhentao 
Published: October 2023

AbstractTriggering receptor expressed on myeloid cells 2 (TREM2) is a transmembrane protein that is predominantly expressed by microglia in the brain. The proteolytic shedding of TREM2 results in the release of soluble TREM2 (sTREM2), which is increased in the cerebrospinal fluid of patients with Alzheimer’s disease (AD). It remains unknown whether sTREM2 regulates the pathogenesis of AD. Here we identified transgelin-2 (TG2) expressed on neurons as the receptor for sTREM2. The microglia-derived sTREM2 binds to TG2, induces RhoA phosphorylation at S188, and deactivates the RhoA-ROCK-GSK3β pathway, ameliorating tau phosphorylation. The sTREM2 (77-89) fragment, which is the minimal active sequence of sTREM2 to activate TG2, mimics the inhibitory effect of sTREM2 on tau phosphorylation. Overexpression of sTREM2 or administration of the active peptide rescues tau pathology and behavioral defects in the tau P301S transgenic mice. Together, these findings demonstrate that the sTREM2-TG2 interaction mediates the cross-talk between microglia and neurons. sTREM2 and its active peptide may be a potential therapeutic intervention for tauopathies including AD.
High anisotropy in electrical and thermal conductivity through the design of aerogel-like superlattice (NaOH)0.5NbSe2
Authors: Sun Ruijin , Deng Jun , Wu Xiaowei , Hao Munan , Ma Ke , Ma Yuxin , Zhao Changchun , Meng Dezhong , Ji Xiaoyu , Ding Yiyang , Pang Yu , Qian Xin , Yang Ronggui , Li Guodong , Li Zhilin , Dai Linjie , Ying Tianping , zhao Huaizhou , Du Shixuan , Li Gang , Jin Shifeng , Chen Xiaolong 
Published: October 2023

AbstractInterlayer decoupling plays an essential role in realizing unprecedented properties in atomically thin materials, but it remains relatively unexplored in the bulk. It is unclear how to realize a large crystal that behaves as its monolayer counterpart by artificial manipulation. Here, we construct a superlattice consisting of alternating layers of NbSe2 and highly porous hydroxide, as a proof of principle for realizing interlayer decoupling in bulk materials. In (NaOH)0.5NbSe2, the electric decoupling is manifested by an ideal 1D insulating state along the interlayer direction. Vibration decoupling is demonstrated through the absence of interlayer models in the Raman spectrum, dominant local modes in heat capacity, low interlayer coupling energy and out-of-plane thermal conductivity (0.28 W/mK at RT) that are reduced to a few percent of NbSe2’s. Consequently, a drastic enhancement of CDW transition temperature (>110 K) and Pauling-breaking 2D superconductivity is observed, suggesting that the bulk crystal behaves similarly to an exfoliated NbSe2 monolayer. Our findings provide a route to achieve intrinsic 2D properties on a large-scale without exfoliation.
Crystal structure prediction at finite temperatures
Authors: Kruglov Ivan A. , Yanilkin Alexey V. , Propad Yana , Mazitov Arslan B. , Rachitskii Pavel , Oganov Artem R. 
Published: October 2023

AbstractCrystal structure prediction is a central problem of crystallography and materials science, which until mid-2000s was considered intractable. Several methods, based on either energy landscape exploration or, more commonly, global optimization, largely solved this problem and enabled fully non-empirical computational materials discovery. A major shortcoming is that, to avoid expensive calculations of the entropy, crystal structure prediction was done at zero Kelvin, reducing to the search for the global minimum of the enthalpy rather than the free energy. As a consequence, high-temperature phases (especially those which are not quenchable to zero temperature) could be missed. Here we develop an accurate and affordable solution, enabling crystal structure prediction at finite temperatures. Structure relaxation and fully anharmonic free energy calculations are done by molecular dynamics with a forcefield (which can be anything from a parametric forcefield for simpler cases to a trained on-the-fly machine learning interatomic potential), the errors of which are corrected using thermodynamic perturbation theory to yield accurate results with full ab initio accuracy. We illustrate this method by applications to metals (probing the P–T phase diagram of Al and Fe), a refractory covalent solid (WB), an Earth-forming silicate MgSiO3 (at pressures and temperatures of the Earth’s lower mantle), and ceramic oxide HfO2.
Symmetry-driven half-integer conductance quantization in Cobalt–fulvalene sandwich nanowire
Authors: Jiang Zhuoling , Yam Kah-Meng , Ang Yee Sin , Guo Na , Zhang Yongjie , Wang Hao , Zhang Chun 
Published: October 2023

AbstractPrecise manipulation and monitoring spin transport in one-dimensional (1D) systems is a long-sought goal in the field of nano-spintronics. Based on first-principles calculations, we report the observation of half-integer conductance quantization in the Cobalt-fulvalene sandwich nanowire. Compared with a pure monatomic Cobalt wire, the introduction of fulvalene molecules leads to three important features: Firstly, the strong coupling between the fulvalene and the Cobalt prevents the contamination of the ambient air, ensuring both chemical and physical stabilities; Secondly, the fulvalene symmetry-selectively filters out most of the d-type orbitals of the Cobalt while leaving a single d-type orbital to form an open spin channel around the Fermi level, which offers a mechanism to achieve the observed half-integer conductance; Thirdly, it maintains a superexchange coupling between adjacent Co atoms to achieve a high Curie temperature. Spin transport calculations show that this half-metallic nanowire can serve as a perfect spin filter or a spin valve device, thus revealing the potential of Cobalt-fulvalene sandwich nanowire as a promising building block of high-performance spintronics technology.
Rare predicted loss of function alleles in Bassoon (BSN) are associated with obesity
Authors: Zhu Na , LeDuc Charles A. , Fennoy Ilene , Laferrère Blandine , Doege Claudia A. , Shen Yufeng , Chung Wendy K. , Leibel Rudolph L. 
Published: October 2023

AbstractBassoon (BSN) is a component of a hetero-dimeric presynaptic cytomatrix protein that orchestrates neurotransmitter release with Piccolo (PCLO) from glutamatergic neurons throughout the brain. Heterozygous missense variants in BSN have previously been associated with neurodegenerative disorders in humans. We performed an exome-wide association analysis of ultra-rare variants in about 140,000 unrelated individuals from the UK Biobank to search for new genes associated with obesity. We found that rare heterozygous predicted loss of function (pLoF) variants in BSN are associated with higher BMI with p-value of 3.6e-12 in the UK biobank cohort. Additionally, we identified two individuals (one of whom has a de novo variant) with a heterozygous pLoF variant in a cohort of early onset or extreme obesity and report the clinical histories of these individuals with non-syndromic obesity with no history of neurobehavioral or cognitive disability. The BMI association was replicated in the All of Us whole genome sequencing data. Heterozygous pLoF BSN variants constitute a new etiology for obesity.
How do gravity alterations affect animal and human systems at a cellular/tissue level?
Authors: Cialdai Francesca , Brown Austin M. , Baumann Cory W. , Angeloni Debora , Baatout Sarah , Benchoua Alexandra , Bereiter-Hahn Juergen , Bottai Daniele , Buchheim Judith-Irina , Calvaruso Marco , Carnero-Diaz Eugénie , Castiglioni Sara , Cavalieri Duccio , Ceccarelli Gabriele , Choukér Alexander , Ciofani Gianni , Coppola Giuseppe , Cusella Gabriella , Degl’Innocenti Andrea , Desaphy Jean-Francois , Frippiat Jean-Pol , Gelinsky Michael , Genchi Giada , Grano Maria , Grimm Daniela , Guignandon Alain , Hahn Christiane , Hatton Jason , Herranz Raúl , Hellweg Christine E. , Iorio Carlo Saverio , Karapantsios Thodoris , van Loon Jack , Lulli Matteo , Maier Jeanette , Malda Jos , Mamaca Emina , Morbidelli Lucia , van Ombergen Angelique , Osterman Andreas , Ovsianikov Aleksandr , Pampaloni Francesco , Pavezlorie Elizabeth , Pereda-Campos Veronica , Przybyla Cyrille , Puhl Christopher , Rettberg Petra , Risaliti Chiara , Rizzo Angela Maria , Robson-Brown Kate , Rossi Leonardo , Russo Giorgio , Salvetti Alessandra , Santucci Daniela , Sperl Matthias , Strollo Felice , Tabury Kevin , Tavella Sara , Thielemann Christiane , Willaert Ronnie , Szewczyk Nathaniel J. , Monici Monica 
Published: October 2023

AbstractThe present white paper concerns the indications and recommendations of the SciSpacE Science Community to make progress in filling the gaps of knowledge that prevent us from answering the question: “How Do Gravity Alterations Affect Animal and Human Systems at a Cellular/Tissue Level?” This is one of the five major scientific issues of the ESA roadmap “Biology in Space and Analogue Environments”. Despite the many studies conducted so far on spaceflight adaptation mechanisms and related pathophysiological alterations observed in astronauts, we are not yet able to elaborate a synthetic integrated model of the many changes occurring at different system and functional levels. Consequently, it is difficult to develop credible models for predicting long-term consequences of human adaptation to the space environment, as well as to implement medical support plans for long-term missions and a strategy for preventing the possible health risks due to prolonged exposure to spaceflight beyond the low Earth orbit (LEO). The research activities suggested by the scientific community have the aim to overcome these problems by striving to connect biological and physiological aspects in a more holistic view of space adaptation effects.
Estimating pitting descriptors of 316 L stainless steel by machine learning and statistical analysis
Authors: Coelho Leonardo Bertolucci , Torres Daniel , Vangrunderbeek Vincent , Bernal Miguel , Paldino Gian Marco , Bontempi Gianluca , Ustarroz Jon 
Published: October 2023

AbstractA hybrid rule-based/ML approach using linear regression and artificial neural networks (ANNs) determined pitting corrosion descriptors from high-throughput data obtained with Scanning Electrochemical Cell Microscopy (SECCM) on 316 L stainless steel. Non-parametric density estimation determined the central tendencies of the Epit/log(jpit) and Epass/log(jpass) distributions. Descriptors estimated using conditional mean or median curves were compared to their central tendency values, with the conditional medians providing more accurate results. Due to their lower sensitivity to high outliers, the conditional medians were more robust representations of the log(j) vs.Edistributions. An observed trend of passive range shortening with increasing testing aggressiveness was attributed to delayed stabilisation of the passive film, rather than early passivity breakdown.
Expanding causal genes for Parkinson’s disease via multi-omics analysis
Authors: Gu Xiao-Jing , Su Wei-Ming , Dou Meng , Jiang Zheng , Duan Qing-Qing , Yin Kang-Fu , Cao Bei , Wang Yi , Li Guo-Bo , Chen Yong-Ping 
Published: October 2023

AbstractGenome‑wide association studies (GWASs) have revealed numerous loci associated with Parkinson’s disease (PD). However, some potential causal/risk genes were still not revealed and no etiological therapies are available. To find potential causal genes and explore genetically supported drug targets for PD is urgent. By integrating the expression quantitative trait loci (eQTL) and protein quantitative trait loci (pQTL) datasets from multiple tissues (blood, cerebrospinal fluid (CSF) and brain) and PD GWAS summary statistics, a pipeline combing Mendelian randomization (MR), Steiger filtering analysis, Bayesian colocalization, fine mapping, Protein-protein network and enrichment analysis were applied to identify potential causal genes for PD. As a result, GPNMB displayed a robust causal role for PD at the protein level in the blood, CSF and brain, and transcriptional level in the brain, while the protective role of CD38 (in brain pQTL and eQTL) was also identified. We also found inconsistent roles of DGKQ on PD between protein and mRNA levels. Another 9 proteins (CTSB, ARSA, SEC23IP, CD84, ENTPD1, FCGR2B, BAG3, SNCA, FCGR2A) were associated with the risk for PD based on only a single pQTL after multiple corrections. We also identified some proteins’ interactions with known PD causative genes and therapeutic targets. In conclusion, this study suggested GPNMB, CD38, and DGKQ may act in the pathogenesis of PD, but whether the other proteins involved in PD needs more evidence. These findings would help to uncover the genes underlying PD and prioritize targets for future therapeutic interventions.
Spin-orbit coupled spin-polarised hole gas at the CrSe2-terminated surface of AgCrSe2
Authors: Siemann Gesa-R. , Kim Seo-Jin , Morales Edgar Abarca , Murgatroyd Philip A. E. , Zivanovic Andela , Edwards Brendan , Marković Igor , Mazzola Federico , Trzaska Liam , Clark Oliver J. , Bigi Chiara , Zhang Haijing , Achinuq Barat , Hesjedal Thorsten , Watson Matthew D. , Kim Timur K. , Bencok Peter , van der Laan Gerrit , Polley Craig M. , Leandersson Mats , Fedderwitz Hanna , Ali Khadiza , Balasubramanian Thiagarajan , Schmidt Marcus , Baenitz Michael , Rosner Helge , King Phil D. C. 
Published: October 2023

AbstractIn half-metallic systems, electronic conduction is mediated by a single spin species, offering enormous potential for spintronic devices. Here, using microscopic-area angle-resolved photoemission, we show that a spin-polarised two-dimensional hole gas is naturally realised in the polar magnetic semiconductor AgCrSe2 by an intrinsic self-doping at its CrSe2-terminated surface. Through comparison with first-principles calculations, we unveil a striking role of spin-orbit coupling for the surface hole gas, unlocked by both bulk and surface inversion symmetry breaking, suggesting routes for stabilising complex magnetic textures in the surface layer of AgCrSe2.
An ocean front dataset for the Mediterranean sea and southwest Indian ocean
Authors: Sudre Floriane , Hernández-Carrasco Ismael , Mazoyer Camille , Sudre Joel , Dewitte Boris , Garçon Véronique , Rossi Vincent 
Published: October 2023

AbstractFronts are ubiquitous discrete features of the global ocean often associated with enhanced vertical velocities, in turn boosting primary production. Fronts thus form dynamical and ephemeral ecosystems where numerous species meet across all trophic levels. Fronts are also targeted by fisheries. Capturing ocean fronts and studying their long-term variability in relation with climate change is thus key for marine resource management and spatial planning. The Mediterranean Sea and the Southwest Indian Ocean are natural laboratories to study front-marine life interactions due to their energetic flow at sub-to-mesoscales, high biodiversity (including endemic and endangered species) and numerous conservation initiatives. Based on remotely-sensed Sea Surface Temperature and Height, we compute thermal fronts (2003–2020) and attracting Lagrangian coherent structures (1994–2020), in both regions over several decades. We advocate for the combined use of both thermal fronts and attracting Lagrangian coherent structures to study front-marine life interactions. The resulting front dataset differs from other alternatives by its high spatio-temporal resolution, long time coverage, and relevant thresholds defined for ecological provinces.
Contact Endoscopy – Narrow Band Imaging (CE-NBI) data set for laryngeal lesion assessment
Authors: Esmaeili Nazila , Davaris Nikolaos , Boese Axel , Illanes Alfredo , Navab Nassir , Friebe Michael , Arens Christoph 
Published: October 2023

AbstractThe endoscopic examination of subepithelial vascular patterns within the vocal fold is crucial for clinicians seeking to distinguish between benign lesions and laryngeal cancer. Among innovative techniques, Contact Endoscopy combined with Narrow Band Imaging (CE-NBI) offers real-time visualization of these vascular structures. Despite the advent of CE-NBI, concerns have arisen regarding the subjective interpretation of its images. As a result, several computer-based solutions have been developed to address this issue. This study introduces the CE-NBI data set, the first publicly accessible data set that features enhanced and magnified visualizations of subepithelial blood vessels within the vocal fold. This data set encompasses 11144 images from 210 adult patients with pathological vocal fold conditions, where CE-NBI images are annotated using three distinct label categories. The data set has proven invaluable for numerous clinical assessments geared toward diagnosing laryngeal cancer using Optical Biopsy. Furthermore, given its versatility for various image analysis tasks, we have devised and implemented diverse image classification scenarios using Machine Learning (ML) approaches to address critical clinical challenges in assessing laryngeal lesions.