bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Development of Spatial Attention U‐Net for the Recovery of Ionospheric Measurements and Extraction of Ionospheric Parameters
Authors: Huang Guan‐Han , Dmitriev Alexei V. , Lin Chia‐Hsien , Chang Yu‐Chi , Hsieh Mon‐Chai , Tsogtbaatar Enkhtuya , Mendoza Merlin M. , Hsu Hao‐Wei , Lin Yu‐Chiang , Tsai Lung‐Chih , Li Yung‐Hui 
Published: July 2022

AbstractWe train a deep learning artificial neural network model, Spatial Attention U‐Net, to recover useful ionospheric signals from noisy ionogram data measured by Hualien's Vertical Incidence Pulsed Ionospheric Radar. Our results show that the model can well identify F2 layer ordinary and extraordinary modes (F2o and F2x) and the combined signals of the E layer (ordinary and extraordinary modes and sporadic Es). The model is also capable of identifying some signals that were not labeled. The performance of the model can be significantly degraded by insufficient number of samples in the data set. From the recovered signals, we determine the critical frequencies of F2o and F2x and the intersection frequency between the two signals. The difference between the two critical frequencies is peaking at 0.63 MHz, with the uncertainty being 0.18 MHz.
The effect of citalopram treatment on amyloid-β precursor protein processing and oxidative stress in human hNSC-derived neurons
Authors: Elsworthy R. J. , Crowe J. A. , King M. C. , Dunleavy C. , Fisher E. , Ludlam A. , Parri H. R. , Hill E. J. , Aldred S. 
Published: July 2022

AbstractSelective Serotonin Reuptake Inhibitors (SSRIs) may hold therapeutic benefits for people with Alzheimer’s disease (AD). SSRIs may perturb AD progression, or the conversion from MCI to AD, via increased neurogenesis, reduced oxidative stress and/or favourable Amyloid-β Precursor Protein (AβPP) processing. This study used iPSC derived cortical neuronal cells carrying 3 different PSEN1 mutations, to investigate the effect of treatment with the SSRI, Citalopram on AβPP processing and oxidative stress. Control and PSEN1 mutation (L286V, A246E, M146L) iPSC-derived neurons were treated with Citalopram for 45 days. ADAM10 activity, AβPP processing and Aβ generation was measured in addition to cellular redox status. Citalopram treatment reduced the Aβ1-42:40 ratio in control but not in fAD PSEN1 cells. ADAM10 activity was increased with Citalopram treatments in fAD PSEN1 cell lines, which was also seen for sAβPPα secretion. Lower superoxide generation in fAD PSEN1 cells following Citalopram treatment was identified, although there was no effect on end markers of oxidative stress. Treatment with Citalopram appears to have little effect on Aβ generation in fADPSEN1 cells, but our findings suggest that treatment can significantly increase non-amyloidogenic AβPP processing and reduce oxidative stress. These changes may explain why SSRIs appear most effective in the prodromal period of the disease progression, as opposed to reducing established AD pathology. Further investigation of specific pathways conferring the beneficial effects of SSRIs treatment are warranted.
Bone remodeling: an operational process ensuring survival and bone mechanical competence
Authors: Bolamperti Simona , Villa Isabella , Rubinacci Alessandro 
Published: July 2022

AbstractBone remodeling replaces old and damaged bone with new bone through a sequence of cellular events occurring on the same surface without any change in bone shape. It was initially thought that the basic multicellular unit (BMU) responsible for bone remodeling consists of osteoclasts and osteoblasts functioning through a hierarchical sequence of events organized into distinct stages. However, recent discoveries have indicated that all bone cells participate in BMU formation by interacting both simultaneously and at different differentiation stages with their progenitors, other cells, and bone matrix constituents. Therefore, bone remodeling is currently considered a physiological outcome of continuous cellular operational processes optimized to confer a survival advantage. Bone remodeling defines the primary activities that BMUs need to perform to renew successfully bone structural units. Hence, this review summarizes the current understanding of bone remodeling and future research directions with the aim of providing a clinically relevant biological background with which to identify targets for therapeutic strategies in osteoporosis.
Osteocytes regulate bone anabolic response to mechanical loading in male mice via activation of integrin α5
Authors: Zhao Dezhi , Hua Rui , Riquelme Manuel A. , Cheng Hongyun , Guda Teja , Xu Huiyun , Gu Sumin , Jiang Jean X. 
Published: July 2022

AbstractPhysical mechanical stimulation can maintain and even increase bone mass. Here, we report an important role of osteocytic integrin α5 in regulating the anabolic response of bone to mechanical loading using an Itga5 conditional gene knockout (cKO) mouse model. Integrin α5 gene deletion increased apoptotic osteocytes and reduced cortical anabolic responses to tibial compression including decreased endosteal osteoblasts and bone formation, and increased endosteal osteoclasts and bone resorption, contributing to the decreased bone area fraction and biomechanical properties, leading to an enlarged bone marrow area in cKO mice. Similar disruption of anabolic responses to mechanical loading was also detected in cKO trabecular bone. Moreover, integrin α5 deficiency impeded load-induced Cx43 hemichannel opening, and production and release of PGE2, an anabolic factor, resulting in attenuated effects of the loading on catabolic sclerostin (SOST) reduction and anabolic β-catenin increase. Together, this study shows an indispensable role of integrin α5 in osteocytes in the anabolic action of mechanical loading on skeletal tissue through activation of hemichannels and PGE2-evoked gene expression. Integrin α5 could act as a potential new therapeutic target for bone loss, especially in the elderly population with impeded mechanical sensitivity.
Structural basis for the activation and ligand recognition of the human oxytocin receptor
Authors: Waltenspühl Yann , Ehrenmann Janosch , Vacca Santiago , Thom Cristian , Medalia Ohad , Plückthun Andreas 
Published: July 2022

AbstractThe small cyclic neuropeptide hormone oxytocin (OT) and its cognate receptor play a central role in the regulation of social behaviour and sexual reproduction. Here we report the single-particle cryo-electron microscopy structure of the active oxytocin receptor (OTR) in complex with its cognate ligand oxytocin. Our structure provides high-resolution insights into the OT binding mode, the OTR activation mechanism as well as the subtype specificity within the oxytocin/vasopressin receptor family.
Spongy all-in-liquid materials by in-situ formation of emulsions at oil-water interfaces
Authors: Bazazi Parisa , Stone Howard A. , Hejazi S. Hossein 
Published: July 2022

AbstractPrinting a structured network of functionalized droplets in a liquid medium enables engineering collectives of living cells for functional purposes and promises enormous applications in processes ranging from energy storage to tissue engineering. Current approaches are limited to drop-by-drop printing or face limitations in reproducing the sophisticated internal features of a structured material and its interactions with the surrounding media. Here, we report a simple approach for creating stable liquid filaments of silica nanoparticle dispersions and use them as inks to print all-in-liquid materials that consist of a network of droplets. Silica nanoparticles stabilize liquid filaments at Weber numbers two orders of magnitude smaller than previously reported in liquid-liquid systems by rapidly producing a concentrated emulsion zone at the oil-water interface. We experimentally demonstrate the printed aqueous phase is emulsified in-situ; consequently, a 3D structure is achieved with flexible walls consisting of layered emulsions. The tube-like printed features have a spongy texture resembling miniaturized versions of “tube sponges” found in the oceans. A scaling analysis based on the interplay between hydrodynamics and emulsification kinetics reveals that filaments are formed when emulsions are generated and remain at the interface during the printing period. Stabilized filaments are utilized for printing liquid-based fluidic channels.
Molecular signatures of in situ to invasive progression for basal-like breast cancers: An integrated mouse model and human DCIS study
Authors: Thennavan Aatish , Garcia-Recio Susana , Liu Siyao , He Xiaping , Perou Charles M. 
Published: July 2022

AbstractDuctal carcinoma in situ (DCIS) of the breast is a non-obligate precursor of Invasive Ductal Carcinoma (IDC) and thus the identification of features that may predict DCIS progression would be of potential clinical value. Experimental mouse models can be used to address this challenge by studying DCIS-to-IDC biology. Here we utilize single cell RNA sequencing (scRNAseq) on the C3Tag genetically engineered mouse model that forms DCIS-like precursor lesions and for which many lesions progress into end-stage basal-like molecular subtype IDC. We also perform bulk RNAseq analysis on 10 human synchronous DCIS-IDC pairs comprised of estrogen receptor (ER) positive and ER-negative subsets and utilize 2 additional public human DCIS data sets for comparison to our mouse model. By identifying malignant cells using inferred DNA copy number changes from the murine C3Tag scRNAseq data, we show the existence of cancer cells within the C3Tag pre-DCIS, DCIS, and IDC-like tumor specimens. These cancer cells were further classified into proliferative, hypoxic, and inflammatory subpopulations, which change in frequency in DCIS versus IDC. The C3Tag tumor progression model was also associated with increase in Cancer-Associated Fibroblasts and decrease in activated T cells in IDC. Importantly, we translate the C3Tag murine genomic findings into human DCIS where we find common features only with human basal-like DCIS, suggesting there are intrinsic subtype unique DCIS features. This study identifies several tumor and microenvironmental features associated with DCIS progression and may also provide genomic signatures that can identify progression-prone DCIS within the context of human basal-like breast cancers.
Third-order topological insulators with wallpaper fermions in Tl4PbTe3 and Tl4SnTe3
Authors: Mao Ning , Wang Hao , Dai Ying , Huang Baibiao , Niu Chengwang 
Published: July 2022

AbstractNonsymmorphic symmetries open up horizons of exotic topological boundary states and even generalize the bulk–boundary correspondence, which, however, the third-order topological insulator in electronic materials are still unknown. Here, by means of the symmetry analysis and k · p models, we uncover the emergence of long-awaited third-order topological insulators and the wallpaper fermions in space group I4/mcm (No.140). Based on this, we present the hourglass fermion, fourfold-degenerate Dirac fermion, and Möbius fermion in the (001) surface of Tl4XTe3 (X = Pb/Sn) with a nonsymmorphic wallpaper group p4g. Remarkably, 16 helical corner states reside on eight corners in Kramers pair, rendering the real electronic material of third-order topological insulators. More importantly, a time-reversal polarized octupole polarization is defined to uncover the nontrivial third-order topology, as is implemented by the 2nd and 3rd order Wilson loop calculations. Our results could considerably broaden the range of wallpaper fermions and lay the foundation for future experimental investigations of third-order topological insulators.
On the role of the microstructure in the deformation of porous solids
Authors: Patnaik Sansit , Jokar Mehdi , Ding Wei , Semperlotti Fabio 
Published: July 2022

AbstractThis study explores the role that the microstructure plays in determining the macroscopic static response of porous elastic continua and exposes the occurrence of position-dependent nonlocal effects that are strictly correlated to the configuration of the microstructure. Then, a nonlocal continuum theory based on variable-order fractional calculus is developed in order to accurately capture the complex spatially distributed nonlocal response. The remarkable potential of the fractional approach is illustrated by simulating the nonlinear thermoelastic response of porous beams. The performance, evaluated both in terms of accuracy and computational efficiency, is directly contrasted with high-fidelity finite element models that fully resolve the pores’ geometry. Results indicate that the reduced-order representation of the porous microstructure, captured by the synthetic variable-order parameter, offers a robust and accurate representation of the multiscale material architecture that largely outperforms classical approaches based on the concept of average porosity.
Intrinsically flexible all-carbon-nanotube electronics enabled by a hybrid organic–inorganic gate dielectric
Authors: Huang Qiuyue , Wang Jialiang , Li Chenglin , Zhu Jiahao , Wang Wanting , Huang Youchao , Zhang Yiming , Jiao Hailong , Zhang Shengdong , Meng Hong , Zhang Min , Wang Xinwei 
Published: July 2022

AbstractThe advancement of Internet of Things has stimulated huge demands on low-voltage flexible electronics. Carbon-nanotube (CNT)-based electronics are of great promise to this end for their intrinsic flexibility, high carrier mobility, and capability to synthesize as semiconducting or metallic to serve as the channels, electrodes, and interconnects of circuits. However, the gate dielectric often has to adopt brittle oxides, which can seriously limit the device flexibility. Herein, we show that a hybrid polyimide-Al2O3 material can serve as a good gate dielectric to realize truly intrinsic flexibility of transistors and circuits based on CNTs. With this hybrid dielectric, high-performance all-CNT transistors and integrated circuits of inverters, ring oscillators, and logic gates are demonstrated. Particularly, the inverters exhibit a remarkably high gain of 342.5 and can be used as an analog amplifier for millivolt small signals. Ultralow voltage (50 mV) operation is also feasible, which highlights the great promise for low-power applications.
Rapid battery cost declines accelerate the prospects of all-electric interregional container shipping
Authors: Kersey Jessica , Popovich Natalie D. , Phadke Amol A. 
Published: July 2022

AbstractInternational maritime shipping—powered by heavy fuel oil—is a major contributor to global CO2, SO2, and NOx emissions. The direct electrification of maritime vessels has been underexplored as a low-emission option despite its considerable efficiency advantage over electrofuels. Past studies on ship electrification have relied on outdated assumptions on battery cost, energy density values and available on-board space. We show that at battery prices of US$100 kWh−1 the electrification of intraregional trade routes of less than 1,500 km is economical, with minimal impact to ship carrying capacity. Including the environmental costs increases the economical range to 5,000 km. If batteries achieve a US$50 kWh−1 price point, the economical range nearly doubles. We describe a pathway for the battery electrification of containerships within this decade that electrifies over 40% of global containership traffic, reduces CO2 emissions by 14% for US-based vessels, and mitigates the health impacts of air pollution on coastal communities.
Transcriptomic study of anastasis for reversal of ethanol-induced apoptosis in mouse primary liver cells
Authors: Tang Ho Man , Talbot C. Conover , Fung Ming Chiu , Tang Ho Lam 
Published: July 2022

AbstractAnastasis is a cell recovery mechanism that rescues dying cells from the brink of death. Reversal of apoptosis is the first example of anastasis. Here, we describe a comprehensive dataset containing time-course mRNA expression profiles for reversal of ethanol-induced apoptosis in mouse primary liver cells in νitro. This transcriptome dataset includes the conditions of the untreated cells, cells undergoing apoptosis triggered by incubating with cell death inducer of 4.5% ethanol for 5 hours, and apoptosis reversal of ethanol-induced cells at the early (3rd hour), middle (6th hour), and late (24th, 48th hour) stages after being washed with and incubated in fresh cell culture medium. By comparing this dataset with the transcriptomic profiles of other anastasis models generated with different combinations of cell types and cell death inducers, investigators can identify the key regulators governing reversal of apoptosis and other reversible cell death processes. Therefore, reusing or reanalysing this dataset will facilitate the future studies on the physiological, pathological, and therapeutic implications of anastasis.
High accuracy barrier heights, enthalpies, and rate coefficients for chemical reactions
Authors: Spiekermann Kevin , Pattanaik Lagnajit , Green William H. 
Published: July 2022

AbstractQuantitative chemical reaction data, including activation energies and reaction rates, are crucial for developing detailed kinetic mechanisms and accurately predicting reaction outcomes. However, such data are often difficult to find, and high-quality datasets are especially rare. Here, we use CCSD(T)-F12a/cc-pVDZ-F12//ωB97X-D3/def2-TZVP to obtain high-quality single point calculations for nearly 22,000 unique stable species and transition states. We report the results from these quantum chemistry calculations and extract the barrier heights and reaction enthalpies to create a kinetics dataset of nearly 12,000 gas-phase reactions. These reactions involve H, C, N, and O, contain up to seven heavy atoms, and have cleaned atom-mapped SMILES. Our higher-accuracy coupled-cluster barrier heights differ significantly (RMSE of ∼5 kcal mol−1) relative to those calculated at ωB97X-D3/def2-TZVP. We also report accurate transition state theory rate coefficients $${k}_{\infty }(T)$$

k

∞

(

T

)

between 300 K and 2000 K and the corresponding Arrhenius parameters for a subset of rigid reactions. We believe this data will accelerate development of automated and reliable methods for quantitative reaction prediction.
Microdosimetry performance of the first multi-arrays of 3D-cylindrical microdetectors
Authors: Bachiller-Perea Diana , Zhang Mingming , Fleta Celeste , Quirion David , Bassignana Daniela , Gómez Faustino , Guardiola Consuelo 
Published: July 2022

AbstractThe present work reports on the microdosimetry measurements performed with the two first multi-arrays of microdosimeters with the highest radiation sensitive surface covered so far. The sensors are based on new silicon-based radiation detectors with a novel 3D cylindrical architecture. Each system consists of arrays of independent microdetectors covering 2 mm$$\times$$
×
2 mm and 0.4 mm$$\times$$
×
12 cm radiation sensitive areas, the sensor distributions are arranged in layouts of 11$$\times$$
×
11 microdetectors and 3$$\times$$
×
3 multi-arrays, respectively. We have performed proton irradiations at several energies to compare the microdosimetry performance of the two systems, which have different spatial resolution and detection surface. The unitcell of both arrays is a 3D cylindrical diode with a 25 $$\mu$$
μ
m diameter and a 20 $$\mu$$
μ
m depth that results in a welldefined and isolated radiation sensitive micro-volume etched inside a silicon wafer. Measurements were carried out at the Accélérateur Linéaire et Tandem à Orsay (ALTO) facility by irradiating the two detection systems with monoenergetic proton beams from 6 to 20 MeV at clinical-equivalent fluence rates. The microdosimetry quantities were obtained with a spatial resolution of 200 $$\mu$$
μ
m and 600 $$\mu$$
μ
m for the 11$$\times$$
×
11 system and for the 3$$\times$$
×
3 multi-array system, respectively. Experimental results were compared with Monte Carlo simulations and an overall good agreement was found. The good performance of both microdetector arrays demonstrates that this architecture and both configurations can be used clinically as microdosimeters for measuring the lineal energy distributions and, thus, for RBE optimization of hadron therapy treatments. Likewise, the results have shown that the devices can be also employed as a multipurpose device for beam monitoring in particle accelerators.
iCodon customizes gene expression based on the codon composition
Authors: Diez Michay , Medina-Muñoz Santiago Gerardo , Castellano Luciana Andrea , da Silva Pescador Gabriel , Wu Qiushuang , Bazzini Ariel Alejandro 
Published: July 2022

AbstractMessenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon optimality. We have developed iCodon (www.iCodon.org), an algorithm for customizing mRNA expression through the introduction of synonymous codon substitutions into the coding sequence. iCodon is optimized for four vertebrate transcriptomes: mouse, human, frog, and fish. Users can predict the mRNA stability of any coding sequence based on its codon composition and subsequently generate more stable (optimized) or unstable (deoptimized) variants encoding for the same protein. Further, we show that codon optimality predictions correlate with both mRNA stability using a massive reporter library and expression levels using fluorescent reporters and analysis of endogenous gene expression in zebrafish embryos and/or human cells. Therefore, iCodon will benefit basic biological research, as well as a wide range of applications for biotechnology and biomedicine.