bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observation and control of the weak topological insulator state in ZrTe5
Authors: Zhang Peng , Noguchi Ryo , Kuroda Kenta , Lin Chun , Kawaguchi Kaishu , Yaji Koichiro , Harasawa Ayumi , Lippmaa Mikk , Nie Simin , Weng Hongming , Kandyba V. , Giampietri A. , Barinov A. , Li Qiang , Gu G. D. , Shin Shik , Kondo Takeshi 
Published: January 2021

AbstractA quantum spin Hall (QSH) insulator hosts topological states at the one-dimensional (1D) edge, along which backscattering by nonmagnetic impurities is strictly prohibited. Its 3D analogue, a weak topological insulator (WTI), possesses similar quasi-1D topological states confined at side surfaces. The enhanced confinement could provide a route for dissipationless current and better advantages for applications relative to strong topological insulators (STIs). However, the topological side surface is usually not cleavable and is thus hard to observe. Here, we visualize the topological states of the WTI candidate ZrTe5 by spin and angle-resolved photoemission spectroscopy (ARPES): a quasi-1D band with spin-momentum locking was revealed on the side surface. We further demonstrate that the bulk band gap is controlled by external strain, realizing a more stable WTI state or an ideal Dirac semimetal (DS) state. The highly directional spin-current and the tunable band gap in ZrTe5 will provide an excellent platform for applications.
Core transcription regulatory circuitry orchestrates corneal epithelial homeostasis
Authors: Li Mingsen , Huang Huaxing , Li Lingyu , He Chenxi , Zhu Liqiong , Guo Huizhen , Wang Li , Liu Jiafeng , Wu Siqi , Liu Jingxin , Xu Tao , Mao Zhen , Cao Nan , Zhang Kang , Lan Fei , Ding Junjun , Yuan Jin , Liu Yizhi , Ouyang Hong 
Published: January 2021

AbstractAdult stem cell identity, plasticity, and homeostasis are precisely orchestrated by lineage-restricted epigenetic and transcriptional regulatory networks. Here, by integrating super-enhancer and chromatin accessibility landscapes, we delineate core transcription regulatory circuitries (CRCs) of limbal stem/progenitor cells (LSCs) and find that RUNX1 and SMAD3 are required for maintenance of corneal epithelial identity and homeostasis. RUNX1 or SMAD3 depletion inhibits PAX6 and induces LSCs to differentiate into epidermal-like epithelial cells. RUNX1, PAX6, and SMAD3 (RPS) interact with each other and synergistically establish a CRC to govern the lineage-specific cis-regulatory atlas. Moreover, RUNX1 shapes LSC chromatin architecture via modulating H3K27ac deposition. Disturbance of RPS cooperation results in cell identity switching and dysfunction of the corneal epithelium, which is strongly linked to various human corneal diseases. Our work highlights CRC TF cooperativity for establishment of stem cell identity and lineage commitment, and provides comprehensive regulatory principles for human stratified epithelial homeostasis and pathogenesis.
A database framework for rapid screening of structure-function relationships in PFAS chemistry
Authors: Su An , Rajan Krishna 
Published: January 2021

AbstractThis paper describes a database framework that enables one to rapidly explore systematics in structure-function relationships associated with new and emerging PFAS chemistries. The data framework maps high dimensional information associated with the SMILES approach of encoding molecular structure with functionality data including bioactivity and physicochemical property. This ‘PFAS-Map’ is a 3-dimensional unsupervised visualization tool that can automatically classify new PFAS chemistries based on current PFAS classification criteria. We provide examples on how the PFAS-Map can be utilized, including the prediction and estimation of yet unmeasured fundamental physical properties of PFAS chemistries, uncovering hierarchical characteristics in existing classification schemes, and the fusion of data from diverse sources.
Impact of tumor-parenchyma biomechanics on liver metastatic progression: a multi-model approach
Authors: Wang Yafei , Brodin Erik , Nishii Kenichiro , Frieboes Hermann B. , Mumenthaler Shannon M. , Sparks Jessica L. , Macklin Paul 
Published: January 2021

AbstractColorectal cancer and other cancers often metastasize to the liver in later stages of the disease, contributing significantly to patient death. While the biomechanical properties of the liver parenchyma (normal liver tissue) are known to affect tumor cell behavior in primary and metastatic tumors, the role of these properties in driving or inhibiting metastatic inception remains poorly understood, as are the longer-term multicellular dynamics. This study adopts a multi-model approach to study the dynamics of tumor-parenchyma biomechanical interactions during metastatic seeding and growth. We employ a detailed poroviscoelastic model of a liver lobule to study how micrometastases disrupt flow and pressure on short time scales. Results from short-time simulations in detailed single hepatic lobules motivate constitutive relations and biological hypotheses for a minimal agent-based model of metastatic growth in centimeter-scale tissue over months-long time scales. After a parameter space investigation, we find that the balance of basic tumor-parenchyma biomechanical interactions on shorter time scales (adhesion, repulsion, and elastic tissue deformation over minutes) and longer time scales (plastic tissue relaxation over hours) can explain a broad range of behaviors of micrometastases, without the need for complex molecular-scale signaling. These interactions may arrest the growth of micrometastases in a dormant state and prevent newly arriving cancer cells from establishing successful metastatic foci. Moreover, the simulations indicate ways in which dormant tumors could “reawaken” after changes in parenchymal tissue mechanical properties, as may arise during aging or following acute liver illness or injury. We conclude that the proposed modeling approach yields insight into the role of tumor-parenchyma biomechanics in promoting liver metastatic growth, and advances the longer term goal of identifying conditions to clinically arrest and reverse the course of late-stage cancer.
A shift towards early-age desexing of cats under veterinary care in Australia
Authors: Mazeau Loic , Wylie Claire , Boland Lara , Beatty Julia A. 
Published: January 2021

AbstractThe global problem of unowned domestic cats, driven by their phenomenal reproductive success, carries significant economic, animal welfare and biodiversity costs. Desexing owned cats prior to puberty prevents unwanted litters that contribute to unowned cat populations. The prevalence and predictors of desexing, and the age at which surgery was carried out were investigated using anonymized electronic patient records in the VetCompass Australia database of cats presented to veterinary practices. Of 52,941 cats born between 2010 and 2017, 83.6% were desexed. Among 7463 desexed females, 21.5% had been desexed by 4 months of age, 59.8% by 6 months and 85.4% by 1 year. Sex, breed, location and socioeconomic indices significantly influenced desexing status and age at surgery. Cats born between 2010 and 2017 had greater odds of being desexed than cats born between 1995and 2009 at each age cut-off (≤ 4 months [OR 1.76, CI951.58–1.97], ≤ 6 months [OR 1.50, CI951.38–1.62] and ≤ 1 year [OR 2.33, CI952.11–2.57]p < 0.001). Most cats presented to veterinarians in Australia are desexed. Compared with cats born before 2010, cats born later are significantly younger at desexing but, even so, many cats would have reached sexual maturity before surgery. These findings will inform the design of front-line strategies promoting prepubertal desexing and they demonstrate, for the first time, a shift towards desexing younger cats.
A comparative study to evaluate CT-based semantic and radiomic features in preoperative diagnosis of invasive pulmonary adenocarcinomas manifesting as subsolid nodules
Authors: Wu Yun-Ju , Liu Yung-Chi , Liao Chien-Yang , Tang En-Kuei , Wu Fu-Zong 
Published: January 2021

AbstractThis study aims to predict the histological invasiveness of pulmonary adenocarcinoma spectrum manifesting with subsolid nodules ≦ 3 cm using the preoperative CT-based radiomic approach. A total of 186 patients with 203 SSNs confirmed with surgically pathologic proof were retrospectively reviewed from February 2016 to March 2020 for training cohort modeling. The validation cohort included 50 subjects with 57 SSNs confirmed with surgically pathologic proof from April 2020 to August 2020. CT-based radiomic features were extracted using an open-source software with 3D nodular volume segmentation manually. The association between CT-based conventional features/selected radiomic features and histological invasiveness of pulmonary adenocarcinoma status were analyzed. Diagnostic models were built using conventional CT features, selected radiomic CT features and experienced radiologists. In addition, we compared diagnostic performance between radiomic CT feature, conventional CT features and experienced radiologists. In the training cohort of 203 SSNs, there were 106 invasive lesions and 97 pre-invasive lesions. Logistic analysis identified that a selected radiomic feature named GLCM_Entropy_log10 was the predictor for histological invasiveness of pulmonary adenocarcinoma spectrum (OR: 38.081, 95% CI 2.735–530.309, p = 0.007). The sensitivity and specificity for predicting histological invasiveness of pulmonary adenocarcinoma spectrum using the cutoff value of CT-based radiomic parameter (GLCM_Entropy_log10) were 84.8% and 79.2% respectively (area under curve, 0.878). The diagnostic model of CT-based radiomic feature was compared to those of conventional CT feature (morphologic and quantitative) and three experienced radiologists. The diagnostic performance of radiomic feature was similar to those of the quantitative CT feature (nodular size and solid component, both lung and mediastinal window) in prediction invasive pulmonary adenocarcinoma (IPA). The AUC value of CT radiomic feature was higher than those of conventional CT morphologic feature and three experienced radiologists. The c-statistic of the training cohort model was 0.878 (95% CI 0.831–0.925) and 0.923 (0.854–0.991) in the validation cohort. Calibration was good in both cohorts. The diagnostic performance of CT-based radiomic feature is not inferior to solid component (lung and mediastinal window) and nodular size for predicting invasiveness. CT-based radiomic feature and nomogram could help to differentiate IPA lesions from preinvasive lesions in the both independent training and validation cohorts. The nomogram may help clinicians with decision making in the management of subsolid nodules.
Effects of symmetry-breaking on electromagnetic backscattering
Authors: Abdelrahman Mohamed Ismail , Slivina Evgeniia , Rockstuhl Carsten , Fernandez-Corbaton Ivan 
Published: January 2021

AbstractSystems with a discrete rotational symmetry $$2\pi /n$$

2
π
/
n

where $$n\ge 3$$

n
≥
3

that also have electromagnetic duality symmetry exhibit zero backscattering. The impact of breaking one of the two symmetries on the emerging backscattering has not yet been systematically studied. Here, we investigate the effect that perturbatively breaking each of the two symmetries has on the backscattering off individual objects and 2D arrays. We find that the backscattering off electromagnetically-small prisms increases with the parameters that determine the symmetry breaking, and that the increase of the backscattering due to the progressive breaking of one of the symmetries can be related to the other symmetry. Further exploration of the interplay between the two symmetries reveals that, in systems lacking enough rotational symmetry, the backscattering can be almost-entirely suppressed for a given linear polarization by deliberately breaking the duality symmetry. This duality breaking can be interpreted as an effective increase of the electromagnetic degree of rotational symmetry for that linear polarization.
Dietary patterns, food groups and nutrients in Crohn’s disease: associations with gut and systemic inflammation
Authors: Naqvi S. Ali , Taylor Lorian M. , Panaccione Remo , Ghosh Subrata , Barkema Herman W. , Hotte Naomi , Shommu Nusrat , Kaur Sandeep , Reimer Raylene A. , Madsen Karen L. , Raman Maitreyi 
Published: January 2021

AbstractThis study examined associations between dietary intake and gut and systemic inflammation assessed by fecal calprotectin ≤ or > 100 μg/mg (FCP), C-reactive protein ≤ or > 5 mg/L (CRP) and serum cytokine profiles in Crohn’s disease (CD) patients in clinical remission. A 3-month observational study was conducted at the University of Calgary in Calgary, Alberta, Canada between 2016 and 2018 in 66 outpatients with CD in clinical remission. FCP was obtained from stool samples at baseline and 3-months and serum CRP and serum cytokines were assessed at 3-months only (n = 41). Dietary intakes were collected using 3-day food records at baseline and 3-months and categorized as: PREDIMED Mediterranean diet scores (pMDS) total and individual components, the dietary inflammatory index (DII), food groups, and common micro- and macro-nutrients. Statistical models were developed to identify relationships between dietary factors and FCP, CRP and cytokine levels. Daily intake of leafy green vegetables was associated with FCP ≤ 100 μg/mg (p < 0.05). Increasing omega 6:3 ratio was associated with CRP ≤ 5 mg/L (p = 0.02). Different cytokines were significantly associated with various dietary variables. Future studies in patients with greater disease activity should be undertaken to explore these relationships.
Dynamics of neuronal oscillations underlying nociceptive response in the mouse primary somatosensory cortex
Authors: Iwamoto Shosuke , Tamura Makoto , Sasaki Atsushi , Nawano Masao 
Published: January 2021

AbstractPain is caused by tissue injury, inflammatory disease, pathogen invasion, or neuropathy. The perception of pain is attributed to the neuronal activity in the brain. However, the dynamics of neuronal activity underlying pain perception are not fully known. Herein, we examined theta-oscillation dynamics of local field potentials in the primary somatosensory cortex of a mouse model of formalin-induced pain, which usually shows a bimodal behavioral response interposed between pain-free periods. We found that formalin injection exerted a reversible shift in the theta-peak frequency toward a slower frequency. This shift was observed during nociceptive phases but not during the pain-free period and was inversely correlated with instantaneous pain intensity. Furthermore, instantaneous oscillatory analysis indicated that the probability of slow theta oscillations increased during nociceptive phases with an association of augmented slow theta power. Finally, cross-frequency coupling between theta and gamma oscillations indicated that the coupling peak frequency of theta oscillations was also shifted toward slower oscillations without affecting coupling strength or gamma power. Together, these results suggest that the dynamic changes in theta oscillations in the mouse primary somatosensory cortex represent the ongoing status of pain sensation.
Hsa-miR-494-3p attenuates gene HtrA3 transcription to increase inflammatory response in hypoxia/reoxygenation HK2 Cells
Authors: Gong Qian , Shen Zhi-ming , Sheng Zhe , Jiang Shi , Ge Sheng-lin 
Published: January 2021

AbstractThe occurrence of cardiac surgery-associated acute kidney injury (CSA-AKI) increases hospital stay and mortality. MicroRNAs has a crucial role in AKI. This objective of the current study is to explore the function of hsa-miR-494-3p in inflammatory response in human kidney tubular epithelial (HK2) cells with hypoxia/reoxygenation. According to KDIGO standard, patients after cardiac surgery with cardiopulmonary bypass were divided into two groups: AKI (n = 10) and non-AKI patients (n = 8). HK2 were raised in the normal and hypoxia/reoxygenation circumstances and mainly treated by overexpression ofmiR-494-3p and HtrA3. The relationship between miR-494-3p and HtrA3 was determined by dual-luciferase reporter assay. Our result showed that Hsa-miR-494-3p was elevated in the serum of patients with CSA-AKI, and also induced in hypoxic reoxygenated HK2 cells. Hsa-miR-494-3p also increased a hypoxia-reoxygenation induced inflammatory response in HK2 cells. Moreover, as a target gene of miR-494-3p, overexpression of HtrA3 downregulated the hypoxia-reoxygenation induced inflammatory response in HK2 cells. Overexpression of hsa-miR-494-3p-induced inflammatory response was inhibited by overexpression of HtrA3. Collectively, we identified that hsa-miR-494-3p, a miRNA induced in both circulation of AKI patients and hypoxia-reoxygenation-treated HK2 cells, enhanced renal inflammation by targeting HtrA3, which may suggest a possible role as a new therapeutic target for CSA-AKI.
Variable- and person-centered approaches to affect-biased attention in infancy reveal unique relations with infant negative affect and maternal anxiety
Authors: Vallorani Alicia , Fu Xiaoxue , Morales Santiago , LoBue Vanessa , Buss Kristin A. , Pérez-Edgar Koraly 
Published: January 2021

AbstractAffect-biased attention is an automatic process that prioritizes emotionally or motivationally salient stimuli. Several models of affect-biased attention and its development suggest that it comprises an individual’s ability to both engage with and disengage from emotional stimuli. Researchers typically rely on singular tasks to measure affect-biased attention, which may lead to inconsistent results across studies. Here we examined affect-biased attention across three tasks in a unique sample of 193 infants, using both variable-centered (factor analysis; FA) and person-centered (latent profile analysis; LPA) approaches. Using exploratory FA, we found evidence for two factors of affect-biased attention: an Engagement factor and a Disengagement factor, where greater maternal anxiety was related to less engagement with faces. Using LPA, we found two groups of infants with different patterns of affect-biased attention: a Vigilant group and an Avoidant group. A significant interaction noted that infants higher in negative affect who also had more anxious mothers were most likely to be in the Vigilant group. Overall, these results suggest that both FA and LPA are viable approaches for studying distinct questions related to the development of affect-biased attention, and set the stage for future longitudinal work examining the role of infant negative affect and maternal anxiety in the emergence of affect-biased attention.
Soil microbial properties of subalpine steppe soils at different grazing intensities in the Chinese Altai Mountains
Authors: Goenster-Jordan Sven , Ingold Mariko , Jannoura Ramia , Buerkert Andreas , Joergensen Rainer Georg 
Published: January 2021

AbstractLong-term provision of ecosystem services by grasslands is threatened by increasing stocking densities. The functions of grassland ecosystems depend on a mutual relationship between aboveground and belowground biota. While the effects of increasing stocking density on plant biomass are well studied, little is known about its impact on soil microbial properties. To fill this knowledge gap a grazing experiment was conducted on a summer pasture in the Chinese Altai Mountains during the summers of 2014 and 2015 using a randomized block design with stocking densities of 0, 8, 16, and 24 sheep ha−1 replicated four times. After two summer grazing periods (each 56 days), topsoil samples (1–7 cm) were taken in September 2015 and analyzed for major physical, chemical, and microbial soil properties. Except for the metabolic quotient (qCO2; p < 0.05), the examined soil properties remained unaffected by the increasing stocking densities, likely due to high spatial variability. The qCO2 declined from 13.5 mg CO2–C g−1 microbial biomass C d−1 at zero grazing to 12.2 mg CO2–C g−1 microbial biomass C d−1 at a stocking density of 24 sheep ha−1. Low values of qCO2 indicate an aged and dormant microbial community that diverts less soil organic carbon (SOC) to catabolic processes within their cells, characteristic for C limiting conditions. The aboveground biomass affected by grazing intensity correlated positively with SOC (rs = 0.60, p = 0.015) and ergosterol (rs = 0.76, p = 0.001) pointing indirectly to the effect of stocking density. Additionally to the relatively high values of qCO2, highest values of SOC (39.2 mg g−1 soil), ergosterol (6.01 µg g−1 soil), and basal respiration (10.7 µg g−1 soil d−1) were observed at a stocking density of 8 sheep ha−1 indicating that a low grazing intensity is recommendable to avoid soil degradation.
A numerical study of fish adaption behaviors in complex environments with a deep reinforcement learning and immersed boundary–lattice Boltzmann method
Authors: Zhu Yi , Tian Fang-Bao , Young John , Liao James C. , Lai Joseph C. S. 
Published: January 2021

AbstractFish adaption behaviors in complex environments are of great importance in improving the performance of underwater vehicles. This work presents a numerical study of the adaption behaviors of self-propelled fish in complex environments by developing a numerical framework of deep learning and immersed boundary–lattice Boltzmann method (IB–LBM). In this framework, the fish swimming in a viscous incompressible flow is simulated with an IB–LBM which is validated by conducting two benchmark problems including a uniform flow over a stationary cylinder and a self-propelled anguilliform swimming in a quiescent flow. Furthermore, a deep recurrent Q-network (DRQN) is incorporated with the IB–LBM to train the fish model to adapt its motion to optimally achieve a specific task, such as prey capture, rheotaxis and Kármán gaiting. Compared to existing learning models for fish, this work incorporates the fish position, velocity and acceleration into the state space in the DRQN; and it considers the amplitude and frequency action spaces as well as the historical effects. This framework makes use of the high computational efficiency of the IB–LBM which is of crucial importance for the effective coupling with learning algorithms. Applications of the proposed numerical framework in point-to-point swimming in quiescent flow and position holding both in a uniform stream and a Kármán vortex street demonstrate the strategies used to adapt to different situations.
Super-resolution time-resolved imaging using computational sensor fusion
Authors: Callenberg C. , Lyons A. , Brok D. den , Fatima A. , Turpin A. , Zickus V. , Machesky L. , Whitelaw J. , Faccio D. , Hullin M. B. 
Published: January 2021

AbstractImaging across both the full transverse spatial and temporal dimensions of a scene with high precision in all three coordinates is key to applications ranging from LIDAR to fluorescence lifetime imaging. However, compromises that sacrifice, for example, spatial resolution at the expense of temporal resolution are often required, in particular when the full 3-dimensional data cube is required in short acquisition times. We introduce a sensor fusion approach that combines data having low-spatial resolution but high temporal precision gathered with a single-photon-avalanche-diode (SPAD) array with data that has high spatial but no temporal resolution, such as that acquired with a standard CMOS camera. Our method, based on blurring the image on the SPAD array and computational sensor fusion, reconstructs time-resolved images at significantly higher spatial resolution than the SPAD input, upsampling numerical data by a factor $$12 \times 12$$

12
×
12

, and demonstrating up to $$4 \times 4$$

4
×
4

upsampling of experimental data. We demonstrate the technique for both LIDAR applications and FLIM of fluorescent cancer cells. This technique paves the way to high spatial resolution SPAD imaging or, equivalently, FLIM imaging with conventional microscopes at frame rates accelerated by more than an order of magnitude.