bluuebunny/crossref_metadata_2025 huggingface dataset:
Volcanology, Geochemistry, and Petrology Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science
Authors: Arora Bhavna , Currin Adriana , Dwivedi Dipankar , Fru Mary I. N. , Kumar Naresh , McLeod Claire L. , Roman Diana C.
Published: April 2022

This article is composed of a commentary about the state of Integrated, Coordinated, Open, and Networked (ICON) principles (Goldman et al., 2021, https://doi.org/10.1029/2021ea002099) in Volcanology, Geochemistry, and Petrology (VGP), and discussion on the opportunities and challenges of adopting them. VGP encompasses a broad field that addresses volcanic, magmatic, hydrothermal, geomicrobial systems; process investigations that span the physical, geochemical and biological realms, including planetary geology; and one that is extensively supported by state‐of‐the‐art research facilities. We suggest that an open, inclusive, collaborative and evolving model of an international coordinated network is critical to answering the most pressing challenges in VGP. In this commentary piece, we begin to discuss the elements of, challenges to, and path forward in developing such a model. For this team, ICON means collaboration, equitable access to data for the entire scientific community, and forging of partnerships that potentially contribute to more innovative ways of coordinating and sharing research. It also means bringing more equity to science, by implementing effective measures which consider access to funding, analytical equipment, resources, and mentors. More importantly, ICON to us means having important conversations around what we value in the advancement of science, perhaps exploring outside the idea of meritocracy and evaluating what individual traits can contribute to science outside what has traditionally been considered the norm.
Temporal Evolution of Radiated Energy to Seismic Moment Scaling During the Preparatory Phase of the Mw 6.1, 2009 L’Aquila Earthquake (Italy)
Authors: Picozzi M. , Spallarossa D. , Iaccarino A. G. , Bindi D.
Published: April 2022

We investigate the preparatory phase of the 2009, Mw 6.1 L’Aquila earthquake in central Italy by analyzing the temporal evolution and spatial distribution of the seismic moment, M0, to radiated energy, ES. Our approach focuses on monitoring the deviations of the scaling between M0 and ES with respect to a model calibrated for the background seismicity. The temporal evolution of these deviations, defined as Energy Index (EI), identifies the onset of the activation phase 1 week before the mainshock. We show that foreshocks are characterized by a progressive increase in slip per unit stress, in agreement with the diffusion of highly pressurized fluids before the L’Aquila earthquake proposed by previous studies. Our results suggest that the largest events occur where energy index (EI) is highest, in agreement with the existing link between energy index (EI) and the mean loading stress.
Small Scale Magnetic Structure in the Induced Martian Ionosphere and Lower Magnetic Pile‐Up Region
Authors: Hamil O. , Cravens T. E. , Renzaglia A. , Andersson L.
Published: April 2022

Small‐scale magnetic structures have been observed in the induced Martian ionosphere by magnetometers onboard the Mars Global Surveyor (MGS) and the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft. The origin and evolution of these structures remain poorly understood and the goal of the current paper is to better characterize them and their distribution in the dayside ionosphere using Mars Atmosphere and Volatile EvolutioN (MAVEN) data. Mars Atmosphere and Volatile EvolutioN (MAVEN) Langmuir probe data is used to find thermal pressures in the ionosphere. The structures studied range in size from about 20 km up to a couple of hundred km. We constrain our investigation to the northern hemisphere, dayside Martian ionosphere in order to minimize crustal magnetic field interference. Magnetic pressure spikes (and/or field component variations), along with thermal pressure behavior can also sometimes characterize small‐scale structures. In addition to pressures and field components, minimum variance analyses are carried out for each structure in order to help classify them (e.g., horizontal slabs, ionopause‐like structures, flux tube and flux ropes). A “statistical” catalog of properties (pressure, field amplitude, ellipticity, width, etc.) is generated for about 1,000 structures. One conclusion we reached from this survey is that slab‐like features are more likely to be found than rope‐like features for altitudes above 250 km.
Electron Diffusion by Magnetosonic Waves in the Earth’s Radiation Belts
Authors: Wong Jin‐Mann , Meredith Nigel P. , Horne Richard B. , Glauert Sarah A. , Ross Johnathan P. J.
Published: April 2022

We conduct a global survey of magnetosonic waves and compute the associated bounce‐ and drift‐averaged diffusion coefficients, taking into account colocated measurements of fpe/fce, to assess the role of magnetosonic waves in radiation belt dynamics. The average magnetosonic wave intensities increase with increasing geomagnetic activity and decreasing relative frequency with the majority of the wave power in the range fcp < f < 0.3fLHR during active conditions. In the region 4.0 ≤ L* ≤ 5.0, the bounce‐ and drift‐averaged energy diffusion rates due to magnetosonic waves never exceed those due to whistler mode chorus, suggesting that whistler mode chorus is the dominant mode for electron energization to relativistic energies in this region. Further in, in the region 2.0 ≤ L* ≤ 3.5, the bounce‐ and drift‐averaged pitch angle diffusion rates due to magnetosonic waves can exceed those due to plasmaspheric hiss and very low frequency (VLF) transmitters over energy‐dependent ranges of intermediate pitch angles. We compute electron lifetimes by solving the 1D pitch angle diffusion equation including the effects of plasmaspheric hiss, VLF transmitters, and magnetosonic waves. We find that magnetosonic waves can have a significant effect on electron loss timescales in the slot region reducing the loss timescales during active times from 5.6 to 1.5 days for 500 keV electrons at L* = 2.5 and from 140.4 to 35.7 days for 1 MeV electrons at L* = 2.0.
Thermal Properties of Liquid Iron at Conditions of Planetary Cores
Authors: Li Qing , Xian Jia‐Wei , Zhang Yigang , Sun Tao , Vočadlo Lidunka
Published: April 2022

Thermal properties of iron at high pressures (P) and temperatures (T) are essential for determining the internal structure and evolution of planetary cores. Compared to its solid counterpart, the liquid phase of iron is less studied and existing results exhibit large discrepancies, hindering a proper understanding of planetary cores. Here we use the formally exact thermodynamic integration approach to calculate thermal properties of liquid iron up to 3.0 TPa and 25000 K. Uncertainties associated with theory are compensated by introducing a T‐independent pressure shift based on experimental data. The resulting thermal equation of state agrees well with the diamond anvil cell (DAC) data in the P‐T range of measurements. At higher P‐T it matches the reduced shock wave data yet deviates considerably from the extrapolations of DAC measurements, indicating the latter may require further examinations. Moreover, the calculated heat capacity and thermal expansivity are substantially lower than some recent reports, which have important ramifications for understanding thermal evolutions of planetary cores. Using Kepler‐36b as a prototype, we examine how a completely molten core may affect the P‐T profiles of massive exoplanets. By comparing the melting slope and the adiabatic slope along the iron melting line, we propose that crystallization of the cores of massive planets proceeds from the bottom‐up rather than the top‐down.
Short‐Term Precipitation Prediction for Contiguous United States Using Deep Learning
Authors: Chen Guoxing , Wang Wei‐Chyung
Published: April 2022

Accurate short‐term weather prediction, essential for many aspects of life, relies mainly on forecasts from numerical weather models. Here, we report results supporting strongly deep learning as a viable, alternative approach. A 3D convolutional neural network, which uses a single frame of meteorology fields as input to predict the precipitation spatial distribution, is developed based on 39‐years (1980–2018) data of meteorology and daily precipitation over the contiguous United States. Results show that the trained network outperforms the state‐of‐the‐art weather models in predicting daily total precipitation, and the superiority of the network extends to forecast leads up to 5 days. Combining the network predictions with the weather‐model forecasts significantly improves the accuracy of model forecasts, especially for heavy‐precipitation events. Furthermore, the millisecond‐scale inference time of the network facilitates large ensemble predictions for extra accuracy improvement. These results demonstrate the promising prospects of deep learning in short‐term weather predictions.
Maximum Latewood Density Analysis Solves Long‐Standing Mystery Between Temperature Reconstructions and Historical Records
Authors: Kleemann K.
Published: April 2022

Edwards et al. (2022, https://doi.org/10.1029/2021pa004386) take tree ring samples from Scots pine trees in Sämtland, Sweden, and analyze them to reconstruct the summer temperatures for 1783. The maximum latewood density data for 1783 are low, suggesting cooler temperatures. The authors conclude that anatomical anomalies in their samples resulted from acidic damage caused by the Laki haze, a dry and sulfuric smelling fog emitted by the Laki fissure in Iceland during its eruption, which lasted from 8 June 1783 to 7 February 1784. This finding resolves a long‐standing discrepancy between historical documents that indicate an unusually warm summer in 1783 and temperature reconstructions based on tree rings that often suggested a cooler summer. The paper by Edwards et al. (2022, https://doi.org/10.1029/2021pa004386) thereby shows the potential of interdisciplinary collaborations: Only by studying historical records does it becomes apparent that the summer was not cold but warm. Historical records indicate further that the Laki haze also affected the vegetation in other parts of Europe, such as England, the Low Countries, and Germany. Further study of tree rings to reconstruct the temperature of other regions is desirable.
Cyclin-dependent kinase inhibitor fadraciclib (CYC065) depletes anti-apoptotic protein and synergizes with venetoclax in primary chronic lymphocytic leukemia cells
Authors: Chen Rong , Chen Yuling , Xiong Ping , Zheleva Daniella , Blake David , Keating Michael J. , Wierda William G. , Plunkett William
Published: April 2022

Fadraciclib (CYC065) is a second-generation aminopurine CDK2/9 inhibitor with increased potency and selectivity toward CDK2 and CDK9 compared to seliciclib (R-roscovitine). In chronic lymphocytic leukemia (CLL), a disease that depends on the over-expression of anti-apoptotic proteins for its survival, inhibition of CDK9 by fadraciclib reduced phosphorylation of the C-terminal domain of RNA polymerase II and blocked transcription in vitro; these actions depleted the intrinsically short-lived anti-apoptotic protein Mcl-1 and induced apoptosis. While the simulated bone marrow and lymph node microenvironments induced Mcl-1 expression and protected CLL cells from apoptosis, these conditions did not prolong the turnover rate of Mcl-1, and fadraciclib efficiently abrogated the protective effect. Further, fadraciclib was synergistic with the Bcl-2 antagonist venetoclax, inducing more profound CLL cell death, especially in samples with 17p deletion. While fadraciclib, venetoclax, and the combination each had distinct kinetics of cell death induction, their activities were reversible, as no additional cell death was induced upon removal of the drugs. The best combination effects were achieved when both drugs were maintained together. Altogether, this study provides a rationale for the clinical development of fadraciclib in CLL, either alone or in combination with a Bcl-2 antagonist.
A potent human monoclonal antibody with pan-neutralizing activities directly dislocates S trimer of SARS-CoV-2 through binding both up and down forms of RBD
Authors: Wang Xiaofei , Hu Ao , Chen Xiangyu , Zhang Yixin , Yu Fei , Yue Shuai , Li Arong , Zhang Junsong , Pan Zhiwei , Yang Yang , Lin Yao , Gao Leiqiong , Zhou Jing , Zhao Jing , Li Fang , Shi Yaling , Huang Feng , Yang Xiaofan , Peng Yi , Tu Luoyang , Zhang Huan , Zheng Huanying , He Jun , Zhang Hui , Xu Lifan , Huang Qizhao , Zhu Yongqun , Deng Kai , Ye Lilin
Published: April 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of novel coronavirus disease (COVID-19). The neutralizing monoclonal antibodies (mAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 are among the most promising strategies to prevent and treat COVID-19. However, SARS-CoV-2 variants of concern (VOCs) profoundly reduced the efficacies of most of mAbs and vaccines approved for clinical use. Herein, we demonstrated mAb 35B5 efficiently neutralizes both wild-type (WT) SARS-CoV-2 and VOCs, including B.1.617.2 (delta) variant, in vitro and in vivo. Cryo-electron microscopy (cryo-EM) revealed that 35B5 neutralizes SARS-CoV-2 by targeting a unique epitope that avoids the prevailing mutation sites on RBD identified in circulating VOCs, providing the molecular basis for its pan-neutralizing efficacy. The 35B5-binding epitope could also be exploited for the rational design of a universal SARS-CoV-2 vaccine.
Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline
Authors: Pinseel Eveline , Nakov Teofil , Van den Berge Koen , Downey Kala M , Judy Kathryn J , Kourtchenko Olga , Kremp Anke , Ruck Elizabeth C , Sjöqvist Conny , Töpel Mats , Godhe Anna , Alverson Andrew J
Published: April 2022

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of acclimated S. marinoi grown in a common garden. Our experiment included eight strains from source populations spanning the Baltic Sea salinity cline. Gene expression analysis revealed that low salinities induced changes in the cellular metabolism of S. marinoi, including upregulation of photosynthesis and storage compound biosynthesis, increased nutrient demand, and a complex response to oxidative stress. However, the strain effect overshadowed the salinity effect, as strains differed significantly in their response, both regarding the strength and the strategy (direction of gene expression) of their response. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond to environmental change.
The in-practice prevention programme: an example of flexible commissioning from Yorkshire and the Humber
Authors: Sandom Fiona , Hearnshaw Simon , Grant Siobhan , Williams Lynne , Brocklehurst Paul
Published: April 2022

Introduction An In-Practice Prevention (IPP) programme was developed by the Local Dental Network in the North Yorkshire and the Humber area in England in response to an oral health needs assessment. The underpinning logic model drew on a flexible commissioning approach and aimed to incentivise dental teams with NHS contracts to promote the delivery of prevention. This used care pathways that involved the whole dental team and was cost-neutral.

Aim The programme was evaluated using realist methodology to identify 'what works, in which circumstances, how and for who?'.

Design Realist evaluations are explanatory in nature and attempt to understand the factors that appear to influence the success (or not) of an intervention, rather than demonstrating causality.

Methods and results Following a review of the pertinent literature, semi-structured interviews and focus groups, five theory areas were considered to be critical to the delivery of IPP. In order of stated priority, these were: 1) clinical leadership; 2) 'skill mix'; 3) financial incentives; 4) institutional logic/practice culture; and 5) behaviour change.

Conclusion The results appear to show that clinically-led programmes could offer value to dental commissioners within a flexible commissioning model, although this would need to be further tested using an experiment design.
KLF5 inhibition overcomes oxaliplatin resistance in patient-derived colorectal cancer organoids by restoring apoptotic response
Authors: Shen Xiaohui , Zhang Yuchen , Xu Zhuoqing , Gao Han , Feng Wenqing , Li Wenchang , Miao Yiming , Xu Zifeng , Zong Yaping , Zhao Jingkun , Lu Aiguo
Published: April 2022

Oxaliplatin resistance is a major challenge in the treatment of colorectal cancer (CRC). Many molecular targeted drugs for refractory CRC have been developed to solve CRC drug resistance, but their effectiveness and roles in the progression of CRC and oxaliplatin resistance remain unclear. Here, we successfully constructed CRC PDOs and selected the Kruppel-like factor 5 (KLF5) inhibitor ML264 as the research object based on the results of the in vitro drug screening assay. ML264 significantly restored oxaliplatin sensitivity in CRC PDOs by restoring the apoptotic response, and this effect was achieved by inhibiting the KLF5/Bcl-2/caspase3 signaling pathway. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays verified that KLF5 promoted the transcription of Bcl-2 in CRC cells. KLF5 inhibition also overcame oxaliplatin resistance in xenograft tumors. Taken together, our study demonstrated that ML264 can restore oxaliplatin sensitivity in CRC PDOs by restoring the apoptotic response. KLF5 may be a potential therapeutic target for oxaliplatin-resistant CRC. PDOs have a strong potential for evaluating inhibitors and drug combination therapy in a preclinical environment.
The lncRNA MIAT regulates CPT-1a mediated cardiac hypertrophy through m6A RNA methylation reading protein Ythdf2
Authors: Yang Yiqing , Mbikyo Muisha B. , Zhang Junzhe , Zhang Yuan , Zhang Naijin , Li Zhao
Published: April 2022

Abstracts

Pathological cardiac hypertrophy is a key contributor in heart failure (HF). Long non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A) modification play a vital role in cardiac hypertrophy respectively. Nevertheless, the interaction between lncRNA and m6A methylase in cardiac hypertrophy is scarcely reported. Here, we constructed a cardiac hypertrophy mouse model by transverse aortic constriction (TAC) surgery and H9c2 cell model by stimulating with AngII. We found that lncRNA MIAT mRNA level, and m6A RNA methylation reading protein Ythdf2 mRNA and protein levels, were significantly increased in the cardiac hypertrophy model both in vivo and vitro. MIAT or Ythdf2 overexpression aggravated cardiac hypertrophy, and vice versa. Through bioinformatics prediction, western blotting, FISH, RNA pull-down, and RIP, we found that MIAT bound to Ythdf2 and regulated its expression. Furthermore, we discovered that Ythdf2 function was a downstream of MIAT in cardiac hypertrophy. Finally, we found that MIAT was a necessary regulator of cardiac hypertrophy due to its regulation of the Ythdf2/PPARα/CPT-1a axis. This study indicated a new hypertrophic signaling pathway: MIAT/Ythdf2/PPARα/CPT-1a. The results provided a new understanding of the MIAT and m6A RNA methylation reading protein, Ythdf2, function and mechanism in cardiac hypertrophy and highlighted the potential therapeutic benefits in the heart.
Akt-GSK3β-mPTP pathway regulates the mitochondrial dysfunction contributing to odontoblasts apoptosis induced by glucose oxidative stress
Authors: Wu Danni , Yan Liya , Zheng Chuchu , Ren Xuekun , Pan Yihuai , Huang Shengbin , Pan Lijun , Li Zongli
Published: April 2022

Diabetes Mellitus can cause dental pulp cells apoptosis by oxidative stress, and affect the integrity and function of dental pulp tissue. Mitochondria are the main attack targets of oxidative stress and have a critical role in apoptosis. However, whether mitochondria are involved in dental pulp damage caused by diabetes mellitus remains unclear. This study aimed to investigate the role of mitochondria in the apoptosis of odontoblast-like cell line (mDPC6T) induced by glucose oxidative stress, and to explore its possible mechanism. We established an oxidative stress model in vitro using glucose oxidase/glucose to simulate the pathological state under diabetic conditions. We found that the opening of mitochondrial permeability transition pore (mPTP) contributed to the apoptosis of mDPC6T treated with glucose oxidase, as evidenced by enhanced mitochondrial reactive oxygen species (mtROS) and intracellular Ca2+ disorder, significantly reduced mitochondrial membrane potential (MMP) and ATP production. Antioxidant N-acetylcysteine (NAC) or Cyclosporine A (mPTP inhibitor) blocked the mPTP opening, which significantly attenuated mitochondrial dysfunction and apoptosis induced by glucose oxidative stress. In addition, we found that glucose oxidative stress stimulated mPTP opening may through inhibition of Akt-GSK3β pathway. This study provides a new insight into the mitochondrial mechanism underlying diabetes-associated odontoblast-like cell apoptosis, laying a foundation for the prevention and treatment of diabetes-associated pulp injury.
DUB3/KLF4 combats tumor growth and chemoresistance in hepatocellular carcinoma
Authors: Jia Xuebing , Li Lei , Wang Fan , Xue Ying , Wu Tongde , Jia Qianqian , Li Yunhui , Wu Chenming , Chen Yuping , Wu Jinhuan , Su Yang , Wang Xinshu , Zhuang Tao , Dong Xiao , Ling Jing , Yuan Jian , Li Qi
Published: April 2022

This study aimed to investigate the role of deubiquitinating enzyme 3 (DUB3) in the regulation of Krüppel-like factor 4 (KLF4) expression in hepatocellular carcinoma (HCC). Gain- and loss-of-function assay, luciferase reporter assay, co-immunoprecipitation, and intracellular and extracellular deubiquitination assays were conducted in vitro. A tumor xenograft mouse model was established. The expression of DUB3 and KLF4 was examined in HCC patient specimens. The results showed that DUB3 upregulated KLF4 expression by deubiquitinating and stabilizing KLF4 protein in HCC cells through binding with KLF4. DUB3 inhibited HCC cell proliferation in vitro and tumor growth in vivo while enhancing the chemosensitivity of HCC cells in a KLF4-dependent manner. Furthermore, KLF4 promoted DUB3 transcription by binding to the DUB3 promoter. In HCC patients, DUB3 expression positively correlated with KLF4 expression in HCC tissues. Low DUB3 expression predicted worse overall survival and recurrence in HCC patients. In conclusion, this study revealed a positive DUB3/KLF4 feedback loop that inhibits tumor growth and chemoresistance in HCC. These results suggest that DUB3/KLF4 activation might be a potential therapeutic approach for HCC treatment.
A metafluid with multistable density and internal energy states
Authors: Peretz Ofek , Ben Abu Ezra , Zigelman Anna , Givli Sefi , Gat Amir D.
Published: April 2022

Investigating and tailoring the thermodynamic properties of different fluids is crucial to many fields. For example, the efficiency, operation range, and environmental safety of applications in energy and refrigeration cycles are highly affected by the properties of the respective available fluids. Here, we suggest combining gas, liquid and multistable elastic capsules to create an artificial fluid with a multitude of stable states. We study, theoretically and experimentally, the suspension’s internal energy, equilibrium pressure-density relations, and their stability for both adiabatic and isothermal processes. We show that the elastic multistability of the capsules endows the fluid with multistable thermodynamic properties, including the ability of capturing and storing energy at standard atmospheric conditions, not found in naturally available fluids.
Atomic-scale visualization of chiral charge density wave superlattices and their reversible switching
Authors: Song Xuan , Liu Liwei , Chen Yaoyao , Yang Han , Huang Zeping , Hou Baofei , Hou Yanhui , Han Xu , Yang Huixia , Zhang Quanzhen , Zhang Teng , Zhou Jiadong , Huang Yuan , Zhang Yu , Gao Hong-Jun , Wang Yeliang
Published: April 2022

Chirality is essential for various phenomena in life and matter. However, chirality and its switching in electronic superlattices, such as charge density wave (CDW) superlattices, remain elusive. In this study, we characterize the chirality switching with atom-resolution imaging in a single-layer NbSe2 CDW superlattice by the technique of scanning tunneling microscopy. The atomic arrangement of the CDW superlattice is found continuous and intact although its chirality is switched. Several intermediate states are tracked by time-resolved imaging, revealing the fast and dynamic chirality transition. Importantly, the switching is reversibly realized with an external electric field. Our findings unveil the delicate switching process of chiral CDW superlattice in a two-dimensional (2D) crystal down to the atomic scale.
Recent advances and applications of deep learning methods in materials science
Authors: Choudhary Kamal , DeCost Brian , Chen Chi , Jain Anubhav , Tavazza Francesca , Cohn Ryan , Park Cheol Woo , Choudhary Alok , Agrawal Ankit , Billinge Simon J. L. , Holm Elizabeth , Ong Shyue Ping , Wolverton Chris
Published: April 2022

Deep learning (DL) is one of the fastest-growing topics in materials data science, with rapidly emerging applications spanning atomistic, image-based, spectral, and textual data modalities. DL allows analysis of unstructured data and automated identification of features. The recent development of large materials databases has fueled the application of DL methods in atomistic prediction in particular. In contrast, advances in image and spectral data have largely leveraged synthetic data enabled by high-quality forward models as well as by generative unsupervised DL methods. In this article, we present a high-level overview of deep learning methods followed by a detailed discussion of recent developments of deep learning in atomistic simulation, materials imaging, spectral analysis, and natural language processing. For each modality we discuss applications involving both theoretical and experimental data, typical modeling approaches with their strengths and limitations, and relevant publicly available software and datasets. We conclude the review with a discussion of recent cross-cutting work related to uncertainty quantification in this field and a brief perspective on limitations, challenges, and potential growth areas for DL methods in materials science.
Materials structure–property factorization for identification of synergistic phase interactions in complex solar fuels photoanodes
Authors: Guevarra Dan , Zhou Lan , Richter Matthias H. , Shinde Aniketa , Chen Di , Gomes Carla P. , Gregoire John M.
Published: April 2022

Properties can be tailored by tuning composition in high-order composition spaces. For spaces with complex phase behavior, modeling the properties as a function of composition and phase distribution remains a formidable challenge. We present materials structure–property factorization (MSPF) as an approach to automate modeling of such data and identify synergistic phase interactions. MSPF is an interpretable machine learning algorithm that couples phase mapping via Deep Reasoning Networks (DRNets) to matrix factorization-based modeling of the representative properties of each phase in a dataset. MSPF is demonstrated for Bi–Cu–V oxide photoanodes for solar fuel generation, which contains 25 different phase combinations and correspondingly exhibits complex composition-structure-photoactivity relationships. Comparing the measured photoactivity to a learned model for non-interacting phases, synergistic phase interactions are identified to guide further photoactivity optimization and understanding. MSPF identifies synergistic interactions of a BiVO4-like phase with both Cu2V2O7-like and CuV2O6-like phases, creating avenues for understanding complex photoelectrocatalysts.
fastMRI+, Clinical pathology annotations for knee and brain fully sampled magnetic resonance imaging data
Authors: Zhao Ruiyang , Yaman Burhaneddin , Zhang Yuxin , Stewart Russell , Dixon Austin , Knoll Florian , Huang Zhengnan , Lui Yvonne W. , Hansen Michael S. , Lungren Matthew P.
Published: April 2022

Improving speed and image quality of Magnetic Resonance Imaging (MRI) using deep learning reconstruction is an active area of research. The fastMRI dataset contains large volumes of raw MRI data, which has enabled significant advances in this field. While the impact of the fastMRI dataset is unquestioned, the dataset currently lacks clinical expert pathology annotations, critical to addressing clinically relevant reconstruction frameworks and exploring important questions regarding rendering of specific pathology using such novel approaches. This work introduces fastMRI+, which consists of 16154 subspecialist expert bounding box annotations and 13 study-level labels for 22 different pathology categories on the fastMRI knee dataset, and 7570 subspecialist expert bounding box annotations and 643 study-level labels for 30 different pathology categories for the fastMRI brain dataset. The fastMRI+ dataset is open access and aims to support further research and advancement of medical imaging in MRI reconstruction and beyond.
A three-year dataset supporting research on building energy management and occupancy analytics
Authors: Luo Na , Wang Zhe , Blum David , Weyandt Christopher , Bourassa Norman , Piette Mary Ann , Hong Tianzhen
Published: April 2022

This paper presents the curation of a monitored dataset from an office building constructed in 2015 in Berkeley, California. The dataset includes whole-building and end-use energy consumption, HVAC system operating conditions, indoor and outdoor environmental parameters, as well as occupant counts. The data were collected during a period of three years from more than 300 sensors and meters on two office floors (each 2,325 m2) of the building. A three-step data curation strategy is applied to transform the raw data into research-grade data: (1) cleaning the raw data to detect and adjust the outlier values and fill the data gaps; (2) creating the metadata model of the building systems and data points using the Brick schema; and (3) representing the metadata of the dataset using a semantic JSON schema. This dataset can be used in various applications—building energy benchmarking, load shape analysis, energy prediction, occupancy prediction and analytics, and HVAC controls—to improve the understanding and efficiency of building operations for reducing energy use, energy costs, and carbon emissions.
Influence of wind and light on the floating and sinking process of Microcystis
Authors: Xue Zongpu , Zhu Wei , Zhu Yuyang , Fan Xihui , Chen Huaimin , Feng Ganyu
Published: April 2022

The vertical migration and accumulation of Microcystis colonies is a critical process in algal bloom formation. This work explored the effect of wind and light intensity on the vertical migration of Microcystis colonies. The wind-driven currents, light-driven changes in mass density of colonies, and the effect of colony size was coupled to simulate the vertical motion of colonies via Ansys Fluent and MATLAB. Results showed that light causes Microcystis to exhibit a ‘day-sinking and night-floating’ (d-n) phenomenon, however, wind weakens the phenomenon by forming a turbulent drag force that inhibits the vertical movement of Microcystis. This study proposed a kinetic ratio-based method, that there is a specific equilibrium turbulent kinetic energy and when turbulent kinetic energy of the water body is greater than the equilibrium turbulent kinetic energy, the d-n phenomenon does not occur. For Lake Taihu, the wind-driven turbulent kinetic energy is usually greater than the equilibrium turbulent kinetic energy. Therefore, Microcystis colonies may not exhibit the d-n phenomenon. Our findings provide a new theoretical basis for current process-based models in simulating algal blooms in large shallow lakes.
Short-term effects of different PM2.5 ranges on daily all-cause mortality in Jinan, China
Authors: Ma Zhixiang , Meng Xiangwei , Chen Cai , Chao Baoting , Zhang Chuanzhen , Li Wei
Published: April 2022

To examine the effects of different PM2.5 concentration ranges on daily all-cause mortality, 8768 all-cause deaths were recorded in the database of the Shandong Provincial Hospital Affiliated to Shandong First Medical University. Data of air pollutants (PM2.5 and O3) concentration were provided by the Jinan Environment Monitoring Center. The relative risk of all-cause mortality was assessed using a quasi-Poisson regression model after adjusting for confounding factors. The concentrations of PM2.5 were divided into four ranges 0–35 μg/m3; 35–75 μg/m3; 75–115 μg/m3; 115–150 μg/m3. There was no significant relationship between PM2.5 exposure and all-cause deaths in individuals aged < 60 years. However, for individuals aged ≥ 60 years, there was a significant positive association between exposure concentrations and all-cause deaths within the ranges 0–35 μg/m3, 35–75 μg/m3, and 115–150 μg/m3 with a mortality increase of 1.07 (1.01, 1.13), 1.03 (1.00, 1.05), and 1.05 (1.01, 1.08), respectively. When the population aged ≥ 60 years was stratified into gender groups, exposure to PM2.5 in the range 0–35 μg/m3 increased the mortality risk in men but not women. All-cause mortality in women, but not men, increased significantly with exposure to PM2.5 in the ranges of 35–75, 75–115, and 115–150 μg/m3.
Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan
Authors: Saeed Muhammad , Rais Muhammad , Akram Ayesha , Williams Maggie R. , Kellner Kenneth F. , Hashsham Syed A. , Davis Drew R.
Published: April 2022

Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for bothA. hazarensisandN. vicinathan for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly forA. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.
A microbiome study reveals the potential relationship between the bacterial diversity of a gymnastics hall and human health
Authors: Liang Z. , Dong C. B. , Liang H. , Zhen Y. X. , Zhou R. L. , Han Y. F. , Liang Z. Q.
Published: April 2022

Currently, investigations on the microbiota of sports centers and related facilities have been carried out in some countries, which showed that Microsporum gypseum, Trichophyton mentagrophytes and T. tonsurans are important dermatoprotofungi. In China, some research on athletes and sports equipment between the fungal community and public health has made some interesting achievements. However, the bacterial group among them has not been reported. Therefore, The aim of this study was to uncover (I) gymnastic equipment is there potential pathogenic factors and (ii) is there any difference in the biomarker of bacterial in different types of gymnastic room? The samples were collected from the gymnastics halls of one university in western China and main sports equipment, including gymnastics carpets, moving barres, hoops and balls, as well as wall bars, parallel bars and horizontal bars. The 16S rDNA of all the samples was sequenced, and the analyses were performed using FaproTax, Bug base function prediction and Line Discriminant Analysis (LDA) Effect Size. A 16S rDNA sequence analysis revealed abundant bacterial species biodiversity on gymnasts and apparatuses from two gymnastics halls at a university in western China. An analysis using the FaproTax and Bugbase functional prediction platforms showed that there were some opportunistic pathogens on the athletes and equipment from the Rhythmic Gymnastics (RG) and Artistic Gymnastics (AG) halls, such as Staphylococcus and Corynebacteiaceae. Infectious agents associated with cancer induction and development, such as Ruminococcaceae, Veillonellaceae and Moraxellaceae, as well as microbial toxin producers with a potential impact on human health, were also detected. According to a line discriminant analysis (LDA effect size), the bacterial biomarker groups of the two gymnasiums were different at the phylum-genus level: for RG, Erysipelatoclostridium, Lachnospiraceae and Bacteroidales, while for AG, Rhizobiales. Based on the results of the investigation, we suggest that more comprehensive consideration should be given to indoor microbial biodiversity and related public health problems in school gymnasiums.
Large landslides cluster at the margin of a deglaciated mountain belt
Authors: Pánek Tomáš , Břežný Michal , Harrison Stephan , Schönfeldt Elisabeth , Winocur Diego
Published: April 2022

Landslides in deglaciated and deglaciating mountains represent a major hazard, but their distribution at the spatial scale of entire mountain belts has rarely been studied. Traditional models of landslide distribution assume that landslides are concentrated in the steepest, wettest, and most tectonically active parts of the orogens, where glaciers reached their greatest thickness. However, based on mapping large landslides (> 0.9 km2) over an unprecedentedly large area of Southern Patagonia (~ 305,000 km2), we show that the distribution of landslides can have the opposite trend. We show that the largest landslides within the limits of the former Patagonian Ice Sheet (PIS) cluster along its eastern margins occupying lower, tectonically less active, and arid part of the Patagonian Andes. In contrast to the heavily glaciated, highest elevations of the mountain range, the peripheral regions have been glaciated only episodically, leaving a larger volume of unstable sedimentary and volcanic rocks that are subject to ongoing slope instability.
Effect of pulse laser frequency on PLD growth of LuFeO3 explained by kinetic simulations of in-situ diffracted intensities
Authors: Gabriel Vít , Kocán Pavel , Bauer Sondes , Nergis Berkin , Rodrigues Adriana , Horák Lukáš , Jin Xiaowei , Schneider Reinhard , Baumbach Tilo , Holý Václav
Published: April 2022

Atomistic processes during pulsed-laser deposition (PLD) growth influence the physical properties of the resulting films. We investigated the PLD of epitaxial layers of hexagonal LuFeO$$_3$$

3

by measuring the X-ray diffraction intensity in the quasiforbidden reflection 0003 in situ during deposition. From measured X-ray diffraction intensities we determined coverages of each layer and studied their time evolution which is described by scaling exponent $$\beta$$
β
directly connected to the surface roughness. Subsequently we modelled the growth using kinetic Monte Carlo simulations. While the experimentally obtained scaling exponent $$\beta$$
β
decreases with the laser frequency, the simulations provided the opposite behaviour. We demonstrate that the increase of the surface temperature caused by impinging ablated particles satisfactorily explains the recorded decrease in the scaling exponent with the laser frequency. This phenomena is often overlooked during the PLD growth.
Assessing mechanical catheter dysfunction in automated tidal peritoneal dialysis using cycler software: a case control, proof-of-concept study
Authors: Oviedo Flores Krystell , Kaltenegger Lukas , Eibensteiner Fabian , Unterwurzacher Markus , Kratochwill Klaus , Aufricht Christoph , König Franz , Vychytil Andreas
Published: April 2022

New recommendations on evaluation of peritoneal membrane function suggest ruling out catheter dysfunction when evaluating patients with low ultrafiltration capacity. We introduce the use of a combination of parameters obtained from the cycler software PD Link with HomeChoicePro (Baxter International Inc., Illinois, United States) cyclers for predicting catheter dysfunction in automated peritoneal dialysis patients (APD). Out of 117 patients treated at the Medical University of Vienna between 2015 and 2021, we retrospectively identified all patients with verified catheter dysfunction (n = 14) and compared them to controls without clinical evidence of mechanical catheter problems and a recent X-ray confirming PD catheter tip in the rectovesical/rectouterine space (n = 19). All patients had a coiled single-cuff PD catheter, performed tidal PD, and received neutral pH bicarbonate/lactate-buffered PD fluids with low-glucose degradation products on APD. Icodextrin-containing PD fluids were used for daytime dwells. We retrieved cycler data for seven days each and tested parameters' predictive capability of catheter dysfunction. Total number of alarms/week > 7 as single predictive parameter of catheter dislocation identified 85.7% (sensitivity) of patients with dislocated catheter, whereas 31.6% (1-specificity) of control patients were false positive. A combination of parameters (number of alarms/week > 7, total drain time > 22 min, ultrafiltration of last fill < 150 mL) where at least two of three parameters appeared identified the same proportion of patients with catheter dislocation, but was more accurate in identifying controls (21.1% false positive). In contrast to yearly PET measurements, an easily applicable combination of daily cycler readout parameters, also available in new APD systems connected to remote monitoring platforms shows potential for diagnosis of catheter dysfunction during routine follow-up.
Perceptions of weight status and energy balance behaviors among patients with non-alcoholic fatty liver disease
Authors: Heredia Natalia I. , Gaba Ruchi , Liu Yan , Jain Shilpa , Rungta Manasi , Rungta Manav , El-Serag Hashem B. , Kanwal Fasiha , Thrift Aaron P. , Balakrishnan Maya
Published: April 2022

Weight loss through behavioral modification is central to treating non-alcoholic fatty liver disease (NAFLD). To achieve this, patients need to accurately self-perceive their health behaviors. We aimed to identify predictors of concordance between self-perception and objective measures of body weight, physical activity (PA) and dietary behaviors. We used data from the Harris County NAFLD Cohort, an ongoing prospective study in a regional safety-net healthcare system. Patients completed self-administered baseline questionnaires on demographics, diet, PA, and self-perceptions. We assessed concordance between actual and self-perceived body weight and energy-balance behaviors. Multivariable logistic regression identified predictors of concordance. Patients (n = 458; average age 46.5 years) were 90% Hispanic and 76% female. PA and fruit/vegetable intake guidelines were met among 37% and 9%, respectively. Most (89%) overweight/obese patients accurately perceived themselves as such. However, 41% of insufficiently-active and 34% of patients not meeting fruit/vegetable intake guidelines inaccurately self-perceived their behaviors as “just right”. Women were 3 times more likely to accurately self-perceive weight status (adjusted odds ratio [AOR] 3.24; 95% CI 1.68–6.25) but 51% less likely to accurately self-perceive PA levels than men (AOR 0.49; 95% CI 0.29–0.81). Lower acculturation was associated with higher odds of accurate PA self-perception. Patients with prediabetes or diabetes vs normoglycemia were more likely to accurately self-perceive their fruit/vegetable intake. Most NAFLD patients accurately self-perceived their body weight. A third or more of those not meeting fruit/vegetable intake or PA guidelines had inaccurate perceptions about their behaviors. Our findings highlight key areas to target in NAFLD-specific behavioral modification programs.
Sparse pixel image sensor
Authors: Mennel Lukas , Polyushkin Dmitry K. , Kwak Dohyun , Mueller Thomas
Published: April 2022

As conventional frame-based cameras suffer from high energy consumption and latency, several new types of image sensors have been devised, with some of them exploiting the sparsity of natural images in some transform domain. Instead of sampling the full image, those devices capture only the coefficients of the most relevant spatial frequencies. The number of samples can be even sparser if a signal only needs to be classified rather than being fully reconstructed. Based on the corresponding mathematical framework, we developed an image sensor that can be trained to classify optically projected images by reading out the few most relevant pixels. The device is based on a two-dimensional array of metal–semiconductor–metal photodetectors with individually tunable photoresponsivity values. We demonstrate its use for the classification of handwritten digits with an accuracy comparable to that achieved by readout of the full image, but with lower delay and energy consumption.
Convergence of virulence and resistance in international clones of WHO critical priority enterobacterales isolated from Marine Bivalves
Authors: Bueris Vanessa , Sellera Fábio P. , Fuga Bruna , Sano Elder , Carvalho Marcelo P. N. , Couto Samuel C. F. , Moura Quézia , Lincopan Nilton
Published: April 2022

The global spread of critical-priority antimicrobial-resistant Enterobacterales by food is a public health problem. Wild-caught seafood are broadly consumed worldwide, but exposure to land-based pollution can favor their contamination by clinically relevant antimicrobial-resistant bacteria. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we performed genomic surveillance and cell culture-based virulence investigation of WHO critical priority Enterobacterales isolated from marine bivalves collected in the Atlantic Coast of South America. Broad-spectrum cephalosporin-resistant Klebsiella pneumoniae and Escherichia coli isolates were recovered from eight distinct geographical locations. These strains harbored blaCTX-M-type or blaCMY-type genes. Most of the surveyed genomes confirmed the convergence of wide virulome and resistome (i.e., antimicrobials, heavy metals, biocides, and pesticides resistance). We identified strains belonging to the international high-risk clones K. pneumoniae ST307 and E. coli ST131 carrying important virulence genes, whereas in vitro experiments confirmed the high virulence potential of these strains. Thermolabile and thermostable toxins were identified in some strains, and all of them were biofilm producers. These data point to an alarming presence of resistance and virulence genes in marine environments, which may favor horizontal gene transfer and the spread of these traits to other bacterial species.