bluuebunny/crossref_metadata_2025 huggingface dataset:
Farm productivity and social sustainability in formalized value chain governance: the case of the potato industry in Pakistan
Authors: Rasool Azhar , Badar Hammad , Blare Trent D , Ghafoor Abdul , Mushtaq Khalid
Published: December 2023

Farm productivity and social sustainability are essential to realizing agro-based value chains’ full potential. This paper aims to empirically conduct an analysis of the impact of formal value chain governance practices on farm productivity and social sustainability in Pakistan's potato industry. A multi-stage sampling method was employed from 10 villages to examine growers’ motivations to adopt the contract and its effect on their income and farm employment. The main findings of this study stipulate that buyers’ technical assistance and provision of quality inputs are the growers’ primary motives for contracting, non-contracted farms earned 40% less than contracted farms from each unit invested, contracted farms employed more labor with better wages, and welfare arrangements than the non-contracting farms. The study concluded that formal value chain governance practices significantly affect farm productivity and social sustainability and can spur growth in the agricultural sector in developing countries. The results reveal that any governmental initiative aiming to support formal value chain governance should consider the role that intermediaries play in the value chain and accordingly minimize their risks and food losses and improve social outcomes.
Observational Uncertainty for Global Drought‐Pluvial Volatility
Authors: Li Yichan , Cheng Linyin , Miao Chiyuan , Liu Zhiyong
Published: December 2023

Droughts and pluvials have occurred in most regions in the past. However, what calls growing attention is the additive effects of these two opposite extreme events occurring in spatial‐temporal proximity to one another, sometimes beyond either of the hazards individually. This study examines the likelihood of global drought‐pluvial volatility which involves both meteorological drought‐to‐pluvial (DTP) and pluvial‐to‐meteorological drought transitions; meanwhile, identifies discrepancies and agreements among the widely used observations for such events, an aspect that remains currently overlooked. Globally, we find that the observation‐based data sets including Global Precipitation Climatology Center (GPCC), Climate Research Unit (CRU) and ERA5 reach a good agreement in estimating the event transition rates, with an average 15.46% (15.49%) of all meteorological droughts (pluvials) being succeeded by pluvials (meteorological droughts) in the following season. At the regional scale, our results reveal that the spatial variability and frequency associated with meteorological DTP transitions are slightly larger than that with pluvial‐to‐ meteorological drought transitions, but the observational uncertainty is more pronounced in the latter case as a result of greater uncertainty in the univariate drought depiction and enhanced regional divergence among the observed data. In general, GPCC and CRU exhibit higher consistency, albeit with less agreement under pluvial‐to‐ meteorological drought transitions, while ERA5 yields underestimations and reduced spatial variability considering both transition scenarios. The study highlights a need of using multiple independent observation‐based data sets for compound/multivariate extreme analysis, particularly in the context of climate‐related decision‐making, water resources planning, and future model validation studies.
Hydration State and Rheologic Stratification of the Lithospheric Mantle Beneath the North Anatolian Fault, Turkey
Authors: Lusk A. D. , Chatzaras V. , Aldanmaz E. , Tikoff B.
Published: December 2023

We present constraints on the hydration state and rheology of the lithospheric mantle beneath the North Anatolian fault zone (NAFZ). Peridotite xenoliths from the Biyikali and Çorlu volcanic centers record deformational microstructures consistent with shearing in a lithosphere‐scale transcurrent fault system. Analysis by Fourier transform infrared spectroscopy indicates that nominally anhydrous phases retain some OH−, but bulk rock concentrations are generally restricted to <50 ppm H2O by weight. From the rock microstructure, we determined differential stress magnitude and active deformation mechanism(s); combined with estimates of hydration state, we constrained the rheology. Recrystallized grain size piezometry shows that the mantle beneath the NAFZ sustained differential stresses of 10–20 MPa, largely independent of depth. The dominant deformation mechanism(s) change with depth; xenoliths extracted from shallower depths record evidence for grain size‐sensitive creep possibly in the presence of melt. At intermediate depths, both dislocation creep and grain size‐sensitive mechanisms were active, and we did not observe evidence for deformation in the presence of melt. The deepest samples were dominated by dislocation creep. The strong temperature sensitivity of creep mechanisms, combined with the low variability in differential stress, contributes to a stratified viscosity profile ranging from 1018 Pa s for the deepest samples to >1022 Pa s at shallower depths (assuming a melt‐free rheology). Although difficult to quantify from the rock record, melt likely reduced the viscosity of the shallow lithospheric mantle. Vertical stratification in viscosity beneath the NAFZ, the result of melt‐present deformation and/or transitions in the dominant deformation mechanism, has important consequences for the seismic cycle of strike‐slip fault systems.
Are Plant Functional Types Fit for Purpose?
Authors: Cranko Page Jon , Abramowitz Gab , De Kauwe Martin. G. , Pitman Andy J.
Published: December 2023

For over 40 years, Plant Functional Types (PFTs) have been used to discretize the ∼400,000 species of terrestrial plants into “similar” classes. Within Earth System Models (ESMs), PFTs simplify terrestrial biosphere modeling in combination with soil information and other site characteristics. However, in flux analysis studies, PFT schemes are often implemented as the sole analytical lens to clarify complex behavior. This usage assumes that PFTs adequately enable a mapping between climate inputs and flux outputs. Here, we show that random forest models, trained using aggregated climate and flux measurements from 245 eddy‐covariance sites, cannot accurately predict PFT groupings, regardless of the nature of the PFT scheme. Similarly, PFTs provide negligible benefit when using site climate to predict site flux regimes and vice versa. While use of PFT classifications is convenient, our results suggest they do not aid analytical skill, which has important implications for future terrestrial flux studies.
Rapid Sea Level Rise in the Tropical Southwest Indian Ocean in the Recent Two Decades
Authors: Huang Lei , Zhuang Wei , Lu Wenfang , Zhang Yang , Edwing Deanna , Yan Xiao‐Hai
Published: December 2023

It has been reported that the sea level falls in the tropical Southwest Indian Ocean (SWIO) from the 1960s to the early 2000s. However, a rising trend of 4.05 ± 0.56 cm/decade has occurred during the recent two decades with our analysis showing that manometric sea level contributes 41% to this sea level rise. 30% of this rise is due to steric sea level (SSL) change in the upper 2,000 m with SSL rise in the upper 300 m of secondary importance. Conversely, thermal expansion below the thermocline (300–2,000 m), likely caused by water mass spread from the Southern Ocean, induces major contribution to SSL changes. Compared to existing studies demonstrating the contribution of thermal variations above the thermocline to sea level variability in the tropical SWIO, this study emphasizes the importance of ocean mass and deeper ocean changes in a warming climate.
Quantifying Magma Overpressure Beneath a Submarine Caldera: A Mechanical Modeling Approach to Tsunamigenic Trapdoor Faulting Near Kita‐Ioto Island, Japan
Authors: Sandanbata Osamu , Saito Tatsuhiko
Published: December 2023

Submarine volcano monitoring is vital for assessing volcanic hazards but challenging in remote and inaccessible environments. In the vicinity of Kita‐Ioto Island, south of Japan, unusual M ∼ 5 non‐double‐couple volcanic earthquakes exhibited quasi‐regular recurrence near a submarine caldera. Following the earthquakes in 2008 and 2015, a distant ocean bottom pressure sensor recorded distinct tsunami signals. In this study, we aim to find a source model of the tsunami‐generating earthquake and quantify the pre‐seismic magma overpressure within the caldera's magma reservoir. Based on the earthquake's characteristic focal mechanism and efficient tsunami generation, we hypothesize that submarine trapdoor faulting occurred due to highly pressurized magma. To investigate this hypothesis, we establish mechanical earthquake models that link pre‐seismic magma overpressure to the size of the resulting trapdoor faulting, by considering stress interaction between a ring‐fault system and a reservoir of the caldera. The trapdoor faulting with large fault slip due to magma‐induced shear stress in the submarine caldera reproduces well the observed tsunami waveform. Due to limited data, uncertainties in the fault geometry persist, leading to variations of magma overpressure estimation: the pre‐seismic magma overpressure ranging approximately from 5 to 20 MPa, and the co‐seismic pressure drop ratio from 10% to 40%. Although better constraints on the fault geometry are required for robust magma pressure quantification, this study shows that magmatic systems beneath calderas are influenced significantly by intra‐caldera fault systems and that tsunamigenic trapdoor faulting provides rare opportunities to obtain quantitative insights into remote submarine volcanism hidden under the ocean.
The Impacts of Dust Storms With Different Transport Pathways on Aerosol Chemical Compositions and Optical Hygroscopicity of Fine Particles in the Yangtze River Delta
Authors: Song Xiaorui , Wang Yuying , Huang Xin , Wang Yuxiang , Li Zhanqing , Zhu Bin , Ren Rongmin , An Junlin , Yan Jiade , Zhang Rui , Shang Yi , Zhan Puning
Published: December 2023

Aerosol physicochemical properties during two dust storms (DS1: March 30–31, and DS2: May 7–8) are measured in 2021 in Nanjing, aiming to investigate the impacts of dust storms on aerosol chemical compositions and optical hygroscopicity in the Yangtze River Delta (YRD). During DS1, the dust air masses are transported in the lower atmosphere and pass through the inlands and sea areas before reaching the YRD region. During DS2, the dust air masses are transported in the upper atmosphere and pass through the inlands only. Both of them are accompanied by an increase in black carbon (BC) mass fraction and a decrease in nitrate mass fraction in fine particles (PM2.5, particles with diameters less than 2.5 μm) near the surface. However, the impacts on the mass fractions of organics or sulfate are adverse between DS1 and DS2. During dust‐influence periods the enlarged mass ratios of sulfate to nitrate (greater than 4) promote the occurrence of deliquescent behavior of ambient aerosols although dust aerosols can significantly suppress aerosol optical hygroscopicity. To improve model simulations of aerosol optical hygroscopicity, it is necessary to use a segment parameterization to describe aerosol light scattering enhancement factor during dust‐influence periods. The closure study of optical hygroscopicity parameters with two different methods reveals the impact of aerosol scattering Ångström exponent on the estimation of optical hygroscopicity parameter. The results highlight that the impact of dust storms on aerosol chemical compositions and optical hygroscopicity are different for DS events with different transport pathways.
Coupled Si–Al Biogeochemistry: Occurrence of Aluminum in Diatom‐Derived Biogenic Silica
Authors: Liu Dong , Tian Qian , Li Mengyuan , Mi Mei , Yuan Peng , Yu Rongda , Zhou Junming , Du Peixin , Wei Huihuang , Guo Haozhe , Deng Liangliang
Published: December 2023

Diatoms play an important role in the biogeochemical cycling of aluminum (Al) in oceans. This occurs via the uptake of biological Al (Albio), which is incorporated into the structure of diatom‐derived biogenic silica (DBSi) and the formation of adsorbed Al (Alads) on the DBSi surface of post‐mortem diatoms. Al occurrence influences DBSi dissolution and thus diatom‐driven carbon sequestration. However, the mechanism of Al occurrence in DBSi remains unclear. In this study, Albio and Alads of DBSi from various diatom fossils in marine diatomaceous sediments were identified and quantified by combined focused ion beam thinning, elemental analysis, and the Al K‐edge X‐ray absorption near edge structure. Results showed the coexistence of Albio and Alads in all diatomaceous sediments and Al‐bearing DBSi thus constitutes a biological Al pool. Albio and Alads were mainly fourfold‐ and sixfold‐coordinated, respectively and Alads was much more abundant than Albio. Moreover, even at low concentrations (with an Al/Si atomic ratio of 0.0031), Albio can inhibit DBSi dissolution, effectively decreasing the extent of DBSi dissolution by ∼14%. Albio also significantly increased the mechanical strength of DBSi. The average Young's modulus (a measure of the stiffness of a material) of cribrum layers in Al‐incorporated DBSi was ∼1.4 times higher than that of Al‐free DBSi. Our results further demonstrate that diatoms play a dominant role in the biogeochemical cycling of Al in oceans, and the Al of DBSi participates in diatom‐driven Si and C coupled cycles in oceans, influencing the effectiveness of diatom‐driven carbon export by regulating the dissolution and mechanical strength of DBSi.
Responses of Soil Fungi to Long‐Term Nitrogen‐Water Interactions Depend on Fungal Guilds in a Mixed Pinus koraiensis Forest
Authors: Guo W. , Wang C. , Brunner I. , Zhou Y. , Tang Q. , Wang J. , Li M.‐H.
Published: December 2023

Different fungal guilds within the soil fungal community regulate forest ecosystem processes. Soil fungi are dictated by edaphic factors such as soil water and nutrient availabilities. However, how the total number of fungi and the composition of different fungal guilds in the soil vary under covarying pattern of nitrogen deposition and precipitation regime in temperate forests has not been well documented. In this study, we explored the effects of long‐term nitrogen‐water interactions on the diversity and composition of soil overall fungi and different fungal guilds, and their relationships with fine‐root and soil fungal mycelial traits in a temperate forest. The diversity of the totality of soil fungi or any fungal guilds did not change, but the community composition of saprotrophic and symbiotrophic fungi was significantly changed by nitrogen addition (N), showing increased abundance of soil symbiotrophic fungi but decreased abundance of soil saprotrophic fungi. Precipitation reduction (W) significantly altered soil overall and pathotrophic fungal community. Precipitation reduction combined with nitrogen addition (WN) significantly changed soil overall, pathotrophic and symbiotrophic fungal community composition. Soil pathotrophic, saprotrophic and symbiotrophic fungal community composition was variously related to fine‐root diameter, root tissue density, nitrogen and/or phosphorus concentration. Long‐term nitrogen‐water interactions decreased the complexity of soil fungal networks, reflected by the lower edges and average degree, but the higher average path distance and modularity. These findings of soil fungal guild‐specific responses to nitrogen‐water interactions will deepen our understanding of soil carbon sequestration potential and nutrient cycling in temperate forest ecosystems under future climate changes.
Forward‐Looking Study of Solar Maximum Impact in 2025: Effects of Satellite Navigation Failure on Aviation Network Operation in the Greater Bay Area, China
Authors: Xue Dabin , Yang Jian , Liu Zhizhao , Cong Wei
Published: December 2023

Satellite navigation based on the Global Navigation Satellite System can provide aircraft with more precise guidance and increase flight efficiency. However, severe space weather events can cause satellite navigation failure due to the dramatic increase in total electron content and irregularities in the ionosphere. Consequently, ground navigation has to be used to replace satellite navigation, increasing aircraft separation standards and reducing airspace capacity. As a result, numerous flights may be delayed or even canceled, incurring significant financial losses. The occurrence peak of space weather events generally coincides with the 11‐year‐cycle solar maximum, and 2025 is expected to be the upcoming solar maximum. The Greater Bay Area (GBA), located in the equatorial ionization anomaly region of China, is particularly vulnerable to space weather impacts. To explore the effects of satellite navigation failure on flight operation, we conduct this looking‐forward study and propose solution methods from the standpoint of Air Traffic Management, by simulating satellite navigation failure scenarios. Based on the projected flight volume in 2025 related to the GBA airports, simulation results show that the economic costs can be tens of millions of Euros, which is dependent on the duration of satellite navigation failure and the time interval of ground navigation‐based landing. We believe that this study can be a benchmark for evaluating the potential economic effects of forthcoming space weather on flight operations.
Assessing the cyclic fatigue resistance and sterilization effects on replica-like endodontic instruments compared to Reciproc Blue
Authors: dos Reis Fernando Antonio Siano , Abu Hasna Amjad , Ragozzini Gustavo , de Moura Felipe Bernardo , Campos Tiago Moreira Bastos , de Martin Alexandre Sigrist , Carvalho Cláudio Antonio Talge , Bueno Carlos Eduardo Silveira
Published: December 2023

This study aimed to evaluate the effect of the number of uses and autoclave sterilization on the cyclic fatigue resistance of four replica-like instruments RC Blue; Only One File Blue; Recip One Blue; and Micro Blue compared to the original system Reciproc Blue (VDW, Munich, Germany). The instruments were analyzed by scanning electron microscope (SEM) before being used in root canal instrumentation (baseline). Fifty molars were instrumented by ten instruments (n=10). After sterilization in an autoclave, the  instruments were analyzed by SEM. This procedure was repeated twice more using different molars, totaling 3 rounds of instrumentation, sterilization and SEM analysis. Then, ten different instruments from each brand were tested for cyclic fatigue resistance. Number of uses data were analyzed using Chi-squared analysis, and cyclic fatigue data were analyzed by one-way Anova followed by Tukey’s test as the data had normal distribution. The fracture times for all systems had no significant difference, but Micro Blue had significantly lower values than the other systems (p < 0.05). The SEM analysis showed distortions in the instruments after the 3rd use. Therefore, all tested instruments except of Micro Blue have similar resistance to cyclic fatigue, and all are reliable for use in up to 2-cases.
Trichostatin A enhances the titanium rods osseointegration in osteoporotic rats by the inhibition of oxidative stress through activating the AKT/Nrf2 pathway
Authors: Zhou Zhi , Jiang Wenkai , Yan Junjie , Liu Hedong , Ren Maoxian , Li Yang , Liu Zhiyi , Yao Xuewei , Li Tianlin , Ma Nengfeng , Chen Bing , Guan Wengang , Yang Min
Published: December 2023

The use of titanium implants as fixed supports following fractures in patients with OP can often result in sterile loosening and poor osseointegration. Oxidative stress has been shown to play a particularly important role in this process. While TSA has been reported to facilitate in vivo osteogenesis, the underlying mechanisms remain to be clarified. It also remains unclear whether TSA can improve the osseointegration of titanium implants. This study investigated whether TSA could enhance the osseointegration of titanium rods by activating AKT/Nrf2 pathway signaling, thereby suppressing oxidative stress. MC3T3-E1 cells treated with CCCP to induce oxidative stress served as an in vitro model, while an OVX-induced OP rat model was employed for in vivo analysis of titanium rod implantation. In vitro, TSA treatment of CCCP-treated MC3T3-E1 cells resulted in the upregulation of osteogenic proteins together with increased AKT, total Nrf2, nuclear Nrf2, HO-1, and NQO1 expression, enhanced mitochondrial functionality, and decreased oxidative damage. Notably, the PI3K/AKT inhibitor LY294002 reversed these effects. In vivo, TSA effectively enhanced the microstructural characteristics of distal femur trabecular bone, increased BMSCs mineralization capacity, promoted bone formation, and improved the binding of titanium implants to the surrounding tissue. Finally, our results showed that TSA could reverse oxidative stress-induced cell damage while promoting bone healing and improving titanium rods' osseointegration through AKT/Nrf2 pathway activation.
Cannabis Sativa targets mediobasal hypothalamic neurons to stimulate appetite
Authors: Wheeler Emma C. , Choi Pique , De Howitt Joanne , Gill Sumeen , Watson Shane , Yu Sue , Wahl Peyton , Diaz Cecilia , Mohr Claudia , Zinski Amy , Jiang Zhihua , Rossi David , Davis Jon F.
Published: December 2023

The neurobiological mechanisms that regulate the appetite-stimulatory properties of cannabis sativa are unresolved. This work examined the hypothesis that cannabinoid-1 receptor (CB1R) expressing neurons in the mediobasal hypothalamus (MBH) regulate increased appetite following cannabis vapor inhalation. Here we utilized a paradigm where vaporized cannabis plant matter was administered passively to rodents. Initial studies in rats characterized meal patterns and operant responding for palatable food following exposure to air or vapor cannabis. Studies conducted in mice used a combination of in vivo optical imaging, electrophysiology and chemogenetic manipulations to determine the importance of MBH neurons for cannabis-induced feeding behavior. Our data indicate that cannabis vapor increased meal frequency and food seeking behavior without altering locomotor activity. Importantly, we observed augmented MBH activity within distinct neuronal populations when mice anticipated or consumed food. Mechanistic experiments demonstrated that pharmacological activation of CB1R attenuated inhibitory synaptic tone onto hunger promoting Agouti Related Peptide (AgRP) neurons within the MBH. Lastly, chemogenetic inhibition of AgRP neurons attenuated the appetite promoting effects of cannabis vapor. Based on these results, we conclude that MBH neurons contribute to the appetite stimulatory properties of inhaled cannabis.
Testing the effects of photobiomodulation on angiogenesis in a newly established CAM burn wound model
Authors: Firouz Bardia , Faihs Lorenz , Slezak Paul , Ghaffari Tabrizi-Wizsy Nassim , Schicho Kurt , Winter Raimund , Kamolz Lars Peter , Dungel Peter
Published: December 2023

Burn wounds are a common challenge for medical professionals. Current burn wound models hold several limitations, including a lack of comparability due to the heterogeneity of wounds and differences in individual wound healing. Hence, there is a need for reproducible in vivo models. In this study, we established a new burn wound model using the chorioallantoic membrane assay (CAM) as a surrogate model for animal experiments. The new experimental setup was tested by investigating the effects of the auspicious biophysical therapy, photobiomodulation (PBM), on the wound healing of an induced CAM burn wound with a metal stamp. PBM has been shown to positively influence wound healing through vascular proliferative effects and the increased secretion of chemotactic substances. The easily accessible burn wounds can be treated with various therapies. The model enables the analysis of ingrowing blood vessels (angiogenesis) and diameter and area of the wounds. The established model was used to test the effects of PBM on burn wound healing. PBM promoted angiogenesis in burn wounds on day 4 (p = 0.005). Furthermore, there was a not significant trend toward a higher number of vessels for day 6 (p = 0.065) in the irradiated group. Changes in diameter (p = 0.129) and the burn area (p = 0.131) were not significant. Our results suggest that CAM can be a suitable model for studying burn wounds. The novel experimental design enables reproducible and comparable studies on burn wound treatment.
Weight loss outcomes are generally worse for dogs and cats with class II obesity, defined as > 40% overweight
Authors: Broome H. A. O. , Woods-Lee G. R. T. , Flanagan J. , Biourge V. , German A. J.
Published: December 2023

In pet dogs and cats, adiposity is most-often estimated clinically using a 9-category body condition score (BCS), with BCS 9 equating to ~ 40% overweight. Animals that are more overweight (> 40%) are seen in clinical practice but are not appropriately depicted by descriptions in the existing categories. To determine whether being > 40% overweight has clinical relevance, this study aimed to compare the outcomes of weight management in animals that were > 40% overweight with those < 40% overweight. Records of dogs and cats attending a specialist obesity care clinic, where adiposity is determined using dual-energy X-ray absorptiometry (DXA), were reviewed. Animals were assigned to two classes (class I ≤ 40% overweight: 118/398 [40%] dogs and 68/116 [59%] cats; class II, > 40% overweight: 180/398 [60%] dogs and 48/116 [41%] cats) based on DXA results, and weight loss outcomes were compared. Fewer class II dogs obesity completed weight management than class I dogs (P < 0.001), rate of weight loss was also slower (P = 0.012) and lean tissue loss greater (P < 0.001). Compared with class I, cats with class II obesity lost more weight (P = 0.048) albeit over a longer period (P = 0.043) leading to greater lean tissue loss (P = 0.004). Approximately half the pets presenting to a specialist clinic were have class II obesity (> 40% overweight), and some weight loss outcomes are worse for these animals.
Exploring the infiltrative and degradative ability of Fusarium oxysporum on polyethylene terephthalate (PET) using correlative microscopy and deep learning
Authors: Cognigni Flavio , Temporiti Marta Elisabetta Eleonora , Nicola Lidia , Gueninchault Nicolas , Tosi Solveig , Rossi Marco
Published: December 2023

Managing the worldwide steady increase in the production of plastic while mitigating the Earth’s global pollution is one of the greatest challenges nowadays. Fungi are often involved in biodegradation processes thanks to their ability to penetrate into substrates and release powerful catabolic exoenzymes. However, studying the interaction between fungi and plastic substrates is challenging due to the deep hyphal penetration, which hinders visualisation and evaluation of fungal activity. In this study, a multiscale and multimodal correlative microscopy workflow was employed to investigate the infiltrative and degradative ability of Fusarium oxysporum fungal strain on polyethylene terephthalate (PET) fragments. The use of non-destructive high-resolution 3D X-ray microscopy (XRM) coupled with a state-of-art Deep Learning (DL) reconstruction algorithm allowed optimal visualisation of the distribution of the fungus on the PET fragment. The fungus preferentially developed on the edges and corners of the fragment, where it was able to penetrate into the material through fractures. Additional analyses with scanning electron microscopy (SEM), Raman and energy dispersive X-ray spectroscopy (EDX) allowed the identification of the different phases detected by XRM. The correlative microscopy approach unlocked a more comprehensive understanding of the fungus-plastic interaction, including elemental information and polymeric composition.
Automated tracking of cell migration in phase contrast images with CellTraxx
Authors: Holme Børge , Bjørnerud Birgitte , Pedersen Nina Marie , de la Ballina Laura Rodriguez , Wesche Jørgen , Haugsten Ellen Margrethe
Published: December 2023

The ability of cells to move and migrate is required during development, but also in the adult in processes such as wound healing and immune responses. In addition, cancer cells exploit the cells’ ability to migrate and invade to spread into nearby tissue and eventually metastasize. The majority of cancer deaths are caused by metastasis and the process of cell migration is therefore intensively studied. A common way to study cell migration is to observe cells through an optical microscope and record their movements over time. However, segmenting and tracking moving cells in phase contrast time-lapse video sequences is a challenging task. Several tools to track the velocity of migrating cells have been developed. Unfortunately, most of the automated tools are made for fluorescence images even though unlabelled cells are often preferred to avoid phototoxicity. Consequently, researchers are constrained with laborious manual tracking tools using ImageJ or similar software. We have therefore developed a freely available, user-friendly, automated tracking tool called CellTraxx. This software makes it easy to measure the velocity and directness of migrating cells in phase contrast images. Here, we demonstrate that our tool efficiently recognizes and tracks unlabelled cells of different morphologies and sizes (HeLa, RPE1, MDA-MB-231, HT1080, U2OS, PC-3) in several types of cell migration assays (random migration, wound healing and cells embedded in collagen). We also provide a detailed protocol and download instructions for CellTraxx.
Synthesis and detonation characters of 3,4,5-1H-trinitropyrazole and its nitrogen-rich energetic salts
Authors: Lin Chenchen , Yi Pingping , Yi Xiaoyi , He Piao , Wang Tingwei , Zhang Jianguo
Published: December 2023

Two novel nitrogen-rich energetic salts of HTNP were synthesized and studied. They exhibit excellent thermostability and detonation performance, making them promising green energetic materials.
Modulation of cecal microbiota and fecal metabolism in mice by walnut protein
Authors: Si Huang , Yan Wang , Jun Sheng , Hongyu Mu , Xia Zhang , Kuan Wu , Cunchao Zhao
Published: December 2023

The characteristic functional groups of WP exhibit obvious absorption peaks, with >30% α-helix and β-folding content in the secondary structure. WP is a typical spherical particle with a denaturation temperature of 73.6 °C, which indicates its good structural stability and thermal stability.
Investigating the mechanism of phosphorene nanoribbon synthesis by discharging black phosphorus intercalation compounds
Authors: Shutt Rebecca R. C. , Aw Eva S. Y. , Liu Qili , Berry-Gair Jasper , Lancaster Hector J. , Said Samia , Miller Thomas S. , Corà Furio , Howard Christopher A. , Clancy Adam J.
Published: December 2023

Phosphorene nanoribbons can be synthesised in by intercalation of black phosphorus with Li followed by dissolution in amides. Our result suggest that the first step does not cut the sheets to ribbons, indicating they are cut by solvent interactions.
The use of multicomponent reactions in the development of bis-boronic acids for the detection of β-sialic acid
Authors: Chou Tzu-Ching , Hu Ying-Li , Xie Guan-Cheng , Jiang Jyh-Chiang , Peng Liang-Ying , Tsai Hsiao-Chun , Yao Chiao-Tien , Tsai Yi-Jie , Huang Ting-Yu , Hu Jing-Wen , Chen Yi-Ching , Tsai Min-Yeh , Chen Yi-Wei , Pan Po-Shen
Published: December 2023

Sialic acid (SA) is a naturally occurring monosaccharide found in glycoproteins and glycolipids.
Accessing a synthetic FeIIIMnIV core to model biological heterobimetallic active sites
Authors: Lee Justin L. , Biswas Saborni , Ziller Joseph W. , Bominaar Emile L. , Hendrich Michael P. , Borovik A. S.
Published: December 2023

Characterization of a synthetic mimic for an enzymatic FeIIIMnIV intermediate and its reactivity with phenolic substrates.
STAE‐YOLO: Intelligent detection algorithm for risk management of construction machinery intrusion on transmission lines based on visual perception
Authors: Ji Chao , Zhang Fan , Huang Xinbo , Song Zhiwei , Hou Wei , Wang Boya , Chen Guoyan
Published: December 2023

The distribution of transmission lines is complex, influenced by terrain and topography, making their maintenance and management challenging. With the advancement of global mechanization, various types of construction machinery and large‐scale mechanical equipment are continually increasing. Accidental contact of construction machinery near transmission lines poses a serious threat to the stability of the power system. Traditional drones and inspection robots face difficulties in achieving real‐time monitoring of construction machinery and equipment around transmission lines, quickly identifying potential risks. Conventional image processing techniques and convolutional neural networks struggle with effective handling of small targets and densely packed detection tasks involving multiple targets. To address these challenges, this paper proposes an intelligent detection algorithm Swin Transformer attention efficient algorithm‐you only look once (YOLO) (STAE‐YOLO). It is based on the Swin Transformer global self‐attention mechanism, cross‐channel fusion attention mechanism, enhanced small object detection framework, and a focused and efficient regression loss function. The experimental results show that the STAE‐YOLO algorithm model improved by 6.3% in mean average precision, 3.7% in precision, and 3.1% in recall compared to the baseline model. Meanwhile, deploying the window multi‐head self‐attention global self‐attention mechanism in the model can strengthen the global multi‐scale semantic information in detection.
Acoustophoresis of monodisperse oil droplets in water: Effect of symmetry breaking and non-resonance operation on oil trapping behavior
Authors: Bazyar H. , Kandemir M. H. , Peper J. , Andrade M. A. B. , Bernassau A. L. , Schroën K. , Lammertink R. G. H.
Published: December 2023

Acoustic manipulation of particles in microchannels has recently gained much attention. Ultrasonic standing wave (USW) separation of oil droplets or particles is an established technology for microscale applications. Acoustofluidic devices are normally operated at optimized conditions, namely, resonant frequency, to minimize power consumption. It has been recently shown that symmetry breaking is needed to obtain efficient conditions for acoustic particle trapping. In this work, we study the acoustophoretic behavior of monodisperse oil droplets (silicone oil and hexadecane) in water in the microfluidic chip operating at a non-resonant frequency and an off-center placement of the transducer. Finite element-based computer simulations are further performed to investigate the influence of these conditions on the acoustic pressure distribution and oil trapping behavior. Via investigating the Gor’kov potential, we obtained an overlap between the trapping patterns obtained in experiments and simulations. We demonstrate that an off-center placement of the transducer and driving the transducer at a non-resonant frequency can still lead to predictable behavior of particles in acoustofluidics. This is relevant to applications in which the theoretical resonant frequency cannot be achieved, e.g., manipulation of biological matter within living tissues.
Performance of point charge embedding schemes for excited states in molecular organic crystals
Authors: Sidat Amir , Ingham Michael , Rivera Miguel , Misquitta Alston J. , Crespo-Otero Rachel
Published: December 2023

Modeling excited state processes in molecular crystals is relevant for several applications. A popular approach for studying excited state molecular crystals is to use cluster models embedded in point charges. In this paper, we compare the performance of several embedding models in predicting excited states and S1–S0 optical gaps for a set of crystals from the X23 molecular crystal database. The performance of atomic charges based on ground or excited states was examined for cluster models, Ewald embedding, and self-consistent approaches. We investigated the impact of various factors, such as the level of theory, basis sets, embedding models, and the level of localization of the excitation. We consider different levels of theory, including time-dependent density functional theory and Tamm–Dancoff approximation (TDA) (DFT functionals: ωB97X-D and PBE0), CC2, complete active space self-consistent field, and CASPT2. We also explore the impact of selection of the QM region, charge leakage, and level of theory for the description of different kinds of excited states. We implemented three schemes based on distance thresholds to overcome overpolarization and charge leakage in molecular crystals. Our findings are compared against experimental data, G0W0-BSE, periodic TDA, and optimally tuned screened range-separated functionals.
Tunable acoustic passive phased array based on double-opening resonant rings
Authors: Gong Shulei , Zhao Jinyu , Yang Mengchun , Liu Yuan , Zhang Haixiao , Li Yongchang
Published: December 2023

The special structural design of acoustic metamaterials further extends acoustic properties of the materials. We design a tunable acoustic passive phased array based on double-opening resonant rings, which modulates the acoustic waves only by the rotational angle, making up for the defect of the fixed structure of ordinary metamaterials. The rotation angle is selected based on the generalized Snell’s law, which not only enables focusing in a large frequency band range but also meets the focusing demand of acoustic waves incident at different angles and controls the position of the focal point.
Assessing OPLS-based force fields for investigating the characteristics of imidazolium-based dicationic ionic liquids: A comparative study with AIMD simulations and experimental findings
Authors: Memar Zahra Ostadsharif , Moosavi Majid
Published: December 2023

In this study, we extended the optimized potentials for liquid simulation-ionic-liquid virtual site (OPLS-VSIL) force field (FF) to imidazolium-based dicationic ionic liquids (DILs) and evaluated the ability of different OPLS-based FFs (i.e., OPLS-2009IL, 0.8*OPLS-2009IL, and OPLS-VSIL) in predicting different properties of the studied DIL by comparing their results with ab initio molecular dynamics (AIMD) simulation and experimental results. To achieve this purpose, MD simulations with three different OPLS-based FFs as well as AIMD simulation were performed for [C3(mim)2][NTF2]2 DIL and its structural, dynamical, vibrational, and volumetric properties were analyzed. Structural properties of the studied DIL, i.e., radial distribution functions (RDFs), structure factor, and hydrogen-bond network, showed that compared to 0.8*OPLS-2009IL FF, there is a much better agreement between the results of both OPLS-2009IL and OPLS-VSIL FFs with the AIMD simulation. On the other hand, the results of dynamical properties, such as mean square displacements, van Hove correlation functions as well as hydrogen bond, ion pair, and ion cage dynamics, depicted that in both 0.8*OPLS-2009IL and OPLS-VSIL FFs, the dynamics of the system is almost similar, and compared to OPLS-2009IL FF, they have better agreements with experimental results where they exist. So, it can be seen that although reducing the total charge of studied DIL by 20% leads to an increase in the dynamics of the system, the type distribution of partial charges on each atom does not significantly affect the system’s dynamics. The calculated infrared (IR) and power spectra showed that the vibrational features of studied DIL in three OPLS-based FFs are mostly the same and reducing total charge and different type distribution of partial charges have no significant effect on the studied system. Furthermore, in volumetric properties, OPLS-VSIL FF shows somehow better agreement with experimental results. Overall, the evaluation of different structural, dynamical, vibrational, and volumetric properties of [C3(mim)2][NTF2]2 DIL shows that the OPLS-VSIL FF may be the best choice among the different studied OPLS FFs.
Evolution of spin coherence of radical pairs due to spin-selective recombination: Comparison of three models
Authors: Bagryansky Victor A. , Chetverikov Artem O. , Borovkov Vsevolod I. , Molin Yuri N.
Published: December 2023

This study looked for a way to evaluate the validity of previously suggested models for describing the spin-selective recombination of radical pairs. As an example, for analysis, we used the conventional model, the model by Jones and Hore [Chem. Phys. Lett. 488, 90 (2010)], and the model by Salikhov [Am. J. Phys. Chem. 11, 67 (2022)]. To do this, analytical solutions to the evolution of the radical pair density matrix due to a radical pair’s spin-selective recombination and singlet–triplet transitions in a strong magnetic field were obtained for the conventional model and the Jones and Hore model. Spin interactions included in the Hamiltonian were time-independent exchange interactions as well as Zeeman and hyperfine interactions. The most striking difference between the models’ predictions appeared when considering the fraction of singlet pairs among all currently existing ones. In the Jones and Hore model, this ratio has the form of damped oscillations for any values of the spin-hamiltonian parameters. The conventional model and the Salikhov model both predicted that this ratio had the form of undamped oscillations in the absence of exchange interaction and at a sufficiently low recombination rate. Besides, the conventional model predicts the possibility of a resonance-like behavior of this ratio when singlet–triplet transitions in a part of the radical pair ensemble are completely suppressed by tuning the magnetic field strength. Possible experimental conditions in which distinguishing between the models seems to be most straightforward were suggested.
Designing the stripe-ordered cuprate phase diagram through uniaxial-stress
Authors: Guguchia Z. , Das D. , Simutis G. , Adachi T. , Küspert J. , Kitajima N. , Elender M. , Grinenko V. , Ivashko O. , Zimmermann M. v. , Müller M. , Mielke C. , Hotz F. , Mudry C. , Baines C. , Bartkowiak M. , Shiroka T. , Koike Y. , Amato A. , Hicks C. W. , Gu G. D. , Tranquada J. M. , Klauss H.-H. , Chang J. J. , Janoschek M. , Luetkens H.
Published: December 2023

The ability to efficiently control charge and spin in the cuprate high-temperature superconductors is crucial for fundamental research and underpins technological development. Here, we explore the tunability of magnetism, superconductivity, and crystal structure in the stripe phase of the cuprate La

2
−
x

Ba

x

CuO

4

, with

x

= 0.115 and 0.135, by employing temperature-dependent (down to 400 mK) muon-spin rotation and AC susceptibility, as well as X-ray scattering experiments under compressive uniaxial stress in the CuO

2

plane. A sixfold increase of the three-dimensional (3D) superconducting critical temperature

T
c

and a full recovery of the 3D phase coherence is observed in both samples with the application of extremely low uniaxial stress of

∼

0.1 GPa. This finding demonstrates the removal of the well-known 1/8-anomaly of cuprates by uniaxial stress. On the other hand, the spin-stripe order temperature as well as the magnetic fraction at 400 mK show only a modest decrease under stress. Moreover, the onset temperatures of 3D superconductivity and spin-stripe order are very similar in the large stress regime. However, strain produces an inhomogeneous suppression of the spin-stripe order at elevated temperatures. Namely, a substantial decrease of the magnetic volume fraction and a full suppression of the low-temperature tetragonal structure is found under stress, which is a necessary condition for the development of the 3D superconducting phase with optimal

T
c

. Our results evidence a remarkable cooperation between the long-range static spin-stripe order and the underlying crystalline order with the three-dimensional fully coherent superconductivity. Overall, these results suggest that the stripe- and the SC order may have a common physical mechanism.
Three-dimensional modelling of maximum fluid load on horizontally rotating cylinder
Authors: Jed Lim Li Xin , Ricardo Bernard
Published: December 2023

It is a well-known fact that when a rod coated with a viscous liquid such as honey is rotated at a sufficiently high speed, the liquid will stop draining. However, when the liquid is left on the rod for a sufficiently long time, fluid will accumulate in bands around the cylinder. When these bands reach a sufficiently large amplitude, the fluid will drain from the rod. While previous literature has explored the formation and growth of these bands, none has explored the conditions under which the fluid in these bands will drain. In this paper, we make use of linear stability analysis to find the growth rate of the band and hence, the time taken for the band to reach the critical amplitude before draining occurs. We verify this approximation with full 3D simulations. Afterwards, this is used to plot a phase plot to identify if the fluid is draining at a specific point in time. We come to the compelling conclusion that the inevitable formation of bands on the rod will invariably lead to fluid drainage. This has important implications for rolling-coating operations where a uniform fluid coating is required as the coating will need to be complete before the fluid accumulates in bands.
Revisiting the damped quantum harmonic oscillator
Authors: Barnett Stephen M , Cresser James D , Croke Sarah
Published: December 2023

We reanalyse the quantum damped harmonic oscillator, introducing three less than common features. These are (i) the use of a continuum model of the reservoir rather than an ensemble of discrete oscillators, (ii) an exact diagonalisation of the Hamiltonian by adapting a technique pioneered by Fano, and (iii) the use of the thermofield technique for describing a finite temperature reservoir. We recover in this way a number of well-known and some, perhaps, less familiar results. An example of the latter is an ab initio proof that the oscillator relaxes to the mean-force Gibbs state. We find that special care is necessary when comparing the damped oscillator with its undamped counterpart as the former has two distinct natural frequencies, one associated with short time evolution and the other with longer times.
Implementing the multistep adams-bashforth numerical approach on magnetohydrodynamic radiated casson fluid with darcy forchheimer, dissipation and activation energy
Authors: Salahuddin T , Awais Muhammad
Published: December 2023

The main goal behind the conduction of this work is to use the Adams-Bashforth method in the field of fluid dynamics to solve the Navier–Stokes equations based on the boundary layer flow of magnetohydrodynamic Casson fluid passing on the upper horizontal parabolic surface with variable fluid characteristics and Darcy-Forchheimer effect. The temperature flow rate and mass rate are also investigated with the help of thermal radiation, viscous dissipation, heat generation and activation energy. The Adams-Bashforth technique is widely used in numerical analysis, scientific computing, fluid dynamics, chemical kinetics, astrophysics and is particularly useful in solving the stiff ODEs, where other methods may fail to converge. It is particularly useful for simulating the flow of fluids around complex geometries, such as aircraft wings or turbine blade. The equations of basic governing laws (Momentum, temperature and concentration) are achieved in the form of PDE’s. These PDEs are then transmuted into ODEs via similarity variables and the numerical behaviors of these ODEs are obtained with Adam-Bashforth (Predictor-Corrector) along with RK-4 technique on the Matlab software. The initial guesses are modified by using secant method. Graphical analyses are used to explain how different parameters affect the temperature, velocity and mass transport rate. The finding of results revealed that the inertia coefficient, Hartmann number and fluid parameter make the decrement in the velocity field. The amplification in temperature of fluid is noted for varying the radiation coefficient, dissipation and thermal generation coefficient. The solutal field drops due to activation energy and reaction coefficient. The findings are useful to observe the flow attributes, behaviors and helpful in the designing of thermal equipment in the thermal industries.