bluuebunny/crossref_metadata_2025 huggingface dataset:
Ionospheric Nighttime Enhancements in the Equatorial Region as Revealed by the Beidou Geostationary TEC Observations
Authors: Wang Yihan , Huang Fuqing , Lei Jiuhou , Luan Xiaoli , Dou Xiankang , Owolabi Charles
Published: July 2022

Ionospheric electron density enhancement at nighttime has been widely studied in the past decades. However, the mechanisms of this anomalous nighttime enhancement are not fully understood. In this study, we took advantage of the fidelity of geostationary total electron contents (GEO TECs) combined with the observations from three equatorial ionosondes to examine the morphology of equatorial ionospheric nighttime enhancements in the Asian‐Australian sector. The equatorial ionospheric nighttime enhancements from GEO TECs during 2016–2018 can be characterized by three categories. Each of these categories showed similar seasonal variations, with the maximal occurrence in the equinoxes. Interestingly, there was a strong correlation between the pre‐reversal enhancement (PRE) of the eastward equatorial electric field and these three types of equatorial ionospheric nighttime enhancements that were mostly accompanied by PRE inferred from foF2 and h'F2 from ionograms around dusk. Nevertheless, the formations of equatorial ionospheric nighttime enhancements could be associated with other factors, such as the equatorial electric fields and neutral winds, as well as associated plasma transports. This study provides a new perspective to explore the variations and the underlying physical processes of ionospheric nighttime enhancements.
Experimental Multiblast Craters and Ejecta—Seismo‐Acoustics, Jet Characteristics, Craters, and Ejecta Deposits and Implications for Volcanic Explosions
Authors: Sonder Ingo , Graettinger Alison , Neilsen Tracianne B. , Matoza Robin S. , Taddeucci Jacopo , Oppenheimer Julie , Lev Einat , Tsunematsu Kae , Waite Greg , Valentine Greg A. , Befus Kenneth S.
Published: July 2022

Blasting experiments were performed that investigate multiple explosions that occur in quick succession in unconsolidated ground and their effects on host material and atmosphere. Such processes are known to occur during phreatomagmatic eruptions at various depths, lateral locations, and energies. The experiments follow a multi‐instrument approach in order to observe phenomena in the atmosphere and in the ground, and measure the respective energy partitioning. The experiments show significant coupling of atmospheric (acoustic)‐ and ground (seismic) signal over a large range of (scaled) distances (30–330 m, 1–10 m J−1/3). The distribution of ejected material strongly depends on the sequence of how the explosions occur. The overall crater sizes are in the expected range of a maximum size for many explosions and a minimum for one explosion at a given lateral location. As previous research showed before, peak atmospheric over‐pressure decays exponentially with scaled depth. An exponential decay rate of was measured. At a scaled explosion depth of 4 × 10−3 m J−1/3 ca. 1% of the blast energy is responsible for the formation of the atmospheric pressure pulse; at a more shallow scaled depth of 2.75 × 10−3 m J−1/3 this ratio lies at ca. 5.5%–7.5%. A first order consideration of seismic energy estimates the sum of radiated airborne and seismic energy to be up to 20% of blast energy. Finally, the transient cavity formation during a blast leads to an effectively reduced explosion depth that was determined. Depth reductions of up to 65% were measured.
Eastward Asthenospheric Flow From NE Tibet Inferred by Joint Inversion of Teleseismic Body and Surface Waves: Insight Into Widespread Continental Deformation in Eastern China
Authors: Guo Zhen , Li Shilin , Yu Yong , Chen Y. John , Yang Yingjie , Xu Bo , Liang Xiaofeng
Published: July 2022

During the last 50 Ma, the eastern Eurasian continent has experienced widespread crustal and lithospheric deformation. However, mechanisms in creating such widespread intra‐continental deformation are still not well understood. Here, we present a 3‐D S‐wave velocity model of the northeastern Tibetan Plateau and adjacent regions by jointly inverting teleseismic body and surface waves. The resulting model clearly suggests that lateral extrusion of asthenosphere from northern Tibet is being blocked by the thick cratonic keels of Ordos and Sichuan, and therefore the asthenosphere is channeled into a strong eastward flow beneath the northern Qinglin between these two cratonic keels. Our results also demonstrate that continental deformation in eastern Eurasia is likely influenced by the small‐scale convection when the lateral asthenospheric flow from NE Tibet encounters preexisting continental lithospheric steps to the east of Ordos.
Intensified Atmospheric Branch of the Hydrological Cycle Over the Tibetan Plateau During the Last Interglacial From a Dynamical Downscaling Perspective
Authors: Jiang Nanxuan , Yan Qing , Wang Huijun
Published: July 2022

Investigation of the variations of hydrological cycles during the Last Interglacial (130–115 ka; LIG) may deepen our understanding of climate change in a warmer‐than‐present world induced by Earth's orbit. Here we revealed an intensified atmospheric branch of the hydrological cycle over the Tibetan Plateau (TP) in summer during the LIG relative to the preindustrial period, using the mesoscale Weather Research and Forecasting model driven by the Community Earth System Model. Our results showed that precipitation over the TP increased by 5.65 × 107 kg s−1, with 63.2% of the increase contributed by advected moisture transports, and the remaining 36.8% caused by local moisture recycling processes. As for advected moisture transports, the inflow increased by 1.93 × 107 kg s−1 and the outflow decreased by 0.87 × 107 kg s−1, respectively. Variations of the moisture transport were more profound at the eastern and northern edges, which were linked with changes in Indian summer monsoon and westerly jets. Regarding local moisture recycling processes, evaporation enhanced by 2.85 × 107 kg s−1 over the TP, influenced by variations in surface air temperature, surface net radiation flux, surface relative humidity, and surface wind fields. Increased evaporation accompanied by enhanced moisture inflow resulted in an enriched precipitation recycling ratio of ∼1% over the TP during the LIG relative to the preindustrial in summer. Our results aid in understanding the atmospheric branch of the hydrological cycle over the TP in an orbit‐induced warmer world and shed light on the future evolution of the hydrological cycle over the TP at multi‐millennial and orbital timescale.
Sulfur Geochemistry Destabilizes Population Oscillations of Wild Rice (Zizania palustris)
Authors: LaFond‐Hudson Sophia , Johnson Nathan W. , Pastor John , Dewey Brad
Published: July 2022

Elevated inputs of sulfate to freshwater systems can increase sulfide concentrations in anoxic soils and subsequently destabilize aquatic plant populations, but the interactions between sulfate, other geochemical cycles, and interannual plant population cycles are poorly understood. Increased sulfate loading increases mineralization of nitrogen from litter, but the sulfide produced during this process can limit nitrogen uptake by plants. In some cases, iron may mitigate sulfide's impacts on plants by precipitating iron sulfide. We examined the interannual effects of sulfate loading on mesocosm populations of wild rice, an emergent aquatic plant that undergoes population oscillations and is sensitive to sulfide. Using experimental mesocosms with self‐perpetuating populations, we investigated how population dynamics respond to manipulations of surface water sulfate (10 mg L−1 or 300 mg L−1), sediment iron (4.3 mg g−1 or 10.9 mg g−1 dry weight), and shoot litter (present or removed). Populations exposed to constant 10 mg L−1 sulfate concentrations had stable biomass oscillations of approximately 3‐year periods, consistent with previous studies that demonstrated litter‐driven oscillations in nitrogen availability. Populations exposed to 300 mg L−1 sulfate concentrations produced fewer and smaller seeds and declined to extinction in 6 years or less. We did not find a strong effect of iron loading or litter removal on wild rice biomass or seed production. Our observations show the potential of elevated surface water sulfate to rapidly destabilize wild rice populations under varying iron and organic carbon concentrations.
Identification Approach of Arriving Wave Model Based on Likelihood Ratio Test With Different Sensor Noise Levels
Authors: Tanaka Yuji , Ota Mamoru , Kasahara Yoshiya
Published: July 2022

k‐vector direction determined by propagation characteristics is crucial for understanding the global features of space plasma. Identifying the arriving wave model is a major factor in obtaining fast and accurate results in the direction finding of various plasma waves. If we can determine whether the observation data contain a significant natural wave or not, we can reduce the computational time for direction finding analysis by excluding noise‐only data. The conventional approach for identifying the arriving wave model assumes that all electromagnetic field sensors have same noise levels. However, the noise levels of electromagnetic field sensors on board scientific satellites can change owing to sensor degradation during long‐term instrument operation. Thus, the arriving wave model should be identified even when the noise levels of all electromagnetic field sensors are not equal. We proposed robustly identifying the arriving wave model by introducing a noise integration kernel that includes information about noise level ratios. Our proposed approach classifies a spectral matrix into three cases: noise model, single plane wave model, and multiple waves model. The proposed approach comprises the likelihood ratio test, and the identification result based on a statistical viewpoint. We conducted Monte Carlo simulations, and it was verified that the proposed approach can correctly derive the arriving wave model with high accuracy even with different sensor noise levels.
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

We 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.
Doped high-entropy glassy materials to create optical coherence from maximally disordered systems
Authors: Marrocco Michele
Published: July 2022

Control over excitation wavelengths, sample size, and doping concentrations in glassy materials with high levels of configuration entropy shows promises of efficient correlation between absorption and build-up of coherent emission of radiation.
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

Selective 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

Bone 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

Physical 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

The 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

Printing 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

Ductal 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

Nonsymmorphic 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

This 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

The 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

International 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

Anastasis 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

Quantitative 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

The 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

Messenger 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.
A systematic review and meta-analysis of weight loss in control group participants of lifestyle randomized trials
Authors: Bouzalmate Hajjaj Amira , Massó Guijarro Paloma , Khan Khalid Saeed , Bueno-Cavanillas Aurora , Cano-Ibáñez Naomi
Published: July 2022

Randomized clinical trials (RCTs) of lifestyle modification have reported beneficial effects of interventions, compared to control. Whether participation in the control group has benefits is unknown. To determine whether control group participants experience weight loss during the course of RCTs. After prospective registration (PROSPERO CRD42021233070), we conducted searches in Medline, Scopus, Web of Science, Cochrane library and Clinicaltrials.gov databases from inception to May 2021 without language restriction to capture RCTs on dietary advice or physical activity interventions in adults with overweight, obesity or metabolic syndrome. Data extraction and study quality assessment was performed by two independent reviewers. Weight loss in the control group, i.e., the difference between baseline and post-intervention, was pooled using random effects model generating mean difference and 95% confidence interval (CI). Heterogeneity was assessed using the I2 statistical test. Subgroup meta-analysis was performed stratifying by follow-up period, type of control group protocols and high-quality studies. Among the 22 included studies (4032 participants), the risk of bias was low in 9 (40%) studies. Overall, the controls groups experienced weight loss of − 0.41 kg (95% CI − 0.53 to − 0.28; I2 = 73.5% p < 0.001). To identify a result that is an outlier, we inspected the forest plot for spread of the point estimates and the confidence intervals. The magnitude of the benefit was related to the duration of follow-up (− 0.51 kg, 95% CI − 0.68, − 0.3, for 1–4 months follow-up; − 0.32 kg, 95% CI − 0.58, − 0.07, 5–12 months; − 0.20 kg, 95% CI − 0.49, 0.10, ≥ 12 months). In high-quality studies we found an overall weight loss mean difference of − 0.16 (95% CI − 0.39, 0.09) with a considerable heterogeneity (I2 = 74%; p < 0.000). Among studies including control group in waiting lists and combining standard care, advice and material, no heterogeneity was found (I2 = 0%, p = 0.589) and (I2 = 0%, p = 0.438); and the mean difference was − 0.84 kg (95% CI − 2.47, 0.80) and − 0.65 kg (95% CI − 1.03, − 0.27) respectively. Participation in control groups of RCTs of lifestyle interventions had a benefit in terms of weight loss in meta-analysis with heterogeneity. These results should be used to interpret the benefits observed with respect to intervention effect in trials. That control groups accrue benefits should be included in patient information sheets to encourage participation in future trials among patients with overweight and obesity.
The fall of vulnerability to sleep disturbances in evening chronotypes when working from home and its implications for depression
Authors: Salfi Federico , D’Atri Aurora , Amicucci Giulia , Viselli Lorenzo , Gorgoni Maurizio , Scarpelli Serena , Alfonsi Valentina , Ferrara Michele
Published: July 2022

Eveningness is distinctively associated with sleep disturbances and depression symptoms due to the misalignment between biological and social clocks. The widespread imposition of remote working due to the COVID-19 pandemic allowed a more flexible sleep schedule. This scenario could promote sleep and mental health in evening-type subjects. We investigated the effect of working from home on sleep quality/quantity and insomnia symptoms within the morningness-eveningness continuum, and its indirect repercussions on depressive symptomatology. A total of 610 Italian office workers (mean age ± standard deviation, 35.47 ± 10.17 years) and 265 remote workers (40.31 ± 10.69 years) participated in a web-based survey during the second contagion wave of COVID-19 (28 November–11 December 2020). We evaluated chronotype, sleep quality/duration, insomnia, and depression symptoms through validated questionnaires. Three moderated mediation models were performed on cross-sectional data, testing the mediation effect of sleep variables on the association between morningness-eveningness continuum and depression symptoms, with working modality (office vs. remote working) as moderator of the relationship between chronotype and sleep variables. Remote working was associated with delayed bedtime and get-up time. Working modality moderated the chronotype effect on sleep variables, as eveningness was related to worse sleep disturbances and shorter sleep duration among the office workers only. Working modality also moderated the mediation of sleep variables between chronotype and depression. The above mediation vanished among remote workers. The present study suggests that evening-type people did not show their characteristic vulnerability to sleep problems when working from home. This result could imply a reduction of the proposed sleep-driven predisposition to depression of late chronotypes. A working environment complying with individual circadian preferences might ensure an adequate sleep quantity/quality for the evening-type population, promoting their mental health.
Comparative analysis of high- and low-level deep learning approaches in microsatellite instability prediction
Authors: Park Jeonghyuk , Chung Yul Ri , Nose Akinao
Published: July 2022

Deep learning-based approaches in histopathology can be largely divided into two categories: a high-level approach using an end-to-end model and a low-level approach using feature extractors. Although the advantages and disadvantages of both approaches are empirically well known, there exists no scientific basis for choosing a specific approach in research, and direct comparative analysis of the two approaches has rarely been performed. Using the Cancer Genomic Atlas (TCGA)-based dataset, we compared these two different approaches in microsatellite instability (MSI) prediction and analyzed morphological image features associated with MSI. Our high-level approach was based solely on EfficientNet, while our low-level approach relied on LightGBM and multiple deep learning models trained on publicly available multiclass tissue, nuclei, and gland datasets. We compared their performance and important image features. Our high-level approach showed superior performance compared to our low-level approach. In both approaches, debris, lymphocytes, and necrotic cells were revealed as important features of MSI, which is consistent with clinical knowledge. Then, during qualitative analysis, we discovered the weaknesses of our low-level approach and demonstrated that its performance can be improved by using different image features in a complementary way. We performed our study using open-access data, and we believe this study can serve as a useful basis for discovering imaging biomarkers for clinical application.
Research on the effectiveness of a intersection risk warning system based on driving simulation experiment
Authors: Zhou Yiwen , Guo Fengxiang , Yang Wenchen , Wan Huasen
Published: July 2022

In order to improve the traffic safety condition of intersections, a real-time traffic conflict risk warning system (RTCRWS) is proposed for uncontrolled intersections. To evaluate the effectiveness of this system, a driving simulation experiment was designed and conducted. In this study, a virtual experimental scene including static road, traffic environment and dynamic traffic flow was constructed, and 45 drivers were recruited to complete the driving simulation experiment at 13 intersections. Three different data analysis methods were employed: (1) descriptive analysis of driving behavior characteristics; (2) descriptive analysis of physiological and psychological reactions of drivers; (3) Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS) of RTCRWS. The results show that RTCRWS can effectively control the vehicle speed and reduce the driver's tension. In addition, the following conclusions are also drawn: (1) The early warning signs with better warning effect among the two types signs of RTCRWS were compared; (2) Among the elderly and young and middle-aged drivers, RTCRWS has a better warning effect on the elderly drivers. (3) Among the male and female drivers, RTCRWS has a better warning effect on female drivers.
Microcomputed tomography versus plethysmometer and electronic caliper in the measurements of lymphedema in the hindlimb of mice
Authors: Bucan Amar , Wiinholt Alexander , Dalaei Farima , Gerke Oke , Hansen Christian Rønn , Sørensen Jens Ahm
Published: July 2022

Lymphedema affects 20% of women diagnosed with breast cancer. It is a pathology with no known cure. Animal models are essential to explore possible treatments to understand and potentially cure lymphedema. The rodent hindlimb lymphedema model is one of the most widely used. Different modalities have been used to measure lymphedema in the hindlimb of mice, and these are generally poorly assessed in terms of the interrater agreement; thus, there could be a risk of measuring bias and poor reproducibility. We examined the interrater agreement of µCT-scans, electronic caliper thickness of the paw and plethysmometer in the measurement of lymphedema in the hindlimb of mice. Three independent raters assessed 24 C57BL6 mice using these three modalities four times (week 1, 2, 4 and 8) with a total of 96 samples. The mean interrater differences were then calculated. The interrater agreement was highest in the µCT-scans, with an extremely low risk of measurement bias. The interrater agreement in the plethysmometer and electronic caliper was comparable with a low to moderate risk of measurement bias. The µCT-scanner should be used whenever possible. The electronic caliper should only be used if there is no µCT-scanner available. The plethysmometer should not be used in rodents of this size.
An experimental and theoretical characterization of the electronic structure of doubly ionised disulfur
Authors: Olsson Emelie , Ayari Tarek , Ideböhn Veronica , Wallner Måns , Squibb Richard J. , Andersson Jonas , Roos Andreas Hult , Stranges Stefano , Dyke John M. , Eland John H. D. , Hochlaf Majdi , Feifel Raimund
Published: July 2022

Using time-of-flight multiple electron and ion coincidence techniques in combination with a helium gas discharge lamp and synchrotron radiation, the double ionisation spectrum of disulfur (S$$_2$$

2

) and the subsequent fragmentation dynamics of its dication are investigated. The S$$_2$$

2

sample was produced by heating mercury sulfide (HgS), whose vapour at a suitably chosen temperature consists primarily of two constituents: S$$_2$$

2

and atomic Hg. A multi-particle-coincidence technique is thus particularly useful for retrieving spectra of S$$_2$$

2

from ionisation of the mixed vapour. The results obtained are compared with detailed calculations of the electronic structure and potential energy curves of S$$_2^{2+}$$

2

2
+

which are also presented. These computations are carried out using configuration interaction methodology. The experimental results are interpreted with and strongly supported by the computational results.
The impact of sewage sludge processing on the safety of its use
Authors: Styszko Katarzyna , Durak Justyna , Kończak Beata , Głodniok Marcin , Borgulat Anna
Published: July 2022

Particular attention is devoted to pharmaceutical residues in sewage sludge caused by their potential ecotoxicological effects. Diclofenac, ibuprofen and carbamazepine, 17-α-ethinylestradiol, β-estradiol, were analysed in four types of fertilizers, based on sewage sludge commercial products, in compliance with Polish requirements. The release of active pharmaceutical compounds from fertilizers to water the phase after 24 h and 27 days was analysed. Solid-water partition coefficients (Kd) and partitioning coefficient values normalized on organic carbon content (log KOC) were evaluated. The environmental risk to terrestrial ecosystems, due to the application of fertilizers onto soils, was estimated. Cumulative mass of pharmaceuticals emitted to water from fertilizers ranged from 0.4 to 30.8 µg/kg after 24 h contact. The greatest amount of the material that was released, over 70%, was observed for carbamazepine. No presence of compounds except ibuprofen was observed after 27 days of testing. The highest environmental risk in fertilizers is due to carbamazepine, risk quotation, RQ = 0.93 and diclofenac RQ = 0.17. The values of risk quotation estimated for soil were below RQ = 0.01. This fact means that no risk to terrestrial ecosystems is expected to occur. The important decrease of the concentrations of active compounds after passing from sewage sludge to fertilizers [and] to fertilized soil could be observed.
Angiogenic gene characterization and vessel permeability of dermal microvascular endothelial cells isolated from burn hypertrophic scar
Authors: Molina Esteban A. , Hartmann Brandon , Oliver Mary A. , Kirkpatrick Liam D. , Keyloun John W. , Moffatt Lauren T. , Shupp Jeffrey W. , Travis Taryn E. , Carney Bonnie C.
Published: July 2022

Hypertrophic scar (HTS) formation is a common challenge for patients after burn injury. Dermal microvascular endothelial cells (DMVECs) are an understudied cell type in HTS. An increase in angiogenesis and microvessel density can be observed in HTS. Endothelial dysfunction may play a role in scar development. This study aims to generate a functional and expression profile of HTS DMVECs. We hypothesize that transcript and protein-level responses in HTS DMVECs differ from those in normal skin (NS). HTSs were created in red Duroc pigs. DMVECs were isolated using magnetic-activated cell sorting with ulex europaeus agglutinin 1 (UEA-1) lectin. Separate transwell inserts were used to form monolayers of HTS DMVECs and NS DMVECs. Cell injury was induced and permeability was assessed. Gene expression in HTS DMVECS versus NS DMVECs was measured. Select differentially expressed genes were further investigated. HTS had an increased area density of dermal microvasculature compared to NS. HTS DMVECs were 17.59% less permeable than normal DMVECs (p < 0.05). After injury, NS DMVECs were 28.4% and HTS DMVECs were 18.8% more permeable than uninjured controls (28.4 ± 4.8 vs 18.8 ± 2.8; p = 0.11). PCR array identified 31 differentially expressed genes between HTS and NS DMVECs, of which 10 were upregulated and 21 were downregulated. qRT-PCR and ELISA studies were in accordance with the array. DMVECs expressed a mixed profile of factors that can contribute to and inhibit scar formation. HTS DMVECs have both a discordant response to cellular insults and baseline differences in function, supporting their proposed role in scar pathology. Further investigation of DMVECs is warranted to elucidate their contribution to HTS pathogenesis.