bluuebunny/crossref_metadata_2025_split huggingface dataset:
ProteinGLUE multi-task benchmark suite for self-supervised protein modeling
Authors: Capel Henriette , Weiler Robin , Dijkstra Maurits , Vleugels Reinier , Bloem Peter , Feenstra K. Anton 
Published: September 2022

AbstractSelf-supervised language modeling is a rapidly developing approach for the analysis of protein sequence data. However, work in this area is heterogeneous and diverse, making comparison of models and methods difficult. Moreover, models are often evaluated only on one or two downstream tasks, making it unclear whether the models capture generally useful properties. We introduce the ProteinGLUE benchmark for the evaluation of protein representations: a set of seven per-amino-acid tasks for evaluating learned protein representations. We also offer reference code, and we provide two baseline models with hyperparameters specifically trained for these benchmarks. Pre-training was done on two tasks, masked symbol prediction and next sentence prediction. We show that pre-training yields higher performance on a variety of downstream tasks such as secondary structure and protein interaction interface prediction, compared to no pre-training. However, the larger model does not outperform the smaller model. We expect the ProteinGLUE benchmark dataset introduced here, together with the two baseline pre-trained models and their performance evaluations, to be of great value to the field of protein sequence-based property prediction. Availability: code and datasets fromhttps://github.com/ibivu/protein-glue.
Experimental identification of wheel-surface model parameters: various terrain conditions
Authors: Czapla Tomasz , Fice Marcin , Niestrój Roman 
Published: September 2022

AbstractSince the wheel interaction with a certain terrain cases (asphalt, concrete) are known and well described in case of straightforward motion and non-slip and slip cornering conditions, the skid-steered wheeled vehicles case needs to be analyzed. Side-slip for various attack angle has to be investigated. The main area of interest of research that is shown in the project is energy demand calculation of skid-steered wheeled vehicles in various terrain conditions. Certain cases of all-electric vehicles with individual electric motors per wheel demand a precise assessment of longitudinal and lateral forces in order to perform the fully controlled turn. Experimental stand designed and developed by authors allows to test the wheel-surface interaction for various terrain conditions and different driving directions. Test data were acquired for dry and wet sand and granite pavement. Traction and side forces were acquired and used to identify the wheel-soil interaction model parameters for unpropelled wheel. Results in a form of time series including longitudinal and lateral forces show the relation between attack angle, load and surface conditions in terms of stick and slip phenomenon that is essential for skid-steering dynamics calculations. Measurement results are then used for calculation of longitudinal and lateral forces coefficients as a function of attack angle and vertical load. Test were performed in natural environment, thus they are affected by changeable conditions. Multiple runs are used for elimination of that influence. Described experiments are a part of the project that includes results generalization using test validated FEM model. Described work is not intended to develop new ground-tire interaction models, it is focused on numerically efficient traction effort calculation method for various conditions including passive mode—unpropelled wheel.
Three-dimensional network of nitrogen-doped carbon matrix-encapsulated Si nanoparticles/carbon nanofibers hybrids for lithium-ion battery anodes with excellent capability
Authors: Cong Ruye , Jo Minsang , Martino Angelica , Park Hyun-Ho , Lee Hochun , Lee Chang-Seop 
Published: September 2022

AbstractThree-dimensionally structured silicon (Si)–carbon (C) nanocomposites have great potential as anodes in lithium-ion batteries (LIBs). Here, we report a Nitrogen-doped graphene/carbon-encapsulated Si nanoparticle/carbon nanofiber composite (NG/C@Si/CNF) prepared by methods of surface modification, electrostatic self-assembly, cross-linking with heat treatment, and further carbonization as a potential high-performance anode for LIBs. The N-doped C matrix wrapped around Si nanoparticles improved the electrical conductivity of the composites and buffered the volume change of Si nanoparticles during lithiation/delithiation. Uniformly dispersed CNF in composites acted as conductive networks for the fast transport of ions and electrons. The entire tightly connected organic material of NG/C@Si and CNF prevented the crushing and shedding of particles and maintained the integrity of the electrode structure. The NG/C@Si/CNF composite exhibited better rate capability and cycling performance compared with the other electrode materials. After 100 cycles, the electrode maintained a high reversible specific capacity of 1371.4 mAh/g.
FGF-2 enhances fibrogenetic changes in TGF-β2 treated human conjunctival fibroblasts
Authors: Tsugeno Yuri , Furuhashi Masato , Sato Tatsuya , Watanabe Megumi , Umetsu Araya , Suzuki Soma , Ida Yosuke , Hikage Fumihito , Ohguro Hiroshi 
Published: September 2022

AbstractThe objective of the current study was to examine the effects of fibroblast growth factor-2 (FGF-2) on conjunctival fibrogenesis that was induced by the presence of transforming growth factor-β2 (TGF-β2). Two-dimension (2D) and three-dimension (3D) cultured human conjunctival fibroblasts (HconF) were used for this purpose. The 2D and 3D cultured HconF were characterized by transendothelial electrical resistance (TEER) and FITC dextran permeability measurements (2D), real-time metabolic analyses (2D), size and stiffness measurements (3D), and the mRNA expression of extracellular matrix molecules, their modulators, Tissue inhibitor of metalloproteinases and matrix metalloproteinases and ER-stress related genes (2D and 3D). FGF-2 significantly increased planar proliferation, as evidenced by TEER values and FITC dextran permeability, and shifted glucose metabolism to the energetic phenotype of 2D HconF cells, and the stiffness of the 3D spheroids, and these effects were further enhanced in the presence of TGF-β2. Analyses of the expression of possible candidate molecules involved in cell architecture and stress indicated that some additive effects caused by both factors were also recognized in some of these molecules. The findings reported herein indicate that the FGF-2, either along or additively with TGF- β2 increased the fibrogenetic changes on the plane as well as in the spatial space of HconF cells.
Identification of the effects of COVID-19 on patients with pulmonary fibrosis and lung cancer: a bioinformatics analysis and literature review
Authors: Li Yang , Niu Lipeng 
Published: September 2022

AbstractCoronavirus disease 2019 (COVID-19) poses a serious threat to human health and life. The effective prevention and treatment of COVID-19 complications have become crucial to saving patients’ lives. During the phase of mass spread of the epidemic, a large number of patients with pulmonary fibrosis and lung cancers were inevitably infected with the SARS-CoV-2 virus. Lung cancers have the highest tumor morbidity and mortality rates worldwide, and pulmonary fibrosis itself is one of the complications of COVID-19. Idiopathic lung fibrosis (IPF) and various lung cancers (primary and metastatic) become risk factors for complications of COVID-19 and significantly increase mortality in patients. Therefore, we applied bioinformatics and systems biology approaches to identify molecular biomarkers and common pathways in COVID-19, IPF, colorectal cancer (CRC) lung metastasis, SCLC and NSCLC. We identified 79 DEGs between COVID-19, IPF, CRC lung metastasis, SCLC and NSCLC. Meanwhile, based on the transcriptome features of DSigDB and common DEGs, we identified 10 drug candidates. In this study, 79 DEGs are the common core genes of the 5 diseases. The 10 drugs were found to have positive effects in treating COVID-19 and lung cancer, potentially reducing the risk of pulmonary fibrosis.
Health behavior changes and mortality among South Korean cancer survivors
Authors: Jeong Wonjeong , Park Eun-Cheol , Nam Chung Mo , Park Sohee , Nam Jin Young , Jang Sung-In 
Published: September 2022

AbstractConsidering the rapid growth in the number of cancer survivors, the successful management of their health behaviors requires further attention. However, there are lack of information about cancer survivors’ health behaviors and the risk of mortality using Korean cohort data. This study aimed to examine the effects of health behavior changes on mortality among cancer survivors and to develop a validated nomogram. This cohort study was conducted using claims data. Data from adult cancer survivors from the National Health Insurance Service–National Sample Cohort, conducted between 2002 and 2015, were included. Individuals who were alive for five years after their cancer diagnosis were defined as cancer survivors. Cox proportional-hazards regression was used to estimate the target associations. Discrimination (Harrell’s C-index) and calibration (Hosmer–Lemeshow test) were employed to validate the nomogram. Data from 9300 cancer survivors were used for analysis. Compared to non-smokers, those who started or quit smoking had a higher risk of all-cause mortality. Those who were physically inactive had a higher risk of all-cause mortality than those who were continuously active. In the nomogram, the C-index value was 0.79 in the training data and 0.81 in the testing data. Hosmer–Lemeshow test was not significant, demonstrating a good fit. We found that individuals with unhealthy behaviors had a higher risk of mortality, thereby highlighting the importance of managing health behaviors among cancer survivors. The development of a validated nomogram may provide useful insights regarding official policies and existing practices in healthcare systems, which would benefit cancer survivors. Our study could provide the evidence to inform the priority of guideline for managing the health behavior among cancer survivors.
Synthesis of patient-specific multipoint 4D flow MRI data of turbulent aortic flow downstream of stenotic valves
Authors: Dirix Pietro , Buoso Stefano , Peper Eva S. , Kozerke Sebastian 
Published: September 2022

AbstractWe propose to synthesize patient-specific 4D flow MRI datasets of turbulent flow paired with ground truth flow data to support training of inference methods. Turbulent blood flow is computed based on the Navier–Stokes equations with moving domains using realistic boundary conditions for aortic shapes, wall displacements and inlet velocities obtained from patient data. From the simulated flow, synthetic multipoint 4D flow MRI data is generated with user-defined spatiotemporal resolutions and reconstructed with a Bayesian approach to compute time-varying velocity and turbulence maps. For MRI data synthesis, a fixed hypothetical scan time budget is assumed and accordingly, changes to spatial resolution and time averaging result in corresponding scaling of signal-to-noise ratios (SNR). In this work, we focused on aortic stenotic flow and quantification of turbulent kinetic energy (TKE). Our results show that for spatial resolutions of 1.5 and 2.5 mm and time averaging of 5 ms as encountered in 4D flow MRI in practice, peak total turbulent kinetic energy downstream of a 50, 75 and 90% stenosis is overestimated by as much as 23, 15 and 14% (1.5 mm) and 38, 24 and 23% (2.5 mm), demonstrating the importance of paired ground truth and 4D flow MRI data for assessing accuracy and precision of turbulent flow inference using 4D flow MRI exams.
Semisynthetic teicoplanin derivatives with dual antimicrobial activity against SARS-CoV-2 and multiresistant bacteria
Authors: Bereczki Ilona , Vimberg Vladimir , Lőrincz Eszter , Papp Henrietta , Nagy Lajos , Kéki Sándor , Batta Gyula , Mitrović Ana , Kos Janko , Zsigmond Áron , Hajdú István , Lőrincz Zsolt , Bajusz Dávid , Petri László , Hodek Jan , Jakab Ferenc , Keserű György M. , Weber Jan , Naesens Lieve , Herczegh Pál , Borbás Anikó 
Published: September 2022

AbstractPatients infected with SARS-CoV-2 risk co-infection with Gram-positive bacteria, which severely affects their prognosis. Antimicrobial drugs with dual antiviral and antibacterial activity would be very useful in this setting. Although glycopeptide antibiotics are well-known as strong antibacterial drugs, some of them are also active against RNA viruses like SARS-CoV-2. It has been shown that the antiviral and antibacterial efficacy can be enhanced by synthetic modifications. We here report the synthesis and biological evaluation of seven derivatives of teicoplanin bearing hydrophobic or superbasic side chain. All but one teicoplanin derivatives were effective in inhibiting SARS-CoV-2 replication in VeroE6 cells. One lipophilic and three perfluoroalkyl conjugates showed activity against SARS-CoV-2 in human Calu-3 cells and against HCoV-229E, an endemic human coronavirus, in HEL cells. Pseudovirus entry and enzyme inhibition assays established that the teicoplanin derivatives efficiently prevent the cathepsin-mediated endosomal entry of SARS-CoV-2, with some compounds inhibiting also the TMPRSS2-mediated surface entry route. The teicoplanin derivatives showed good to excellent activity against Gram-positive bacteria resistant to all approved glycopeptide antibiotics, due to their ability to dually bind to the bacterial membrane and cell-wall. To conclude, we identified three perfluoralkyl and one monoguanidine analog of teicoplanin as dual inhibitors of Gram-positive bacteria and SARS-CoV-2.
Effect of Cosmos, Crotalaria, Foeniculum, and Canavalia species, single-cropped or mixes, on the community of predatory arthropods
Authors: Barros Adamastor Pereira , de Carvalho Silva Alessandra , de Souza Abboud Antonio Carlos , Ricalde Marcelo Perrone , Ataide Julielson Oliveira 
Published: September 2022

AbstractSome plants can attract natural enemy by offering resources such as alternative food and refuge. However, studies need to be conducted before agricultural landscape diversification is implement. Our objective was to determine the best floristic compositions of cosmos (Cosmos sulphureus—Asteraceae), showy rattlepod (Crotalaria spectabilis—Fabaceae), fennel (Foeniculum vulgare—Apiaceae), and jack bean (Canavalia ensiformis—Fabaceae) to attract and maintain predatory arthropods, and know the potential of these treatments for future use in diversifying agricultural systems. The experimental design consisted in seven treatments of four species in single-crop, intercrops in three densities called mix1, mix2, and mix3, and the control (weeds). For the arthropod families classified as very frequent and constant, population dynamics in intercropping treatments was plotted according to the plant phenology. We conclude that all plants cultivated in single-cropping and intercropping treatments showed high predator richness and can potentially be used to diversify cultivated areas. Sulfur cosmos as a single crop and three mixes attracts higher numbers and greater family richness. Spider families—Oxyopidae, Araneidae and Thomisidae—and insects—Chrysopidae and Coccinellidae are more frequents. The dynamics of the predator populations varied according to the mixes treatment.
Exceptionally robust magnetism and structure of SrFeO$$_2$$ above 100 GPa
Authors: Balédent V. , Nataf L. , Rueff J.-P. 
Published: September 2022

AbstractWe report the exceptional structural and magnetic stability of SrFeO$$_2$$

2

under pressure by X-Ray Magnetic Circular Dichroism (XMCD) and X-ray Diffraction (XRD) up to the Mbar range. The XMCD data confirm the onset of ferromagnetism above 30 GPa and its stability up to 102 GPa while XRD shows that SrFeO$$_2$$

2

structure remains unchanged from 30 GPa up to 111 GPa without any sign of structural transition. Our results demonstrate the robustness of Fe properties under extreme conditions in the square planar environment.
Striatal D1 and D2 receptor availability are selectively associated with eye-blink rates after methylphenidate treatment
Authors: Demiral Şükrü B. , Manza Peter , Biesecker Erin , Wiers Corinde , Shokri-Kojori Ehsan , McPherson Katherine , Dennis Evan , Johnson Allison , Tomasi Dardo , Wang Gene-Jack , Volkow Nora D. 
Published: September 2022

AbstractEye-blink rate has been proposed as a biomarker of the brain dopamine system, however, findings have not been consistent. This study assessed the relationship between blink rates, measured after oral placebo) (PL) and after a challenge with oral methylphenidate (MP; 60 mg) and striatal D1 receptor (D1R) (measured at baseline) and D2 receptor (D2R) availability (measured after PL and after MP) in healthy participants. PET measures of baseline D1R ([11C]NNC112) (BL-D1R) and D2R availability ([11C]raclopride) after PL (PL-D2R) and after MP (MP-D2R) were quantified in the striatum as non-displaceable binding potential. MP reduced the number of blinks and increased the time participants kept their eyes open. Correlations with dopamine receptors were only significant for the eye blink measures obtained after MP; being positive for BL-D1R in putamen and MP-D2R in caudate (PL-D2R were not significant). MP-induced changes in blink rates (PL minus MP) were negatively correlated with BL-D1R in caudate and putamen. Our findings suggest that eye blink measures obtained while stressing the dopamine system might provide a more sensitive behavioral biomarker of striatal D1R or D2R in healthy volunteers than that obtained at baseline or after placebo.
3D stochastic interferometer detects picometer deformations and minute dielectric fluctuations of its optical volume
Authors: Graciani Guillaume , Filoche Marcel , Amblard François 
Published: September 2022

AbstractSpeckle metrology harnesses the interferometric properties of disordered light to achieve remarkable sensitivities. Often relying on time-domain analysis, it is rate-limited by the acquisition of speckle images. In the present work instead, we use a frequency-domain approach which spans 8 to 10 frequency decades up to 100 MHz, and reveals minute changes of speckle decorrelation spectra. We built a 3D stochastic interferometer using a centimeter-sized quartz-powder cavity with arbitrary shape and high Lambertian reflectivity. Filled with a coherent monochromatic photon gas, it creates statistically isotropic and homogeneous 3D interference patterns, whose variations arise from cavity deformations or fluctuations of the dielectric tensor field inside. Speckle decorrelation depends neither on where the perturbation sits nor on where it is measured. With an average 62 m photon transit path and a finesse of 10500, cavity deformations are detected with a power noise floor of 4 × 10−3 pm2, i.e., 2.7 pm at 1 kHz. We also demonstrate a 100-fold sensitivity gain compared to conventional light scattering techniques when probing thermal motions of single and multiply scattering colloids.
Cave opening and fossil accumulation in Naracoorte, Australia, through charcoal and pollen in dated speleothems
Authors: Weij Rieneke , Woodhead Jon D. , Sniderman J. M. Kale , Hellstrom John C. , Reed Elizabeth , Bourne Steven , Drysdale Russell N. , Pollard Timothy J. 
Published: September 2022

AbstractCaves are important fossil repositories which provide records extending back over million-year timescales. While the physical processes of cave formation are well understood, the timing of initial cave development and opening—a more important parameter to studies of palaeontology, palaeoanthropology and archaeology—has proved more difficult to constrain. Here we investigate speleothems from the Naracoorte Cave Complex in southern Australia, with a rich record of Pleistocene vertebrate fossils (including extinct megafauna) and partly World Heritage-listed, using U-Th-Pb dating and analyses of their charcoal and pollen content. We find that, although speleothem formation began at least 1.34 million years ago, pollen and charcoal only began to be trapped within growing speleothems from 600,000 years ago. We interpret these two ages to represent the timing of initial cave development and the subsequent opening of the caves to the atmosphere respectively. These findings demonstrate the potential of U-Th-Pb dating combined with charcoal and pollen as proxies to assess the potential upper age limit of vertebrate fossil records found within caves.
The effect of Sr doping on the electronic structure and electromagnetic properties of LaCo0.9Fe0.1O3 perovskites
Authors: Wang Fan , Wu Yue , Zhao Yue , Zhou Ming , Tang Shaolong , Ji Guangbin 
Published: September 2022

Herein, different La/Sr molar ratios of LSCFO perovskites were prepared via a sol–gel method. The electronic structure of LSCFO perovskites was investigated by the density functional theory and first principles calculation.
2D NbIrTe4 and TaRhTe4 monolayers: two fascinating topological insulators as electrocatalysts for oxygen reduction
Authors: Lv Mingyue , Yu Guangtao , Chen Wei 
Published: September 2022

2D topological insulator NbIrTe4 and TaRhTe4 monolayers can be high-efficiency oxygen reduction electrocatalysts with good selectivity of 4e pathway for fuel cells. Topological behavior also plays an important role in their oxygen reduction activity.
In vitro reconstitution of kallikrein-kinin system and progress curve analysis
Authors: Favier Bertrand , Bicout Dominique J. , Baroso Rémi , Paclet Marie-Hélène , Drouet Christian 
Published: September 2022

Abstract
Human kallikrein-kinin system (KKS) is a proteolytic cascade with two serine-protease zymogen couples (Factor XII and prekallikrein (PK) and their activated forms, FXIIa, PKa, respectively), releasing bradykinin by cleavage of native high-molecular-weight kininogen (nHK) into cleaved HK. For KKS investigation in human plasma, this cascade is usually triggered on ice eventually by mixing with purified proteins. It has been established that purified FXIIa, PK, and nHK required a fixed order and timing for mixing protein on ice to ensure reproducibility of testing, we investigated the activation kinetics of both enzymes. The activation process of this in vitro minimal reconstitution of KKS was studied by progress curve analysis, in condition of high enzyme/substrate ratio and by using on natural rather than peptide substrates.
FXIIa and PKa were found five-times less active on ice than at 37°C: kcat = 0.133 ± 0.034 and 0.0119 ± 0.0027 s−1, KM = 672 ± 150 and 115 ± 24 nM, respectively. The progress curve analysis of our in vitro KKS reconstitutions differed from a Michaelis–Menten mathematical simulation by a faster initial rate and a slower late rate. These two features were also observed ex vivo by using dextran sulfate-activated plasma and could reinforce the hypothesis of a maximal local effect (bradykinin release) and a minimal systemic consequence (PK preservation) in KKS activation process.
Analyzing the complete curve of cold KKS activation would provide valuable information for ex vivo investigation of KKS in samples from patients presenting with hereditary angioedema and other inflammatory conditions.
ANGPTL1, Foxo3a-Sox2, and colorectal cancer metastasis
Authors: Jiang Kai , Chen Haiyan , Ding Kefeng 
Published: September 2022

Abstract
In the present commentary, we discuss new observations stating that angiopoietin-like protein 1 (ANGPTL1) attenuates cancer metastasis and stemness through Forkhead box O-3a (Foxo3a)–SRY-related HMG-box-2 (Sox2) axis in colorectal cancer (Clin. Sci. (2022) 136, 657–673, https://doi.org/10.1042/CS20220043). ANGPTL1 has been reported to play a critical role in cancer progression and metastasis. However, the underlying mechanisms remain controversial. Here, we integrate the possible mechanisms for ANGPTL1 inhibiting colorectal cancer liver metastasis and discuss the regulation of ANGPTL1 on the Foxo3a–Sox2 pathway. Although ANGPTL1 showed multifunctional potential, there is still a long way to go for ANGPTL1 to be an effective treatment strategy in the clinic.