bluuebunny/crossref_metadata_2025 huggingface dataset:
CREIME—A Convolutional Recurrent Model for Earthquake Identification and Magnitude Estimation
Authors: Chakraborty Megha , Fenner Darius , Li Wei , Faber Johannes , Zhou Kai , Rümpker Georg , Stoecker Horst , Srivastava Nishtha
Published: July 2022

The detection and rapid characterization of earthquake parameters such as magnitude are important in real‐time seismological applications such as Earthquake Monitoring and Earthquake Early Warning (EEW). Traditional methods, aside from requiring extensive human involvement can be sensitive to signal‐to‐noise ratio leading to false/missed alarms depending on the threshold. We here propose a multitasking deep learning model—the Convolutional Recurrent model for Earthquake Identification and Magnitude Estimation (CREIME) that: (a) detects the earthquake signal from background seismic noise, (b) determines the first P wave arrival time, and (c) estimates the magnitude using the raw three‐component waveforms from a single station as model input. Considering, that speed is essential in EEW, we use up to 2 s of P wave information which, to the best of our knowledge, is a significantly smaller data window compared to the previous studies. To examine the robustness of CREIME, we test it on two independent data sets and find that it achieves an average accuracy of 98% for event versus noise discrimination and can estimate first P‐arrival time and local magnitude with average root mean squared errors of 0.13 s and 0.65 units, respectively. We compare CREIME with traditional methods such as short‐term‐average/long‐term‐average (STA/LTA) and show that CREIME has superior performance, for example, the accuracy for signal and noise discrimination is higher by 4.5% and 11.5%, respectively, for the two data sets. We also compare the architecture of CREIME with the architectures of other baseline models, trained on the same data, and show that CREIME outperforms the baseline models.
Snow Equi‐Temperature Metamorphism Described by a Phase‐Field Model Applicable on Micro‐Tomographic Images: Prediction of Microstructural and Transport Properties
Authors: Bouvet L. , Calonne N. , Flin F. , Geindreau C.
Published: July 2022

Representing snow equi‐temperature metamorphism (ETM) is key to model the evolution and properties of the snow cover. Recently, a phase‐field model describing mean curvature flow evolution on 3D microstructures was proposed (Bretin et al., 2019, https://doi.org/10.1051/m2an/2018075). In the present work, this model is used to simulate snow ETM at the pore scale, considering the only process of moving interfaces by sublimation‐deposition driven by curvatures. We take 3D micro‐tomographic images of snow as input in the model and obtain a time series of simulated microstructures as output. Relating the numerical time, as defined in the model, to the real physical time involves the condensation coefficient α, a poorly constrained parameter in literature. A calibration was performed by fitting simulations to experimental data through the evolution of specific surface area (SSA) of snow under ETM at −2°C. A value of the condensation coefficient was obtained: (9.8 ± 0.7) × 10−4 and was used in all the following simulations. We then show that the calibrated model enables to well reproduce an independent time series of ETM at −2°C in terms of SSA, covariance length, and mean curvature distribution. Finally, the calibrated model was used to investigate the effect of ETM on microstructure and effective transport properties (thermal conductivity, vapor diffusion, and permeability) for four different samples. As an interesting preliminary result, simulations show an enhancement of the structural anisotropy of snow in the case of initially anisotropic microstructures, such as depth hoar. Results highlight the potential of such microscale models for the development of snow property predictions for large‐scale snowpack models.
Disassembly of α6β4-mediated hemidesmosomal adhesions promotes tumorigenesis in PTEN-negative prostate cancer by targeting plectin to focal adhesions
Authors: Wenta Tomasz , Schmidt Anette , Zhang Qin , Devarajan Raman , Singh Prateek , Yang Xiayun , Ahtikoski Anne , Vaarala Markku , Wei Gong-Hong , Manninen Aki
Published: July 2022

Loss of α6β4-dependent hemidesmosomal adhesions has been observed during prostate cancer progression. However, the significance and underlying mechanisms by which aberrant hemidesmosome assembly may modulate tumorigenesis remain elusive. Using an extensive CRISPR/Cas9-mediated genetic engineering approaches in different prostate cancer cell lines combined with in vivo tumorigenesis studies in mice, bone marrow-on-chip assays and bioinformatics, as well as histological analysis of prostate cancer patient cohorts, we demonstrated that simultaneous loss of PTEN and hemidesmosomal adhesions induced several tumorigenic properties including proliferation, migration, resistance to anoikis, apoptosis, and drug treatment in vitro, and increased metastatic capacity in vivo. These effects were plectin-depended and plectin was associated with actin-rich adhesions upon hemidesmosome disruption in PTEN-negative prostate cancer cells leading to activation of EGFR/PI3K/Akt- and FAK/Src-pathways. These results suggest that analysis of PTEN and hemidesmosomal proteins may have diagnostic value helping to stratify prostate cancer patients with high risk for development of aggressive disease and highlight actin-associated plectin as a potential therapeutic target specifically in PTEN/hemidesmosome dual-negative prostate cancer.
Homogeneous surrogate virus neutralization assay to rapidly assess neutralization activity of anti-SARS-CoV-2 antibodies
Authors: Kim Sun Jin , Yao Zhong , Marsh Morgan C. , Eckert Debra M. , Kay Michael S. , Lyakisheva Anna , Pasic Maria , Bansal Aiyush , Birnboim Chaim , Jha Prabhat , Galipeau Yannick , Langlois Marc-André , Delgado Julio C. , Elgort Marc G. , Campbell Robert A. , Middleton Elizabeth A. , Stagljar Igor , Owen Shawn C.
Published: July 2022

The COVID-19 pandemic triggered the development of numerous diagnostic tools to monitor infection and to determine immune response. Although assays to measure binding antibodies against SARS-CoV-2 are widely available, more specific tests measuring neutralization activities of antibodies are immediately needed to quantify the extent and duration of protection that results from infection or vaccination. We previously developed a ‘Serological Assay based on a Tri-part split-NanoLuc® (SATiN)’ to detect antibodies that bind to the spike (S) protein of SARS-CoV-2. Here, we expand on our previous work and describe a reconfigured version of the SATiN assay, called Neutralization SATiN (Neu-SATiN), which measures neutralization activity of antibodies directly from convalescent or vaccinated sera. The results obtained with our assay and other neutralization assays are comparable but with significantly shorter preparation and run time for Neu-SATiN. As the assay is modular, we further demonstrate that Neu-SATiN enables rapid assessment of the effectiveness of vaccines and level of protection against existing SARS-CoV-2 variants of concern and can therefore be readily adapted for emerging variants.
Many dissimilar NusG protein domains switch between α-helix and β-sheet folds
Authors: Porter Lauren L. , Kim Allen K. , Rimal Swechha , Looger Loren L. , Majumdar Ananya , Mensh Brett D. , Starich Mary R. , Strub Marie-Paule
Published: July 2022

Folded proteins are assumed to be built upon fixed scaffolds of secondary structure, α-helices and β-sheets. Experimentally determined structures of >58,000 non-redundant proteins support this assumption, though it has recently been challenged by ~100 fold-switching proteins. Though ostensibly rare, these proteins raise the question of how many uncharacterized proteins have shapeshifting–rather than fixed–secondary structures. Here, we use a comparative sequence-based approach to predict fold switching in the universally conserved NusG transcription factor family, one member of which has a 50-residue regulatory subunit experimentally shown to switch between α-helical and β-sheet folds. Our approach predicts that 24% of sequences in this family undergo similar α-helix ⇌ β-sheet transitions. While these predictions cannot be reproduced by other state-of-the-art computational methods, they are confirmed by circular dichroism and nuclear magnetic resonance spectroscopy for 10 out of 10 sequence-diverse variants. This work suggests that fold switching may be a pervasive mechanism of transcriptional regulation in all kingdoms of life.
Viscosity in water from first-principles and deep-neural-network simulations
Authors: Malosso Cesare , Zhang Linfeng , Car Roberto , Baroni Stefano , Tisi Davide
Published: July 2022

We report on an extensive study of the viscosity of liquid water at near-ambient conditions, performed within the Green-Kubo theory of linear response and equilibrium ab initio molecular dynamics (AIMD), based on density-functional theory (DFT). In order to cope with the long simulation times necessary to achieve an acceptable statistical accuracy, our ab initio approach is enhanced with deep-neural-network potentials (NNP). This approach is first validated against AIMD results, obtained by using the Perdew–Burke–Ernzerhof (PBE) exchange-correlation functional and paying careful attention to crucial, yet often overlooked, aspects of the statistical data analysis. Then, we train a second NNP to a dataset generated from the Strongly Constrained and Appropriately Normed (SCAN) functional. Once the error resulting from the imperfect prediction of the melting line is offset by referring the simulated temperature to the theoretical melting one, our SCAN predictions of the shear viscosity of water are in very good agreement with experiments.
Corrosion behavior of pure Ti under continuous NaCl solution spraying at 600 °C
Authors: Li Rui , Liu Li , Cui Yu , Liu Rui , Wang Fuhui
Published: July 2022

The corrosion behavior of pure Ti under continuous NaCl solution spraying at 600 °C, compared with that under solid NaCl deposit film in H2O + O2 environment, has been studied by mass gain curves, detailed microstructural investigation and phase-stability diagram. The results indicate that the oxide scale consists of three repeated multi-layered subscales composed of Na2TiO3 and TiO2. Continuous NaCl increases the volatilization of TiCl4 towards oxide/atmosphere interface as well as introduces pores and cracks. Pores and cracks allow the oxidizing atmosphere to enter and rapidly spread and resulting in a repeat multi-layered oxide scale. Relatively dense repeat TiO2 delayed active oxidation process, which will decrease the corrosion rate of the pure Ti under NaCl spraying.
Similar mechanisms of temporary bindings for identity and location of objects in healthy ageing: an eye-tracking study with naturalistic scenes
Authors: D’Innocenzo Giorgia , Della Sala Sergio , Coco Moreno I.
Published: July 2022

The ability to maintain visual working memory (VWM) associations about the identity and location of objects has at times been found to decrease with age. To date, however, this age-related difficulty was mostly observed in artificial visual contexts (e.g., object arrays), and so it is unclear whether it may manifest in naturalistic contexts, and in which ways. In this eye-tracking study, 26 younger and 24 healthy older adults were asked to detect changes in a critical object situated in a photographic scene (192 in total), about its identity (the object becomes a different object but maintains the same position), location (the object only changes position) or both (the object changes in location and identity). Aging was associated with a lower change detection performance. A change in identity was harder to detect than a location change, and performance was best when both features changed, especially in younger adults. Eye movements displayed minor differences between age groups (e.g., shorter saccades in older adults) but were similarly modulated by the type of change. Latencies to the first fixation were longer and the amplitude of incoming saccades was larger when the critical object changed in location. Once fixated, the target object was inspected for longer when it only changed in identity compared to location. Visually salient objects were fixated earlier, but saliency did not affect any other eye movement measures considered, nor did it interact with the type of change. Our findings suggest that even though aging results in lower performance, it does not selectively disrupt temporary bindings of object identity, location, or their association in VWM, and highlight the importance of using naturalistic contexts to discriminate the cognitive processes that undergo detriment from those that are instead spared by aging.
Dynamics and stabilization mechanism of mitochondrial cristae morphofunction associated with turgor-driven cardiolipin biosynthesis under salt stress conditions
Authors: Nakata Keisuke , Hatakeyama Yuto , Erra-Balsells Rosa , Nonami Hiroshi , Wada Hiroshi
Published: July 2022

Maintaining energy production efficiency is of vital importance to plants growing under changing environments. Cardiolipin localized in the inner mitochondrial membrane plays various important roles in mitochondrial function and its activity, although the regulation of mitochondrial morphology to various stress conditions remains obscure, particularly in the context of changes in cellular water relations and metabolisms. By combining single-cell metabolomics with transmission electron microscopy, we have investigated the adaptation mechanism in tomato trichome stalk cells at moderate salt stress to determine the kinetics of cellular parameters and metabolisms. We have found that turgor loss occurred just after the stress conditions, followed by the contrasting volumetric changes in mitochondria and cells, the accumulation of TCA cycle-related metabolites at osmotic adjustment, and a temporal increase in cardiolipin concentration, resulting in a reversible topological modification in the tubulo-vesicular cristae. Because all of these cellular events were dynamically observed in the same single-cells without causing any disturbance for redox states and cytoplasmic streaming, we conclude that turgor pressure might play a regulatory role in the mitochondrial morphological switch throughout the temporal activation of cardiolipin biosynthesis, which sustains mitochondrial respiration and energy conversion even under the salt stress conditions.
Assessment of hair and cashmere properties and their genetic background of several goat breeds in Southwest China
Authors: Saleh Ahmed A. , Rashad Amr M. A. , Hassanine Nada. N. A. M. , Sharaby Mahmoud A. , Zhao Yongju
Published: July 2022

The aim of this study was to determine the properties and quality characteristics of hair and cashmere fibres of three goat breeds raised in Southwest China, namely; Dazu black goat (DBG, n = 203; ♂99, ♀104), Inner Mongolia cashmere goat (IMCG, n = 65; 21♂, 44♀) and their first cross (F1, n = 79; 39♂, 40♀). Totals of 5219, 2130 and 2981 fibre samples, from the three breeds respectively, were taken prior to shearing at 32.5 ± 01.25 months of age from four body sites; shoulder, side-portion, abdomen and leg. Breed effect was significant (P < 0.01) for most hair and cashmere properties. IMCG and F1 hair lengths were longer (P < 0.001) with less variable lengths than DBG. Shoulder hair diameters of the three breeds were not different (P > 0.05) but biggest of the side-portion and abdomen sites of DBG were bigger (P > 0.01), however, the biggest (P < 0.001) hair diameter was recorded for the leg site of F1 and the smallest (P > 0.01) for IMCG. IMCG recorded the longest value for cashmere lengths followed by DBG, while F1 recorded the lowest (P = 0.001), whilst F1 recorded the biggest (P = 0.001) diameter whereas no differences existed between parents' breeds. The cortical cell lengths of IMCG and DBG were 94.57 and 86.85 μm without significant difference detected between breeds. Differences between hair length and diameter for body sites of the studied goat breeds were significant (P < 0.01) but between whiteness, cashmere diameter and diameter of cortical cells were not. Sex had no significant effect on all hair/cashmere properties. Quality characteristics of cashmere fibres from IMCG and F1 were better (P < 0.001) than from DBG. Leg hair diameter, curl recovery rate and cashmere diameter were superior in the crossbred F1 compared to pure breed parents, and DBG was superior to IMCG for fibre elasticity and intensity traits. FGF-5 gene was detected as a candidate gene for hair and cashmere traits in IMCG breed. Whilst, KIT gene was found to be associated with coat colour in the studied breeds. Extra investigations to examine more cashmere goat breeds and crosses are needed to discover genetic variability in cashmere production locally and worldwide.
Anti-SARS-CoV-2 IgM/IgG antibodies detection using a patch sensor containing porous microneedles and a paper-based immunoassay
Authors: Bao Leilei , Park Jongho , Qin Boyu , Kim Beomjoon
Published: July 2022

Infectious diseases are among the leading causes of mortality worldwide. A new coronavirus named severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) was identified in Wuhan, China in 2019, and the World Health Organization (WHO) declared its outbreak, coronavirus disease 2019 (COVID-19), as a global pandemic in 2020. COVID-19 can spread quickly from person to person. One of the most challenging issues is to identify the infected individuals and prevent potential spread of SARS-CoV-2. Recently, anti-SARS-CoV-2 immunoglobulin M (IgM) and immunoglobulin G (IgG) antibody tests using immunochromatographic methods have been used as a complement to current detection methods and have provided information of the approximate course of COVID-19 infection. However, blood sampling causes pain and poses risks of infection at the needle puncture site. In this study, a novel patch sensor integrating porous microneedles and an immunochromatographic assay (PMNIA) was developed for the rapid detection of anti-SARS-CoV-2 IgM/IgG in dermal interstitial fluid (ISF), which is a rich source of protein biomarkers, such as antibodies. Biodegradable porous microneedles (MNs) made of polylactic acid were fabricated to extract ISF from human skin by capillary effect. The extracted ISF was vertically transported and flowed into the affixed immunoassay biosensor, where specific antibodies could be detected colorimetrically on-site. Anti-SARS-CoV-2 IgM/IgG antibodies were simultaneously detected within 3 min in vitro. Moreover, the limit of detection of anti-SARS-CoV-2 IgM and IgG concentrations was as low as 3 and 7 ng/mL, respectively. The developed device integrating porous MNs and immunochromatographic biosensors is expected to enable minimally invasive, simple, and rapid anti-SARS-CoV-2 IgM/IgG antibody testing. Furthermore, the compact size of the MN and biosensor-integrated device is advantageous for its widespread use. The proposed device has great potential for rapid screening of various infectious diseases in addition to COVID-19 as an effective complementary method with other diagnostic tests.
Quantifying the COVID19 infection risk due to droplet/aerosol inhalation
Authors: Bale Rahul , Iida Akiyoshi , Yamakawa Masashi , Li ChungGang , Tsubokura Makoto
Published: July 2022

The dose-response model has been widely used for quantifying the risk of infection of airborne diseases like COVID-19. The model has been used in the room-average analysis of infection risk and analysis using passive scalars as a proxy for aerosol transport. However, it has not been employed for risk estimation in numerical simulations of droplet dispersion. In this work, we develop a framework for the evaluation of the probability of infection in droplet dispersion simulations using the dose-response model. We introduce a version of the model that can incorporate the higher transmissibility of variant strains of SARS-CoV2 and the effect of vaccination in evaluating the probability of infection. Numerical simulations of droplet dispersion during speech are carried out to investigate the infection risk over space and time using the model. The advantage of droplet dispersion simulations for risk evaluation is demonstrated through the analysis of the effect of ambient wind, humidity on infection risk, and through a comparison with risk evaluation based on passive scalars as a proxy for aerosol transport.
Agreement between continuous cardiac output measured by the fourth-generation FloTrac/Vigileo system and a pulmonary artery catheter in adult liver transplantation
Authors: Murata Yutaka , Imai Takumi , Takeda Chikashi , Mizota Toshiyuki , Kawamoto Shuji
Published: July 2022

In liver transplantation for end-stage liver failure, monitoring of continuous cardiac output (CCO) is used for circulatory management due to hemodynamic instability. CCO is often measured using the minimally invasive FloTrac/Vigileo system (FVS-CCO), instead of a highly invasive pulmonary artery catheter (PAC-CCO). The FVS has improved accuracy due to an updated cardiac output algorithm, but the effect of this change on the accuracy of FVS-CCO in liver transplantation is unclear. In this study, we assessed agreement between fourth-generation FVS-CCO and PAC-CCO in 20 patients aged ≥ 20 years who underwent scheduled or emergency liver transplantation at Kyoto University Hospital from September 2019 to June 2021. Consent was obtained before surgery and data were recorded throughout the surgical period. Pearson correlation coefficient (r), Bland–Altman and 4-quadrant plot analyses were performed on the extracted data. A total of 1517 PAC-CCO vs. FVS-CCO data pairs were obtained. The mean PAC-CCO was 8.73 L/min and the mean systemic vascular resistance was 617.5 dyne·s·cm-5, r was 0.48, bias was 1.62 L/min, the 95% limits of agreement were − 3.04 to 6.27, and the percentage error was 54.36%. These results show that agreement and trending between fourth-generation FVS-CCO and PAC-CCO are low in adult liver transplant recipients.
Nanoparticle-insertion scheme to decouple electron injection from laser evolution in laser wakefield acceleration
Authors: Xu Jiancai , Bae Leejin , Ezzat Mohamed , Kim Hyung Taek , Yang Jeong Moon , Lee Sang Hwa , Yoon Jin Woo , Sung Jae Hee , Lee Seong Ku , Ji Liangliang , Shen Baifei , Nam Chang Hee
Published: July 2022

A localized nanoparticle insertion scheme is developed to decouple electron injection from laser evolution in laser wakefield acceleration. Here we report the experimental realization of a controllable electron injection by the nanoparticle insertion method into a plasma medium, where the injection position is localized within the short range of 100 μm. Nanoparticles were generated by the laser ablation process of a copper blade target using a 3-ns 532-nm laser pulse with fluence above 100 J/cm2. The produced electron bunches with a beam charge above 300 pC and divergence of around 12 mrad show the injection probability over 90% after optimizing the ablation laser energy and the temporal delay between the ablation and the main laser pulses. Since this nanoparticle insertion method can avoid the disturbing effects of electron injection process on laser evolution, the stable high-charge injection method can provide a suitable electron injector for multi-GeV electron sources from low-density plasmas.
Focal epilepsy disrupts spindle structure and function
Authors: Schiller Katharina , Avigdor Tamir , Abdallah Chifaou , Sziklas Viviane , Crane Joelle , Stefani Ambra , Peter-Derex Laure , Frauscher Birgit
Published: July 2022

Sleep spindles are the hallmark of N2 sleep and are attributed a key role in cognition. Little is known about the impact of epilepsy on sleep oscillations underlying sleep-related functions. This study assessed changes in the global spindle rate in patients with epilepsy, analysed the distribution of spindles in relation to the epileptic focus, and performed correlations with neurocognitive function. Twenty-one patients with drug-resistant focal epilepsy (12 females; mean age 32.6 ± 10.7 years [mean ± SD]) and 12 healthy controls (3 females; 24.5 ± 3.3 years) underwent combined whole-night high-density electroencephalography and polysomnography. Global spindle rates during N2 were lower in epilepsy patients compared to controls (mean = 5.78/min ± 0.72 vs. 6.49/min ± 0.71, p = 0.02, d =  − 0.70). Within epilepsy patients, spindle rates were lower in the region of the epileptic focus compared to the contralateral region (median = 4.77/min [range 2.53–6.18] vs. 5.26/min [2.53–6.56], p = 0.02, rank biserial correlation RC =  − 0.57). This decrease was driven by fast spindles (12–16 Hz) (1.50/min [0.62–4.08] vs. 1.65/min [0.51–4.28], p = 0.002, RC =  − 0.76). The focal reduction in spindles was negatively correlated with two scales of attention (r =  − 0.54, p = 0.01; r =  − 0.51, p = 0.025). Patients with focal epilepsy show a reduction in global and local spindle rates dependent on the region of the epileptic focus. This may play a role in impaired cognitive functioning. Future work will show if the local reduction in spindles can be used as potential marker of the epileptic focus.
Biological depolymerization of lignin using laccase harvested from the autochthonous fungus Schizophyllum commune employing various production methods and its efficacy in augmenting in vitro digestibility in ruminants
Authors: Kumar Vidya Pradeep , Sridhar Manpal , Rao Ramya Gopala
Published: July 2022

A laccase-producing hyper performer,Schizophyllum commune,a white-rot fungus, was evaluated for its ability to selectively degrade lignin of diverse crop residues in vitro. Relative analysis of crop residue treatment using laccase obtained from immobilized cells demonstrated degradation of 30–40% in finger millet straw and sorghum stover, 27–32% in paddy straw, 21% in wheat straw, and 26% in maize straw, while 20% lignin degradation was observed when purified and recombinant laccase was used. Further investigations into in vitro dry matter digestibility studies gave promising results recording digestibility of 54–59% in finger millet straw 33–36% in paddy straw and wheat straw, 16% in maize straw for laccase obtained from cell immobilization method, whereas 14% digestibility was observed when purified and recombinant laccase was used. Sorghum stover recorded digestibility of 13–15% across all straws treated with laccase. The results obtained elucidated the positive influence of laccase treatment on lignin degradation and in vitro dry matter digestibility. The present research gave encouraging figures confirming the production of laccase using the cell immobilization method to be an efficient production method commensurate with purified and recombinant laccase under conditions of submerged cultivation, proclaiming a cost-effective, environmentally safe green technology for effectual lignin depolymerization.
Physiological aspects of sex differences and Haldane’s rule in Rumex hastatulus
Authors: Joachimiak Andrzej J. , Libik-Konieczny Marta , Wójtowicz Tomasz , Sliwinska Elwira , Grabowska-Joachimiak Aleksandra
Published: July 2022

Haldane’s rule (HR, impairment of fertility and/or viability of interracial hybrids) seems to be one of few generalizations in evolutionary biology. The validity of HR has been confirmed in animals, and more recently in some dioecious plants (Silene and Rumex). Dioecious Rumex hastatulus has two races differing in the sex chromosome system: Texas (T) and North Carolina (NC), and T × NC males showed both reduced pollen fertility and rarity—two classical symptoms of Haldane’s rule (HR). The reduced fertility of these plants has a simple mechanistic explanation, but the reason for their rarity was not elucidated. Here, we measured selected physiological parameters related to the antioxidant defense system in parental races and reciprocal hybrids of R. hastatulus. We showed that the X-autosome configurations, as well as asymmetries associated with Y chromosomes and cytoplasm, could modulate this system in hybrids. The levels and quantitative patterns of the measured parameters distinguish the T × NC hybrid from the other analyzed forms. Our observations suggest that the rarity of T × NC males is caused postzygotically and most likely related to the higher level of oxidative stress induced by the chromosomal incompatibilities. It is the first report on the physiological aspects of HR in plants.
Sensorimotor performance after high-definition transcranial direct current stimulation over the primary somatosensory or motor cortices in men versus women
Authors: Swissa Yochai , Hacohen Shlomi , Friedman Jason , Frenkel-Toledo Silvi
Published: July 2022

The primary somatosensory (S1) cortex is a central structure in motor performance. However, transcranial direct current stimulation (tDCS) research aimed at improving motor performance usually targets the primary motor cortex (M1). Recently, sex was found to mediate tDCS response. Thus, we investigated whether tDCS with an anodal electrode placed over S1 improves motor performance and sensation perception in men versus women. Forty-five participants randomly received 15-min high-definition tDCS (HD-tDCS) at 1 mA to S1, M1, or sham stimulation. Reaching performance was tested before and immediately following stimulation. Two-point orientation discrimination (TPOD) of fingers and proprioception of a reaching movement were also tested. Although motor performance did not differ between groups, reaching reaction time improved in the M1 group men. Reaching movement time and endpoint error improved in women and men, respectively. Correct trials percentage for TPOD task was higher in the S1 compared to the M1 group in the posttest and improved only in the S1 group. Reaching movement time for the proprioception task improved, overall, and endpoint error did not change. Despite the reciprocal connections between S1 and M1, effects of active tDCS over S1 and M1 may specifically influence sensation perception and motor performance, respectively. Also, sex may mediate effects of HD-tDCS on motor performance.
A novel hamster model of SARS-CoV-2 respiratory infection using a pseudotyped virus
Authors: Yamada Hiroshi , Sasaki So-Ichiro , Tani Hideki , Somekawa Mayu , Kawasuji Hitoshi , Saga Yumiko , Yoshida Yoshihiro , Yamamoto Yoshihiro , Hayakawa Yoshihiro , Morinaga Yoshitomo
Published: July 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a biosafety level (BSL)-3 pathogen; therefore, its research environment is limited. Pseudotyped viruses that mimic the infection of SARS-CoV-2 have been widely used for in vitro evaluation because they are available in BSL-2 containment laboratories. However, in vivo application is inadequate. Therefore, animal models instigated with animal BSL-2 will provide opportunities for in vivo evaluation. Hamsters (6–10-week-old males) were intratracheally inoculated with luciferase-expressing vesicular stomatitis virus (VSV)-based SARS-CoV-2 pseudotyped virus. The lungs were harvested 24–72 h after inoculation and luminescence was measured using an in vivo imaging system. Lung luminescence after inoculation with the SARS-CoV-2 pseudotyped virus increased in a dose-dependent manner and peaked at 48 h. The VSV-G (envelope G) pseudotyped virus also induced luminescence; however, a 100-fold concentration was required to reach a level similar to that of the SARS-CoV-2 pseudotyped virus. The SARS-CoV-2 pseudotyped virus is applicable to SARS-CoV-2 respiratory infections in a hamster model. Because of the single-round infectious virus, the model can be used to study the steps from viral binding to entry, which will be useful for future research on SARS-CoV-2 entry without using live SARS-CoV-2 or transgenic animals.
Improving the diagnosis of thyroid cancer by machine learning and clinical data
Authors: Xi Nan Miles , Wang Lin , Yang Chuanjia
Published: July 2022

Thyroid cancer is a common endocrine carcinoma that occurs in the thyroid gland. Much effort has been invested in improving its diagnosis, and thyroidectomy remains the primary treatment method. A successful operation without unnecessary side injuries relies on an accurate preoperative diagnosis. Current human assessment of thyroid nodule malignancy is prone to errors and may not guarantee an accurate preoperative diagnosis. This study proposed a machine learning framework to predict thyroid nodule malignancy based on our collected novel clinical dataset. The ten-fold cross-validation, bootstrap analysis, and permutation predictor importance were applied to estimate and interpret the model performance under uncertainty. The comparison between model prediction and expert assessment shows the advantage of our framework over human judgment in predicting thyroid nodule malignancy. Our method is accurate, interpretable, and thus useable as additional evidence in the preoperative diagnosis of thyroid cancer.
Impact of COVID-19 emergency on the psychological well-being of susceptible individuals
Authors: Stufano Angela , Lucchese Guglielmo , Stahl Benjamin , Grattagliano Ignazio , Dassisti Liliana , Lovreglio Piero , Flöel Agnes , Iavicoli Ivo
Published: July 2022

The current pandemic has exerted an unprecedented psychological impact on the world population, and its effects on mental health are a growing concern. The present study aims to evaluate psychological well-being (PWB) during the COVID-19 crisis in university workers with one or more diseases likely to increase the risk of severe outcomes in the event of SARS-CoV-2 infection, defined as susceptible. 210 susceptible employees of an Italian University (aged 25–71 years) were recruited during the COVID-19 second wave (October–December 2020). A group comprising 90 healthy university employees (aged 26–69 years) was also recruited. The self-report Psychological General Well Being Index (PGWBI) was used to assess global PWB and the influence on six sub-domains: anxiety, depressed mood, positive well-being, self-control, general health, and vitality. We applied non-linear dimension-reduction techniques and regression methods to 45 variables in order to assess the main demographic, occupational, and general-health-related factors predicting PWB during the COVID-19 crisis. PGWBI score was higher in susceptible than in healthy workers, both as total score (mean 77.8 vs 71.3) and across almost all subscales. Age and jobs involving high social interaction before the pandemic were inversely associated with the PWB total score, general health, and self-control subscores. The current data suggest no decline in PWB during the second wave of COVID-19 health emergency in susceptible individuals of working age. Critically, higher risk for mental-health issues appears to be inversely related to age, particularly among individuals deprived of their previous level of social interaction at work.
RF-CNN-F: random forest with convolutional neural network features for coronary artery disease diagnosis based on cardiac magnetic resonance
Authors: Khozeimeh Fahime , Sharifrazi Danial , Izadi Navid Hoseini , Joloudari Javad Hassannataj , Shoeibi Afshin , Alizadehsani Roohallah , Tartibi Mehrzad , Hussain Sadiq , Sani Zahra Alizadeh , Khodatars Marjane , Sadeghi Delaram , Khosravi Abbas , Nahavandi Saeid , Tan Ru-San , Acharya U. Rajendra , Islam Sheikh Mohammed Shariful
Published: July 2022

Coronary artery disease (CAD) is a prevalent disease with high morbidity and mortality rates. Invasive coronary angiography is the reference standard for diagnosing CAD but is costly and associated with risks. Noninvasive imaging like cardiac magnetic resonance (CMR) facilitates CAD assessment and can serve as a gatekeeper to downstream invasive testing. Machine learning methods are increasingly applied for automated interpretation of imaging and other clinical results for medical diagnosis. In this study, we proposed a novel CAD detection method based on CMR images by utilizing the feature extraction ability of deep neural networks and combining the features with the aid of a random forest for the very first time. It is necessary to convert image data to numeric features so that they can be used in the nodes of the decision trees. To this end, the predictions of multiple stand-alone convolutional neural networks (CNNs) were considered as input features for the decision trees. The capability of CNNs in representing image data renders our method a generic classification approach applicable to any image dataset. We named our method RF-CNN-F, which stands for Random Forest with CNN Features. We conducted experiments on a large CMR dataset that we have collected and made publicly accessible. Our method achieved excellent accuracy (99.18%) using Adam optimizer compared to a stand-alone CNN trained using fivefold cross validation (93.92%) tested on the same dataset.
Diagnostic accuracy of quick SOFA score and inflammatory biomarkers for predicting community-onset bacteremia
Authors: Matono Takashi , Yoshida Maki , Koga Hidenobu , Akinaga Rie
Published: July 2022

The potential use of quick SOFA (qSOFA) score and inflammatory biomarkers as bacteremia predictors is unelucidated. Herein the aim of this study was to evaluate the diagnostic accuracy of the qSOFA score and biomarkers for predicting community-onset bacteremia. We enrolled adult outpatients with blood culture samples drawn between 2018 and 2020. Contamination, intensive care unit admission, and hemodialysis were excluded. We performed a case-control study, and analyzed 115 patients (58 with bacteremia and 57 without bacteremia). The positive likelihood ratio (LR) for bacteremia was 2.46 (95% confidence interval [CI] 0.76–9.05) for a qSOFA score ≥ 2, and 4.07 (95% CI 1.92–9.58) for tachypnea (≥ 22/min). The highest performing biomarkers were procalcitonin (area under the curve [AUC] 0.80; 95% CI 0.72–0.88), followed by presepsin (AUC 0.69; 95% CI 0.60–0.79), and C-reactive protein (AUC 0.60; 95% CI 0.49–0.70). The estimated optimal cut-off value of procalcitonin was 0.377 ng/mL, with a sensitivity of 74.1%, a specificity of 73.7%, and a positive LR of 2.82. Presepsin was 407 pg/mL, with a sensitivity of 60.3%, a specificity of 75.4%, and a positive LR of 2.46. Procalcitonin was found to be a modestly useful biomarker for predicting non-severe community-onset bacteremia. Tachypnea (≥ 22/min) itself, rather than the qSOFA score, can be a diagnostic predictor. These predictors may aid decision-making regarding the collection of blood culture samples in the emergency department and outpatient clinics.
Automated image curation in diabetic retinopathy screening using deep learning
Authors: Nderitu Paul , Nunez do Rio Joan M. , Webster Ms Laura , Mann Samantha S. , Hopkins David , Cardoso M. Jorge , Modat Marc , Bergeles Christos , Jackson Timothy L.
Published: July 2022

Diabetic retinopathy (DR) screening images are heterogeneous and contain undesirable non-retinal, incorrect field and ungradable samples which require curation, a laborious task to perform manually. We developed and validated single and multi-output laterality, retinal presence, retinal field and gradability classification deep learning (DL) models for automated curation. The internal dataset comprised of 7743 images from DR screening (UK) with 1479 external test images (Portugal and Paraguay). Internal vs external multi-output laterality AUROC were right (0.994 vs 0.905), left (0.994 vs 0.911) and unidentifiable (0.996 vs 0.680). Retinal presence AUROC were (1.000 vs 1.000). Retinal field AUROC were macula (0.994 vs 0.955), nasal (0.995 vs 0.962) and other retinal field (0.997 vs 0.944). Gradability AUROC were (0.985 vs 0.918). DL effectively detects laterality, retinal presence, retinal field and gradability of DR screening images with generalisation between centres and populations. DL models could be used for automated image curation within DR screening.
Core cysteine residues in the Plasminogen-Apple-Nematode (PAN) domain are critical for HGF/c-MET signaling
Authors: Pal Debjani , De Kuntal , Shanks Carly M. , Feng Kai , Yates Timothy B. , Morrell-Falvey Jennifer , Davidson Russell B. , Parks Jerry M. , Muchero Wellington
Published: July 2022

The Plasminogen-Apple-Nematode (PAN) domain, with a core of four to six cysteine residues, is found in > 28,000 proteins across 959 genera. Still, its role in protein function is not fully understood. The PAN domain was initially characterized in numerous proteins, including HGF. Dysregulation of HGF-mediated signaling results in multiple deadly cancers. The binding of HGF to its cell surface receptor, c-MET, triggers all biological impacts. Here, we show that mutating four core cysteine residues in the HGF PAN domain reduces c-MET interaction, subsequent c-MET autophosphorylation, and phosphorylation of its downstream targets, perinuclear localization, cellular internalization of HGF, and its receptor, c-MET, and c-MET ubiquitination. Furthermore, transcriptional activation of HGF/c-MET signaling-related genes involved in cancer progression, invasion, metastasis, and cell survival were impaired. Thus, targeting the PAN domain of HGF may represent a mechanism for selectively regulating the binding and activation of the c-MET pathway.
Amino acid sensor GCN2 promotes SARS-CoV-2 receptor ACE2 expression in response to amino acid deprivation
Authors: Hu Xiaoming , Niu Yuguo , Luo Peixiang , Xiao Fei , Yuan Feixiang , Yin Hanrui , Chen Shanghai , Guo Feifan
Published: July 2022

Angiotensin-converting enzyme 2 (ACE2) has been identified as a primary receptor for severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2). Here, we investigated the expression regulation of ACE2 in enterocytes under amino acid deprivation conditions. In this study, we found that ACE2 expression was upregulated upon all or single essential amino acid deprivation in human colonic epithelial CCD841 cells. Furthermore, we found that knockdown of general control nonderepressible 2 (GCN2) reduced intestinal ACE2 mRNA and protein levels in vitro and in vivo. Consistently, we revealed two GCN2 inhibitors, GCN2iB and GCN2-IN-1, downregulated ACE2 protein expression in CCD841 cells. Moreover, we found that increased ACE2 expression in response to leucine deprivation was GCN2 dependent. Through RNA-sequencing analysis, we identified two transcription factors, MAFB and MAFF, positively regulated ACE2 expression under leucine deprivation in CCD841 cells. These findings demonstrate that amino acid deficiency increases ACE2 expression and thereby likely aggravates intestinal SARS-CoV-2 infection.
Secure random number generation from parity symmetric radiations
Authors: Tsurumaru Toyohiro , Sasaki Toshihiko , Tsutsui Izumi
Published: July 2022

The random number generators (RNGs) are an indispensable tool for information security. Among various approaches, the radioactive decay has been considered as a promising candidate of RNGs for over half a century, on account of its seemingly unpredictable decay timings as quantum phenomena. However, the security of these radioactive RNGs has not been proven so far. Here we prove the security by a change of tactics, that is, by rewriting decay timings into decay directions, which allows us to ensure the secrecy with the help of the parity invariance deeply rooted in the fundamental law of nature. Our result demonstrates that the foundational properties of particle physics, such as the symmetry of interactions, can be used as a firm basis for the RNGs.
Universal multilayer network exploration by random walk with restart
Authors: Baptista Anthony , Gonzalez Aitor , Baudot Anaïs
Published: July 2022

The amount and variety of data have been increasing drastically for several years. These data are often represented as networks and explored with approaches arising from network theory. Recent years have witnessed the extension of network exploration approaches to capitalize on more complex and richer network frameworks. Random walks, for instance, have been extended to explore multilayer networks. However, current random walk approaches are limited in the combination and heterogeneity of networks they can handle. New analytical and numerical random walk methods are needed to cope with the increasing diversity and complexity of multilayer networks. We propose here MultiXrank, a method and associated Python package that enables Random Walk with Restart on any kind of multilayer network. We evaluate MultiXrank with leave-one-out cross-validation and link prediction, and measure the impact of the addition or removal of network data on prediction performances. Finally, we measure the sensitivity of MultiXrank to input parameters by in-depth exploration of the parameter space.
Mechanism for particle fractionalization and universal edge physics in quantum Hall fluids
Authors: Bochniak Arkadiusz , Nussinov Zohar , Seidel Alexander , Ortiz Gerardo
Published: July 2022

Advancing a microscopic framework that rigorously unveils the underlying topological hallmarks of fractional quantum Hall (FQH) fluids is a prerequisite for making progress in the classification of strongly-coupled topological matter. We present a second-quantization framework that reveals an exact fusion mechanism for particle fractionalization in FQH fluids, and uncovers the fundamental structure behind the condensation of non-local operators characterizing topological order in the lowest-Landau-level. We show the first exact analytic computation of the quasielectron Berry connections leading to its fractional charge and exchange statistics, and perform Monte Carlo simulations that numerically confirm the fusion mechanism for quasiparticles. We express the sequence of (bosonic and fermionic) Laughlin second-quantized states, highlighting the lack of local condensation, and present a rigorous constructive subspace bosonization dictionary for the bulk fluid. Finally, we establish universal long-distance behavior of edge excitations by formulating a conjecture based on the DNA, or root state, of the FQH fluid.
Over a third of groundwater in USA public-supply aquifers is Anthropocene-age and susceptible to surface contamination
Authors: Jurgens Bryant C. , Faulkner Kirsten , McMahon Peter B. , Hunt Andrew G. , Casile Gerolamo , Young Megan B. , Belitz Kenneth
Published: July 2022

The distribution of groundwater age is useful for evaluating the susceptibility and sustainability of groundwater resources. Here, we compute the aquifer-scale cumulative distribution function to characterize the age distribution for 21 Principal Aquifers that account for ~80% of public-supply pumping in the United States. The aquifer-scale cumulative distribution function for each Principal Aquifer was derived from an ensemble of modeled age distributions (~60 samples per aquifer) based on multiple tracers: tritium, tritiogenic helium-3, sulfur hexafluoride, chlorofluorocarbons, carbon-14, and radiogenic helium-4. Nationally, the groundwater is 38% Anthropocene (since 1953), 34% Holocene (75 – 11,800 years ago), and 28% Pleistocene (>11,800 years ago). The Anthropocene fraction ranges from <5 to 100%, indicating a wide range in susceptibility to land-surface contamination. The Pleistocene fraction of groundwater exceeds 50% in 7 eastern aquifers that are predominately confined. The Holocene fraction of groundwater exceeds 50% in 5 western aquifers that are predominately unconfined. The sustainability of pumping from these Principal Aquifers depends on rates of recharge and release of groundwater stored in fine-grained layers.