bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anchoring Multi‐Scale Models to Micron‐Scale Imaging of Multiphase Flow in Rocks
Authors: Wang Shan , Ruspini Leonardo C. , Øren Pål‐Eric , Van Offenwert Stefanie , Bultreys Tom 
Published: January 2022

AbstractImage‐based pore‐scale modeling is an important method to study multiphase flow in permeable rocks. However, in many rocks, the pore size distribution is so wide that it cannot be resolved in a single pore‐space image, typically acquired using micro‐computed tomography (micro‐CT). Recent multi‐scale models therefore incorporate sub‐voxel porosity maps, created by differential micro‐CT imaging of a contrast fluid in the pores. These maps delineate different microporous flow zones in the model, which must be assigned petrophysical properties as input. The uncertainty on the pore scale physics in these models is therefore heightened by uncertainties on the representation of unresolved pores, also called sub‐rock typing. Here, we address this by validating a multi‐scale pore network model using a drainage experiment imaged with differential micro‐CT on an Estaillades limestone sample. We find that porosity map‐based sub‐rock typing was unable to match the micrometer‐scale experimental fluid distributions. To investigate why, we introduce a novel baseline sub‐rock typing method, based on a 3D map of the experimental capillary pressure function. By incorporating this data, we successfully remove most of the sub‐rock typing uncertainty from the model, obtaining a close fit to the experimental fluid distributions. Comparison between the two methods shows that in this sample, the porosity map is poorly correlated to the multiphase flow behavior of microporosity. The method introduced in this paper can help to constrain the sources of uncertainties in multi‐scale models in reference cases, facilitating the development of simulations in complex reservoir rocks important for for example, geological storage of CO2.
CU06-1004 enhances vascular integrity and improves cardiac remodeling by suppressing edema and inflammation in myocardial ischemia–reperfusion injury
Authors: Zhang Haiying , Kim Hyeok , Park Bong Woo , Noh Minyoung , Kim Yeomyeong , Park Jeongeun , Park Jae-Hyun , Kim Jin-Ju , Sim Woo-Sup , Ban Kiwon , Park Hun-Jun , Kwon Young-Guen 
Published: January 2022

AbstractIschemia–reperfusion (I/R) injury accelerates the cardiomyocytes (CMs) death by oxidative stress, and thereby deteriorates cardiac function. There has been a paradigm shift in the therapeutic perspective more towards the prevention or amelioration of damage caused by reperfusion. Cardiac microvascular endothelial cells (CMECs) are more vulnerable to reperfusion injury and play the crucial roles more than CMs in the pathological process of early I/R injury. In this study, we investigate that CU06-1004, as a vascular leakage blocker, can improve cardiac function by inhibiting CMEC’s hyperpermeability and subsequently reducing the neutrophil’s plugging and infiltration in infarcted hearts. CU06-1004 was delivered intravenously 5 min before reperfusion and the rats were randomly divided into three groups: (1) vehicle, (2) low-CU06-1004 (1 mg/kg, twice at 24 h intervals), and (3) high-CU06-1004 (5 mg/kg, once before reperfusion). CU06-1004 treatment reduced necrotic size and cardiac edema by enhancing vascular integrity, as demonstrated by the presence of intact junction proteins on CMECs and surrounding pericytes in early I/R injury. It also decreased the expression of vascular cell adhesion molecule 1 (VCAM-1) on CMECs, resulting in reduced infiltration of neutrophils and macrophages. Echocardiography showed that the CU06-1004 treatment significantly improved cardiac function compared with the vehicle group. Interestingly, single high-dose treatment with CU06-1004 provided a greater functional improvement than repetitive low-dose treatment until 8 weeks post I/R. These findings demonstrate that CU06-1004 enhances vascular integrity and improves cardiac function by preventing lethal myocardial I/R injury. It can provide a promising therapeutic option, as potential adjunctive therapy to current reperfusion strategies.
The ERα/KDM6B regulatory axis modulates osteogenic differentiation in human mesenchymal stem cells
Authors: Liu Zhenqing , Lee Hye-Lim , Suh Jin Sook , Deng Peng , Lee Chang-Ryul , Bezouglaia Olga , Mirnia Mojan , Chen Vivian , Zhou Michael , Cui Zhong-Kai , Kim Reuben H. , Lee Min , Aghaloo Tara , Hong Christine , Wang Cun-Yu 
Published: January 2022

AbstractOsteoporosis is a highly prevalent public health burden associated with an increased risk of bone fracture, particularly in aging women. Estrogen, an important medicinal component for the preventative and therapeutic treatment of postmenopausal osteoporosis, induces osteogenesis by activating the estrogen receptor signaling pathway and upregulating the expression of osteogenic genes, such as bone morphogenetic proteins (BMPs). The epigenetic regulation of estrogen-mediated osteogenesis, however, is still unclear. In this report, we found that estrogen significantly induced the expression of lysine-specific demethylase 6B (KDM6B) and that KDM6B depletion by shRNAs led to a significant reduction in the osteogenic potential of DMSCs. Mechanistically, upon estrogen stimulation, estrogen receptor-α (ERα) was recruited to the KDM6B promoter, directly enhancing KDM6B expression. Subsequently, KDM6B was recruited to the BMP2 and HOXC6 promoters, resulting in the removal of H3K27me3 marks and activating the transcription of BMP2 and HOXC6, the master genes of osteogenic differentiation. Furthermore, we found that estrogen enhanced DMSC osteogenesis during calvarial bone regeneration and that estrogen’s pro-osteogenic effect was dependent on KDM6B in vivo. Taken together, our results demonstrate the vital role of the ERα/KDM6B regulatory axis in the epigenetic regulation of the estrogen-dependent osteogenic response.
Bioprospecting microwave-alkaline hydrolysate cocktail of defatted soybean meal and jackfruit peel biomass as carrier additive of molasses-alginate-bead biofertilizer
Authors: Roslan Muhamad Aidilfitri Mohamad , Sobri Zulfazli M. , Zuan Ali Tan Kee , Cheak Sim Choon , Rahman Nor Aini Abdul 
Published: January 2022

AbstractThe extraction of soluble hydrolysate protein and sugar from a biomass cocktail of defatted soybean meal (DSM) and jackfruit peel (JP) was examined using microwave-alkaline hydrolysis by varying the NaOH concentrations (0.04–0.11 M) and residence times (2–11 min). Based on the central composite design, the optimized parameters were achieved at 0.084 M NaOH concentration (100 mL), for 8.7 min at 300 W microwave power level to obtain the highest protein (5.31 mg/mL) and sugar concentrations (8.07 mg/mL) with > 75% recovery. Both raw and detoxified hydrolysate (using activated carbon) were correspondingly biocompatible with Enterobacter hormaechei strain 40a (P > 0.05) resulting in maximal cell counts of > 10 log CFU/mL. The optimized hydrolysate was prepared as an additive in molasses-alginate bead encapsulation of strain 40a. Further evaluation on phosphate and potassium solubilization performance of the encapsulated strain 40a exhibited comparable results with those of free cell counterpart (P > 0.05). The DSM-JP hydrolysate cocktail holds potential as a carrier additive of encapsulated-cell bead biofertilizers in order to sustain bacterial cell quality and consequently improve crop growth and productivity.
Negative tension controls stability and structure of intermediate filament networks
Authors: Haimov Ehud , Urbakh Michael , Kozlov Michael M. 
Published: January 2022

AbstractNetworks, whose junctions are free to move along the edges, such as two-dimensional soap froths and membrane tubular networks of endoplasmic reticulum are intrinsically unstable. This instability is a result of a positive tension applied to the network elements. A paradigm of networks exhibiting stable polygonal configurations in spite of the junction mobility, are networks formed by bundles of Keratin Intermediate Filaments (KIFs) in live cells. A unique feature of KIF networks is a, hypothetically, negative tension generated in the network bundles due to an exchange of material between the network and an effective reservoir of unbundled filaments. Here we analyze the structure and stability of two-dimensional networks with mobile three-way junctions subject to negative tension. First, we analytically examine a simplified case of hexagonal networks with symmetric junctions and demonstrate that, indeed, a negative tension is mandatory for the network stability. Another factor contributing to the network stability is the junction elastic resistance to deviations from the symmetric state. We derive an equation for the optimal density of such networks resulting from an interplay between the tension and the junction energy. We describe a configurational degeneration of the optimal energy state of the network. Further, we analyze by numerical simulations the energy of randomly generated networks with, generally, asymmetric junctions, and demonstrate that the global minimum of the network energy corresponds to the irregular configurations.
Neural correlates of integration processes during dynamic face perception
Authors: Alp Nihan , Ozkan Huseyin 
Published: January 2022

AbstractIntegrating the spatiotemporal information acquired from the highly dynamic world around us is essential to navigate, reason, and decide properly. Although this is particularly important in a face-to-face conversation, very little research to date has specifically examined the neural correlates of temporal integration in dynamic face perception. Here we present statistically robust observations regarding the brain activations measured via electroencephalography (EEG) that are specific to the temporal integration. To that end, we generate videos of neutral faces of individuals and non-face objects, modulate the contrast of the even and odd frames at two specific frequencies ($$f_1$$

f
1

and $$f_2$$

f
2

) in an interlaced manner, and measure the steady-state visual evoked potential as participants view the videos. Then, we analyze the intermodulation components (IMs: ($$nf_1\pm mf_2$$

n

f
1

±
m

f
2

), a linear combination of the fundamentals with integer multipliers) that consequently reflect the nonlinear processing and indicate temporal integration by design. We show that electrodes around the medial temporal, inferior, and medial frontal areas respond strongly and selectively when viewing dynamic faces, which manifests the essential processes underlying our ability to perceive and understand our social world. The generation of IMs is only possible if even and odd frames are processed in succession and integrated temporally, therefore, the strong IMs in our frequency spectrum analysis show that the time between frames (1/60 s) is sufficient for temporal integration.
Hydrogen peroxide can be a plausible biomarker in cyanobacterial bloom treatment
Authors: Asaeda Takashi , Rahman Mizanur , Abeynayaka Helayaye Damitha Lakmali 
Published: January 2022

AbstractThe effect of combined stresses, photoinhibition, and nutrient depletion on the oxidative stress of cyanobacteria was measured in laboratory experiments to develop the biomass prediction model. Phormidium ambiguum was exposed to various photosynthetically active radiation (PAR) intensities and phosphorous (P) concentrations with fixed nitrogen concentrations. The samples were subjected to stress assays by detecting the hydrogen peroxide (H2O2) concentration and antioxidant activities of catalase (CAT) and superoxide dismutase (SOD). H2O2 concentrations decreased to 30 µmol m−2 s−1 of PAR, then increased with higher PAR intensities. Regarding P concentrations, H2O2 concentrations (nmol L−1) generally decreased with increasing P concentrations. SOD and CAT activities were proportionate to the H2O2 protein−1. No H2O2 concentrations detected outside cells indicated the biological production of H2O2, and the accumulated H2O2 concentration inside cells was parameterized with H2O2 concentration protein−1. With over 30 µmol m−2 s−1 of PAR, H2O2 concentration protein−1 had a similar increasing trend with PAR intensity, independently of P concentration. Meanwhile, with increasing P concentration, H2O2 protein−1 decreased in a similar pattern regardless of PAR intensity. Protein content decreased with gradually increasing H2O2 up to 4 nmol H2O2 mg−1 protein, which provides a threshold to restrict the growth of cyanobacteria. With these results, an empirical formula—protein (mg L−1) = − 192*Log((H2O2/protein)/4.1), where H2O2/protein (nmol mg−1) = − 0.312*PAR2/(502 + PAR2)*((25/PAR)4 + 1)*Log(P/133,100), as a function of total phosphorus concentration, P (µg L−1)—was developed to obtain the cyanobacteria biomass.
Induced magnetic field and viscous dissipation on flows of two immiscible fluids in a rectangular channel
Authors: Shah Nehad Ali , Alrabaiah Hussam , Vieru Dumitru , Yook Se-Jin 
Published: January 2022

AbstractThe unsteady, magneto-hydrodynamic generalized Couette flows of two immiscible fluids in a rectangular channel with isothermal walls under the influence of an inclined magnetic field and an axial electric field have been investigated. Both fluids are considered electrically conducting and the solid boundaries are electrically insulated. Approximate analytical solutions for the velocity, induced magnetic, and temperature fields have been determined using the Laplace transform method along with the numerical Stehfest's algorithm for the inversion of the Laplace transforms. Also, for the nonlinear differential equation of energy, a numerical scheme based on the finite differences has been developed. A particular case has been numerically and graphically studied to show the evolution of the fluid velocity, induced magnetic field, and viscous dissipation in both flow regions.
Plant canopy may promote seed dispersal by wind
Authors: Qin Xuanping , Liang Wei , Liu Zhimin , Liu Minghu , Baskin Carol C. , Baskin Jerry M. , Xin Zhiming , Wang Zhigang , Zhou Quanlai 
Published: January 2022

AbstractSeed dispersal has received much research attention. The plant canopy can intercept diaspores, but the effect of the plant canopy (the aboveground portion of a plant consisting of branches and leaves) on dispersal distance has not been explored empirically. To determine the effect of plant canopy on seed dispersal distance, a comparison of diaspores falling through open air and through plant canopy was made in a wind tunnel using three wind speeds and diaspores with various traits. Compared with diaspores falling through open air, the dispersal distance of diaspores falling through plant canopy was decreased or increased, depending on wind speed and diaspore traits. When falling through a plant canopy, dispersal distance of diaspores with thorns or those without appendages was promoted at low wind speed (2 m s−1), while that of diaspores with low wing loading (0.5 mg mm−2) and terminal velocity (2.5 m s−1) was promoted by relatively high (6 m s−1) wind speed. A plant canopy could increase seed dispersal distance, which may be due to the complicated updraft generated by canopy. The effect of maternal plants on seed dispersal regulates the distribution pattern and the species composition of the community.
Three-state majority-vote model on small-world networks
Authors: Zubillaga Bernardo J. , Vilela André L. M. , Wang Minggang , Du Ruijin , Dong Gaogao , Stanley H. Eugene 
Published: January 2022

AbstractIn this work, we study the opinion dynamics of the three-state majority-vote model on small-world networks of social interactions. In the majority-vote dynamics, an individual adopts the opinion of the majority of its neighbors with probability 1-q, and a different opinion with chance q, where q stands for the noise parameter. The noise q acts as a social temperature, inducing dissent among individual opinions. With probability p, we rewire the connections of the two-dimensional square lattice network, allowing long-range interactions in the society, thus yielding the small-world property present in many different real-world systems. We investigate the degree distribution, average clustering coefficient and average shortest path length to characterize the topology of the rewired networks of social interactions. By employing Monte Carlo simulations, we investigate the second-order phase transition of the three-state majority-vote dynamics, and obtain the critical noise $$q_c$$

q
c

, as well as the standard critical exponents $$\beta /\nu$$

β
/
ν

, $$\gamma /\nu$$

γ
/
ν

, and $$1/\nu$$

1
/
ν

for several values of the rewiring probability p. We conclude that the rewiring of the lattice enhances the social order in the system and drives the model to different universality classes from that of the three-state majority-vote model in two-dimensional square lattices.
RETRACTED ARTICLE: Performance of
graphene-zinc oxide nanocomposite coated-glassy carbon electrode in the sensitive
determination of para-nitrophenol
Authors: Dar Riyaz Ahmad , Naikoo Gowhar Ahmad , Srivastava Ashwini Kumar , Hassan Israr Ul , Karna Shashi P. , Giri Lily , Shaikh Ahamad M. H. , Rezakazemi Mashallah , Ahmed Waqar 
Published: January 2022

AbstractGraphene: zinc oxide nanocomposite (GN:ZnO NC) platform was tried for
the sensitive determination of para-nitrophenol (p-NP) through the electrochemical
method. ZnO nanoparticles (NPs) were synthesized by the modified wet-chemical method
where in potassium hydroxide and zinc nitrate were used as precursors and starch as
a stabilizing agent. A green and facile approach was applied to synthesize GN:ZnO NC
in which glucose was employed as a reductant to reduce graphene-oxide to graphene in
the presence of ZnO NPs. The synthesized NC was characterized using scanning and
high-resolution transmission electron microscopy, energy dispersive x-ray analysis,
X-ray diffraction and Raman spectroscopic techniques to examine the crystal phase,
crystallinity, morphology, chemical composition and phase structure. GN:ZnO NC layer
deposited over the glassy carbon electrode (GCE) was initially probed for its
electrochemical performance using the standard 1 mM
K3[Fe(CN)6] model complex. GN:ZnO
NC modified GCE was monitored based on p-NP concentration. An enhanced current
response was observed in 0.1 M phosphate buffer of pH 6.8 for the determination of
p-NP in a linear working range of 0.09 × 10–6 to
21.80 × 10–6 M with a lower detection limit of
8.8 × 10–9 M employing square wave adsorptive
stripping voltammetric technique at a deposition-potential and deposition-time of
− 1.0 V and 300 s, respectively. This electrochemical sensor displayed very high
specificity for p-NP with no observed interference from some other possible
interfering substances such as 2, 4-di-NP, ortho-NP, and meta-NP. The developed
strategy was useful for sensitive detection of p-NP quantity in canals/rivers and
ground H2O samples with good recoveries.
Model-free detection of unique events in time series
Authors: Benkő Zsigmond , Bábel Tamás , Somogyvári Zoltán 
Published: January 2022

AbstractRecognition of anomalous events is a challenging but critical task in many scientific and industrial fields, especially when the properties of anomalies are unknown. In this paper, we introduce a new anomaly concept called “unicorn” or unique event and present a new, model-free, unsupervised detection algorithm to detect unicorns. The key component of the new algorithm is the Temporal Outlier Factor (TOF) to measure the uniqueness of events in continuous data sets from dynamic systems. The concept of unique events differs significantly from traditional outliers in many aspects: while repetitive outliers are no longer unique events, a unique event is not necessarily an outlier; it does not necessarily fall out from the distribution of normal activity. The performance of our algorithm was examined in recognizing unique events on different types of simulated data sets with anomalies and it was compared with the Local Outlier Factor (LOF) and discord discovery algorithms. TOF had superior performance compared to LOF and discord detection algorithms even in recognizing traditional outliers and it also detected unique events that those did not. The benefits of the unicorn concept and the new detection method were illustrated by example data sets from very different scientific fields. Our algorithm successfully retrieved unique events in those cases where they were already known such as the gravitational waves of a binary black hole merger on LIGO detector data and the signs of respiratory failure on ECG data series. Furthermore, unique events were found on the LIBOR data set of the last 30 years.
In vitro characterization of a small molecule PD-1 inhibitor that targets the PD-l/PD-L1 interaction
Authors: Lu Chih-Hao , Chung Wei-Min , Tsai Chun-Hao , Cheng Ju-Chien , Hsu Kai-Cheng , Tzeng Huey-En 
Published: January 2022

AbstractTargeting the programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) axis with monoclonal antibodies (mAbs) represents a crucial breakthrough in anticancer therapy, but mAbs are limited by their poor oral bioavailability, adverse events in multiple organ systems, and primary, adaptive, and acquired resistance, amongst other issues. More recently, the advent of small molecule inhibitors that target the PD-1/PD-L1 axis have shown promising cellular inhibitory activity and the potential to counteract the disadvantages of mAbs. In this study, structure-based virtual screening identified small molecule inhibitors that effectively inhibited the PD-1/PD-L1 interaction. Six of those small molecule inhibitors were applied to cell-based experiments targeting PD-1: CH-1, CH-2, CH-3, CH-4, CH-5, and CH-6. Of all 6, CH-4 displayed the lowest cytotoxicity and strongest inhibitory activity towards the PD-1/PD-L1 interaction. The experiments revealed that CH-4 inhibited the interaction of soluble form PD-L1 (sPD-L1) with PD-1 surface protein expressed by KG-1 cells. Investigations into CH-4 analogs revealed that CH-4.7 effectively blocked the PD-1/sPD-L1 interaction, but sustained the secretion of interleukin-2 and interferon-γ by Jurkat cells. Our experiments revealed a novel small molecule inhibitor that blocks the interaction of PD-1/sPD-L1 and potentially offers an alternative PD-1 target for immune checkpoint therapy.
The embryonic transcriptome of Parhyale hawaiensis reveals different dynamics of microRNAs and mRNAs during the maternal-zygotic transition
Authors: Calvo Llilians , Birgaoanu Maria , Pettini Tom , Ronshaugen Matthew , Griffiths-Jones Sam 
Published: January 2022

AbstractParhyale hawaiensis has emerged as the crustacean model of choice due to its tractability, ease of imaging, sequenced genome, and development of CRISPR/Cas9 genome editing tools. However, transcriptomic datasets spanning embryonic development are lacking, and there is almost no annotation of non-protein-coding RNAs, including microRNAs. We have sequenced microRNAs, together with mRNAs and long non-coding RNAs, in Parhyale using paired size-selected RNA-seq libraries at seven time-points covering important transitions in embryonic development. Focussing on microRNAs, we annotate 175 loci in Parhyale, 88 of which have no known homologs. We use these data to annotate the microRNAome of 37 crustacean genomes, and suggest a core crustacean microRNA set of around 61 sequence families. We examine the dynamic expression of microRNAs and mRNAs during the maternal-zygotic transition. Our data suggest that zygotic genome activation occurs in two waves in Parhyale with microRNAs transcribed almost exclusively in the second wave. Contrary to findings in other arthropods, we do not predict a general role for microRNAs in clearing maternal transcripts. These data significantly expand the available transcriptomics resources for Parhyale, and facilitate its use as a model organism for the study of small RNAs in processes ranging from embryonic development to regeneration.