bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urbanization influences the distribution, enrichment, and ecological health risk of heavy metals in croplands
Authors: Rezapour Salar , Siavash Moghaddam Sina , Nouri Amin , Khosravi Aqdam Kamal 
Published: March 2022

AbstractThe contamination of urban soils with heavy elements due to the rapid development of urbanization and urban services has become a major environmental and human health challenge. This study provides insight into the urbanization controls on combined pollution severity and health risk potential of heavy metals in corn-cultivated urban versus non-urban soils. A multifaceted assessment was conducted using enrichment factor (EF), ecological risk (ER), bioconcentration factor (BCF), transmission factor (TF), hazard index (HI), and carcinogenic risk (CR). The results indicate a significant increase in the concentration of all metals in urban farmlands. When compared to the non-urban soils, EF implies a significant increase of all metals in the urban soil, downgrading this index from minimal enrichment (EF < 2) in the control soils to moderate enrichment (2 ≤ EF < 5) in the urban soils. Likewise, the average ER value showed an increase in the urban soils than in the control soils in the order of Fluvisols (66.6%) > Regosols (66.1%) > Cambisols (59.8%) > Calcisols (47%). The BCF and TF values for different elements decreased in the order of Cd (0.41–0.92) > Cu (0.1–0.23) > Zn (0.1–0.18) > Ni (0.01–0.03) > Pb (0.005–0.011) and Zn (0.75–0.94) > Cu (0.72–0.85) > Pb (0.09–0.63) > Cd (0.17–0.22) > Ni (0.01–0.21), respectively, which indicates that certain metals were not mobilized to the extent that they had been accumulated in the plant roots. The total carcinogenic risk was ranged from 5.88E−05 to 1.17E−04 for children and from 1.17E−04 to 2.30E−04 for adults, which implies a greater associated health risk for children.
The Hippo effector YAP1/TEAD1 regulates EPHA3 expression to control cell contact and motility
Authors: Al-Mathkour Marwah M. , Dwead Abdulrahman M. , Alp Esma , Boston Ava M. , Cinar Bekir 
Published: March 2022

AbstractThe EPHA3 protein tyrosine kinase, a member of the ephrin receptor family, regulates cell fate, cell motility, and cell–cell interaction. These cellular events are critical for tissue development, immunological responses, and the processes of tumorigenesis. Earlier studies revealed that signaling via the STK4-encoded MST1 serine-threonine protein kinase, a core component of the Hippo pathway, attenuated EPHA3 expression. Here, we investigated the mechanism by which MST1 regulates EPHA3. Our findings have revealed that the transcriptional regulators YAP1 and TEAD1 are crucial activators of EPHA3 transcription. Silencing YAP1 and TEAD1 suppressed the EPHA3 protein and mRNA levels. In addition, we identified putative TEAD enhancers in the distal EPHA3 promoter, where YAP1 and TEAD1 bind and promote EPHA3 expression. Furthermore, EPHA3 knockout by CRISPR/Cas9 technology reduced cell–cell interaction and cell motility. These findings demonstrate that EPHA3 is transcriptionally regulated by YAP1/TEAD1 of the Hippo pathway, suggesting that it is sensitive to cell contact-dependent interactions.
Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer
Authors: Tran Duy Phuoc , Taira Yuta , Ogawa Takumi , Misu Ryoga , Miyazawa Yoshiki , Kitao Akio 
Published: March 2022

AbstractNon-structural protein 15 (Nsp15) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) forms a homo hexamer and functions as an endoribonuclease. Here, we propose that Nsp15 activity may be inhibited by preventing its hexamerization through drug binding. We first explored the stable conformation of the Nsp15 monomer as the global free energy minimum conformation in the free energy landscape using a combination of parallel cascade selection molecular dynamics (PaCS-MD) and the Markov state model (MSM), and found that the Nsp15 monomer forms a more open conformation with larger druggable pockets on the surface. Targeting the pockets with high druggability scores, we conducted ligand docking and identified compounds that tightly bind to the Nsp15 monomer. The top poses with Nsp15 were subjected to binding free energy calculations by dissociation PaCS-MD and MSM (dPaCS-MD/MSM), indicating the stability of the complexes. One of the identified pockets, which is distinctively bound by inosine analogues, may be an alternative binding site to stabilize viral RNA binding and/or an alternative catalytic site. We constructed a stable RNA structure model bound to both UTP and alternative binding sites, providing a reasonable proposed model of the Nsp15/RNA complex.
Characterizations of botanical attractant of Halyomorpha halys and selection of relevant deorphanization candidates via computational approach
Authors: Zhong Yong-Zhi , Xie Ming-Hui , Huang Cong , Zhang Xue , Cao Li , Chen Hao-Liang , Zhang Feng , Wan Fang-Hao , Han Ri-Chou , Tang Rui 
Published: March 2022

AbstractHalyomorpha halyshas been recognized as a global cross-border pest species. Along with well-established pheromone trapping approaches, there have been many attempts to utilize botanical odorant baits for field monitoring. Due to sensitivity, ecological friendliness, and cost-effectiveness for large-scale implementation, the selection of botanical volatiles as luring ingredients and/or synergists forH. halysis needed. In the current work, botanical volatiles were tested by olfactometer and electrophysiological tests. Results showed that linalool oxide was a potential candidate for application as a behavioral modifying chemical. It drove remarkable attractiveness towardH. halysadults in Y-tube assays, as well as eliciting robust electroantennographic responsiveness towards antennae. A computational pipeline was carried out to screen olfactory proteins related to the reception of linalool oxide. Simulated docking activities of fourH. halysodorant receptors and two odorant binding proteins to linalool oxide and nerolidol were performed. Results showed that all tested olfactory genes were likely to be involved in plant volatile-sensing pathways, and they tuned broadly to tested components. The current work provides insights into the later development of field demonstration strategies using linalool oxide and its molecular targets.
Analysis of swallowing in infants and adults using speckle pattern analysis
Authors: Shahmoon Raz , Tamir Yitav , Beiderman Yevgeny , Agdarov Sergey , Beiderman Yafim , Zalevsky Zeev 
Published: March 2022

AbstractThe ability to detect and evaluate ingestion is especially important in toddlers. The development of new methods for detecting and accurately measuring ingestion is therefore extremely important. One of the methods allowing such measurements is speckle pattern analyses, a well-known phenomenon in coherent imaging. The method allows extraction of various medical parameters, such as blood pulse pressure, temporal signature of heartbeats and breath. The current work contains further development and application of the speckle tracking technique for remote detection and quantification of swallowing and distinguishing between sucking and swallowing to identify feeding disorders in infants and elderly individuals.
A sampling-guided unsupervised learning method to capture percolation in complex networks
Authors: Mimar Sayat , Ghoshal Gourab 
Published: March 2022

AbstractThe use of machine learning methods in classical and quantum systems has led to novel techniques to classify ordered and disordered phases, as well as uncover transition points in critical phenomena. Efforts to extend these methods to dynamical processes in complex networks is a field of active research. Network-percolation, a measure of resilience and robustness to structural failures, as well as a proxy for spreading processes, has numerous applications in social, technological, and infrastructural systems. A particular challenge is to identify the existence of a percolation cluster in a network in the face of noisy data. Here, we consider bond-percolation, and introduce a sampling approach that leverages the core-periphery structure of such networks at a microscopic scale, using onion decomposition, a refined version of the k-core. By selecting subsets of nodes in a particular layer of the onion spectrum that follow similar trajectories in the percolation process, percolating phases can be distinguished from non-percolating ones through an unsupervised clustering method. Accuracy in the initial step is essential for extracting samples with information-rich content, that are subsequently used to predict the critical transition point through the confusion scheme, a recently introduced learning method. The method circumvents the difficulty of missing data or noisy measurements, as it allows for sampling nodes from both the core and periphery, as well as intermediate layers. We validate the effectiveness of our sampling strategy on a spectrum of synthetic network topologies, as well as on two real-word case studies: the integration time of the US domestic airport network, and the identification of the epidemic cluster of COVID-19 outbreaks in three major US states. The method proposed here allows for identifying phase transitions in empirical time-varying networks.
Influence of freezing and heating conditions on grape seed flavan-3-ol extractability, oxidation, and galloylation pattern
Authors: VanderWeide Joshua , Del Zozzo Filippo , Nasrollahiazar Esmaeil , Kennedy James A. , Peterlunger Enrico , Rustioni Laura , Sabbatini Paolo 
Published: March 2022

AbstractIn cool-climate viticulture, the short growing season can influence grape seed maturation by reducing the apparent oxidation of flavan-3-ol monomers and associated increase in seed browning. A reduction in seed maturation increases the potential extraction of flavan-3-ol monomers into wine during maceration operations, heightening bitterness. Here, we carried out a 2 × 2 factorial experiment to test the ability of freezing and heating treatments to advance maturation (decrease flavan-3-ol, improve browning) of (Vitis viniferaL.) Pinot noir and Cabernet Sauvignon seeds over a 24-h incubation period. Only freezing significantly increased seed browning in both cultivars. Subsequent correlations with seed flavan-3-ol monomer concentrations suggest that freezing enhanced the oxidation of these compounds. Interestingly, natural ripening and freezing reduced galloylated flavan-3-ol monomers to a greater extent than non-galloylated ones. This study provides new information regarding the susceptibility of flavan-3-ol monomers to freezing and heating, and also suggests that freezing can advance the maturation the seeds of under-ripe redviniferagrapes.
First-in-class trispecific VHH-Fc based antibody with potent prophylactic and therapeutic efficacy against SARS-CoV-2 and variants
Authors: Titong Allison , Gallolu Kankanamalage Sachith , Dong Jianbo , Huang Betty , Spadoni Nicholas , Wang Bo , Wright Meredith , Pham Keegan L. J. , Le Anh Hai , Liu Yue 
Published: March 2022

AbstractSARS-CoV-2 and its variants have persisted in this ongoing COVID-19 pandemic. While the vaccines have greatly reduced the COVID-19 cases, hospitalizations, and death, about half of the world remain unvaccinated due to various reasons. Furthermore, the duration of the immunity gained from COVID-19 vaccination is still unclear. Therefore, there is a need for innovative prophylactic and treatment measures. In response to this need, we previously reported on the successful computer-aided development of potent VHH-based multispecific antibodies that were characterized in vitro. Here, we evaluated in vivo efficacy and safety of the lead trispecific VHH-Fc, ABS-VIR-001. Importantly, our data showed that ABS-VIR-001 treatment prevented SARS-CoV-2 infection and death when provided as an intranasal prophylaxis in a humanized ACE-2 mouse model. In addition, ABS-VIR-001 post-exposure treatment was shown to greatly reduce viral loads by as much as 50-fold. A detailed panel of metabolic and cellular parameters demonstrated that ABS-VIR-001 treatment was overall comparable to the PBS treatment, indicating a favorable safety profile. Notably, our inhibition studies show that ABS-VIR-001 continued to demonstrate unwavering efficacy against SARS-CoV-2 mutants, associated with key variants including Delta and Omicron, owing to its multiple epitope design. Lastly, we rigorously tested and confirmed the excellent thermostability of ABS-VIR-001 when heated to 45 °C for up to 4 weeks. Taken together, our study suggests that ABS-VIR-001 is an efficacious and durable prophylaxis and post-exposure treatment for COVID-19 with promising safety and manufacturability features for global distribution.
Single versus double bundle in posterior cruciate ligament (PCL) reconstruction: a meta-analysis
Authors: Migliorini Filippo , Pintore Andrea , Spiezia Filippo , Oliva Francesco , Hildebrand Frank , Maffulli Nicola 
Published: March 2022

AbstractPosterior cruciate ligament (PCL) reconstruction can be performed using single bundle (SB) and double bundle (DB) techniques. The present study investigated whether DB PCL reconstruction is superior to SB reconstruction in terms of patient reported outcome measures (PROMs) and joint stability. In December 2021 Embase, Google Scholar, Pubmed, Scopus databases were accessed. All clinical trials comparing SB versus DB reconstruction to address PCL insufficiency in skeletally mature patients were considered. Data from 483 procedures were retrieved. The mean follow-up was 31.0 (28.0 to 107.6) months, and the mean timespan between injury and surgery was 11.3 (6 to 37) months. The mean age of the patients was 29.3 ± 3.8 years. 85 of 483 patients (18%) were women. At a mean of 31.0 months post reconstruction, ROM (P = 0.03) was slightly greater in the SB group, while the Tegner score (P = 0.03) and the Telos stress (P = 0.04) were more favorable in the DB cohort. Similarity was found in instrumental laxity (P = 0.4) and Lysholm score (P = 0.3). The current evidence does not support the use of DB techniques for PCL reconstruction. Both methods could restore knee stability and motion with satisfactory short term patient reported outcome measures. Further high quality clinical trials are required to validate these results on a larger scale.
Implementation of arbitrary polyhedral elements for automatic dynamic analyses of three-dimensional structures
Authors: Zhou Lei , Li Jianbo , Lin Gao 
Published: March 2022

AbstractThe transition from the geometry to the mesh can be rather difficult, manual and time-consuming, especially for the large scale complex structures. The procedure of mesh generation needs massive human intervention making the automatic engineering analyses of structures from CAD geometry models hardly possible. This paper focuses on implementing a polyhedron element with arbitrary convex topology based on the Scaled Boundary Finite Element Method (SBFEM) in ABAQUS on the strength of the interface of UEL (the subroutine to define a general user-defined element) for automatic dynamic analyses of three-dimensional structures. This implementation empowers ABAQUS to analyze any model with arbitrary polyhedron elements. When the geometry of a structure is obtained from CAD, the dynamic analyses can be launched seamlessly and automatically. Cases of a cantilever subjected to a dynamic harmonic excitation with the traditional hexahedron element and this polyhedron element are compared to verify the accuracy of the UEL. Taking a practical example of the Soil-Structure Interaction analysis of a Nuclear Power Plant, the applicability and performance of this implementation are tested. The results of the two examples confirm that this polyhedron element based on SBFEM can be more accurate using much less degrees of freedom and its implementation in ABAQUS is robust and compatible.
A critical role of an oxygen-responsive gene for aerobic nitrogenase activity in Azotobacter vinelandii and its application to Escherichia coli
Authors: Takimoto Ren , Tatemichi Yuki , Aoki Wataru , Kosaka Yuishin , Minakuchi Hiroyoshi , Ueda Mitsuyoshi , Kuroda Kouichi 
Published: March 2022

AbstractSince nitrogenase is irreversibly inactivated within a few minutes after exposure to oxygen, current studies on the heterologous expression of nitrogenase are limited to anaerobic conditions. This study comprehensively identified genes showing oxygen-concentration-dependent expression only under nitrogen-fixing conditions in Azotobacter vinelandii, an aerobic diazotroph. Among the identified genes, nafU, with an unknown function, was greatly upregulated under aerobic nitrogen-fixing conditions. Through replacement and overexpressing experiments, we suggested that nafU is involved in the maintenance of nitrogenase activity under aerobic nitrogenase activity. Furthermore, heterologous expression of nafU in nitrogenase-producing Escherichia coli increased nitrogenase activity under aerobic conditions by 9.7 times. Further analysis of NafU protein strongly suggested its localization in the inner membrane and raised the possibility that this protein may lower the oxygen concentration inside the cells. These findings provide new insights into the mechanisms for maintaining stable nitrogenase activity under aerobic conditions in A. vinelandii and provide a platform to advance the use of nitrogenase under aerobic conditions.
Kluai Hin (Musa sapientum Linn.) peel as a source of functional polyphenols identified by HPLC-ESI-QTOF-MS and its potential antidiabetic function
Authors: Tongkaew Patthamawadee , Tohraman Anna , Bungaramphai Ramlatee , Mitrpant Chalermchai , Aydin Ebru 
Published: March 2022

AbstractTo date, information on the polyphenolic composition of Kluai Hin banana peel and pulp and the potential antidiabetic activity of its major active compounds is limited. This study aimed to identify polyphenols in extracts of fresh and freeze-dried Kluai Hin banana peel and pulp (methanol:water; M:W, 80:20 for flavonoids and acetone:water:acetic acid; A:W:A, 50:49:1 for phenolic acids) by RP-HPLC-DAD and HPLC-ESI-QTOF-MS. Additionally, inhibition of α-amylase and α-glucosidase activities was investigated with crude extracts from Kluai Hin banana peel and pulp, and compared with its major polyphenols ((+)-catechin, (−)-epicatechin and gallic acid) and the antidiabetic drug acarbose. (−)-Gallocatechin was the most abundant polyphenol and was detected in all fresh and freeze-dried pulp and peel extracts by RP-HPLC-DAD. Furthermore, unidentified polyphenol peaks of Kluai Hin were further explored by HPLC-ESI-QTOF-MS. The A:W:A fresh peel extract contained more total phenolic content (811.56 mg GAE/100 g) than the freeze-dried peel (565.03 mg GAE/100 g). A:W:A extraction of the fresh and freeze-dried peel of exhibited IC50 values for α-amylase activity 2.66 ± 0.07 mg/ml and 2.97 ± 0.00 mg/ml, respectively, but its inhibitory activity was lower than acarbose (IC50 = 0.25 ± 0.01 mg/ml). Peel extracts inhibited α-glucosidase activity, whereas pulp extracts had no effect. In addition, all standards, except gallocatechin, activated α-amylase activity, while, gallocatechin inhibited α-glucosidase activity better than acarbose. Therefore, we propose a further investigation into the use of Kluai Hin banana peel as a potential functional food for the management of postprandial glycaemic response to reduce diabetes risk and in the management of diabetes with a commercial drug.
Astrocyte-secreted chordin-like 1 regulates spine density after ischemic injury
Authors: Blanco-Suarez Elena , Allen Nicola J. 
Published: March 2022

AbstractIschemic injury occurs when the brain is deprived of blood flow, preventing cells from receiving essential nutrients. The injury core is the brain region directly deprived and is surrounded by the peri-infarct area, the region with recovery potential. In the peri-infarct area neurons undergo acute loss of dendritic spines, which modifies synaptic plasticity and determines neuronal survival. Astrocytes can be protective or detrimental to the ischemic injury response depending on the specific stage, yet we lack clear understanding of the underlying mechanisms. Chordin-like 1 (Chrdl1) is an astrocyte-secreted protein that promotes synaptic maturation and limits experience-dependent plasticity in the mouse visual cortex. Given this plasticity-limiting function we asked if Chrdl1 regulates the response to ischemic injury, modelled using photothrombosis (PT). We find that Chrdl1 mRNA is upregulated in astrocytes in the peri-infarct area in both acute and sub-acute phases post-PT. To determine the impact of increased Chrdl1 on the response to PT we analyzed Chrdl1 knock-out mice. We find that absence of Chrdl1 prevents ischemia-induced spine loss in the peri-infarct area and reduces cell death in the core, without impacting gliosis. These findings highlight the important role of astrocyte-secreted proteins in regulating structural plasticity in response to brain ischemic injuries.
Yield improvement of Gracilaria tenuistipitata by optimizing different aspects in coast of cox’s bazar, Bangladesh
Authors: Bokhtiar S. M. , Ali M. A. , Chowdhury M. A. Z. , Ahmed K. U. , Hassan M. K. , Ahmed M. , Bhuiyan M. S. , Mashuk O. F. , Rahman M. M. , Salam M. A. , Rafiquzzaman S. M. , Hossain Md Faruque 
Published: March 2022

AbstractThis research was designed to find out the effect of different factors such as influence of lunar cycle, harvesting interval, rope type and seeding gap on the production of G. tenuistipitata in coast of Cox’s Bazar. Duration of these experiments were sixty days and all the parameters were recorded fortnightly. Monitoring of water quality parameters indicated that salinity, temperature, transparency, pH and DO were suitable for seaweed cultivation. In determining lunar cycle effect, results envisaged that fresh yield was 14.43% increased when seeding and harvesting time was selected considering the moon cycle. Regarding the selection of harvesting interval, it was found that T3 (30 days interval) was the best to harvest the seaweed whereas T4 (40 days interval) showed decreasing trend in production. Our study also found that semi floating single line showed better yield performance compared to semi floating double line system. In case of influence on seeding gap, it has been found that 20 cm gap between two seed showed the highest yields followed by 10 cm, 30 cm and 40 cm, respectively. Overall, it can be concluded that yield of G. tenuistipitata in coast of Cox’s Bazar could be improved considering those factors.