bluuebunny/crossref_metadata_2025_split huggingface dataset:
3-Mercaptopyruvate sulfur transferase is a protein persulfidase
Authors: Pedre Brandán , Talwar Deepti , Barayeu Uladzimir , Schilling Danny , Luzarowski Marcin , Sokolowski Mikolaj , Glatt Sebastian , Dick Tobias P. 
Published: February 2023

AbstractProtein S-persulfidation (P-SSH) is recognized as a common posttranslational modification. It occurs under basal conditions and is often observed to be elevated under stress conditions. However, the mechanism(s) by which proteins are persulfidated inside cells have remained unclear. Here we report that 3-mercaptopyruvate sulfur transferase (MPST) engages in direct protein-to-protein transpersulfidation reactions beyond its previously known protein substrates thioredoxin and MOCS3/Uba4, associated with H2S generation and transfer RNA thiolation, respectively. We observe that depletion of MPST in human cells lowers overall intracellular protein persulfidation levels and identify a subset of proteins whose persulfidation depends on MPST. The predicted involvement of these proteins in the adaptation to stress responses supports the notion that MPST-dependent protein persulfidation promotes cytoprotective functions. The observation of MPST-independent protein persulfidation suggests that other protein persulfidases remain to be identified.
Trajetorias: a dataset of environmental, epidemiological, and economic indicators for the Brazilian Amazon
Authors: Rorato Ana C. , Dal’Asta Ana Paula , Lana Raquel Martins , dos Santos Ricardo B. N. , Escada Maria Isabel S. , Vogt Camila M. , Neves Tatiana Campos , Barbosa Milton , Andreazzi Cecilia S. , dos Reis Izabel C. , Fernandes Danilo A. , da Silva-Nunes Mônica , de Souza Anielli R. , Monteiro Antonio M. V. , Codeço Claudia T. 
Published: February 2023

AbstractThe Trajetorias dataset is a harmonized set of environmental, epidemiological, and poverty indicators for all municipalities of the Brazilian Legal Amazon (BLA). This dataset is the result of a scientific synthesis research initiative conducted by scientists from several natural and social sciences fields, consolidating multidisciplinary indicators into a coherent dataset for integrated and interdisciplinary studies of the Brazilian Amazon. The dataset allows the investigation of the association between the Amazonian agrarian systems and their impacts on environmental and epidemiological changes, furthermore enhancing the possibilities for understanding, in a more integrated and consistent way, the scenarios that affect the Amazonian biome and its inhabitants.
Short-term sedimentation dynamics in mesotidal marshes
Authors: Carrasco A. Rita , Kombiadou Katerina , Matias Ana 
Published: February 2023

AbstractOne of the key questions about wetlands resilience to sea-level rise is whether sediment supply will be enough to keep them coping with growing inundation levels. To address this question, researchers have put a lot of effort into field data collection and ecogeomorphic modelling, in an attempt to identify the tipping points of marsh survival. This study uses fieldwork data to characterize the sediment fluxes between the tidal flats and salt marshes, in the Ria Formosa lagoon (Portugal). Sediment fluxes were measured from the tidal channel towards the mid-upper marsh, during neap and spring tide conditions. The flow magnitude was measured, and induced transport was determined based on shear velocities. Deposition rates, instantaneous suspended sediment and near-bed velocities were linked through theoretical formulas and used to characterize time-averaged conditions for sediment delivery and deposition to the site. The results showed that suspended sediment concentrations and sediment deposition varied across the transect with no specific relation to elevation. Maximum water depths were recorded in the vegetated tidal flat, and the maximum currents were flood dominated, in the order of 0.20 m/s, in the low marsh due to flow-plant interactions and an increase of turbulence. Deposition rates ranged between 20 to 45 g/m2/hr, after a complete tidal cycle, and were higher in the mid-upper marsh. Hydroperiod was not the main contributor to sediment deposition in the study area. Sediment transport was tidally driven, strongly two-dimension during the cycle, and highly influenced by the vegetation. Measurements of marsh sediment flux obtained in our work are diverse from the ones found in the literature and evidence the importance of considering spatio-temporal variability of vegetated platforms in assessing overall marsh bed level changes.
Sustainable synthesis of graphene sand composite from waste cooking oil for dye removal
Authors: Abdullah Sani Nor Syazwani , Ang Wei Lun , Mohammad Abdul Wahab , Nouri Alireza , Mahmoudi Ebrahim 
Published: February 2023

AbstractWaste cooking oil (WCO) appears to be a potential carbonaceous source for synthesizing graphene sand composite (GSC) adsorbent in removing pollutants. This study presents a green synthesis method of GSC using WCO as a sustainable carbon source for the synthesis of GSC through the thermal graphitization method. Characterization analysis conducted on GSCWCOverified the successful coating of WCO onto the sand surface and conversion to graphene, which possessed distinct functional groups and features of graphene materials. GSCWCOadsorbent effectiveness in removing Congo Red dye through batch adsorption was studied under the influence of different initial concentrations (20 to 100 mg/L), and the optimum pH (pH 2 to 10), contact time (5 to 240 min), and temperature (25 to 45 °C) were investigated. The GSCWCOshowed removal rates of 91.5% achieved at an initial dye concentration of 20 mg L−1, 1.0 g of adsorbent dosage, a temperature of 25 °C, and 150 min of contact time. The GSCWCOexhibited a maximum capacity of 5.52 mg g−1, was well-fitted to the Freundlich isotherm model with an R2value of 0.989 and had an adsorption mechanism that followed the pseudo-second-order kinetic model. Negative values of enthalpy (ΔH) and Gibbs free energy (ΔG) revealed that CR adsorption onto GSCWCOwas a spontaneous and exothermic process. The presence of functional groups on the surface of GSCWCOwith such interactions (π–π attractive forces, hydrophobic forces, and hydrogen bonding) was responsible for the anionic dye removal. Regeneration of GSCWCOadsorbent declined after four cycles, possibly due to the chemisorption of dyes with GSC that resulted in inefficient adsorption. Being a waste-to-wealth product, GSCWCOpossessed great potential to be used for water treatment and simultaneously benefited the environment through the effort to reduce the excessive discharge of WCO.
Degradation of 1-alkyl-3-methylimidazolium tetrafluoroborate in an ultrasonic zero-valent zinc and activated carbon micro-electrolysis system
Authors: Lyu Ping , Guo Wan , Qi Hang , Yuan Xiang , Ma Jinqi , Xu Xingmin , Zhou Haimei 
Published: February 2023

AbstractIncreased attention has been given to the removal of ionic liquids (ILs) from natural water environments. In this work, 5 kinds of 1-alkyl-3-methylimidazoliumtetrafluoroborate ([Cnmim][BF4] (n = 2, 4, 6, 8, 10)) ILs were degraded in an ultrasonic zero-valent zinc (ZVZ) and activated carbon (AC) micro-electrolysis system. Optimization of degradation conditions and the degradation levels were studied by high performance liquid chromatography, the surface morphology of the ZVZ and AC changed before and after the reaction were observed by scanning electron microscope. The degradation intermediates were detected by gas chromatography- mass spectrometry and ion chromatography, and inferred the degradation pathway. The degradation effect of [C4mim][BF4] was best with ultrasonic assistance, pH 3 and an AC/ZVZ ratio of 1:1. The degradation of [Cnmim][BF4] in aqueous solution exceeded 91.7% in 120 min, and the mineralization level exceeded 88.9%. The surface of smooth and dense ZVZ particles became loose flocculent and the porous surface of AC became larger and rougher after reaction. The degradation pathway suggested that the imidazolium ring was sulfurized or oxidized, and then the ring was opened to form N-alkyl formamide and N-methyl formamide. ZVZ/AC micro-electrolysis combined with ultrasonic irradiation is an effective method to remove ILs, which provides new insight into IL degradation.
Contrasting patterns of population structure of Bulwer’s petrel (Bulweria bulwerii) between oceans revealed by statistical phylogeography
Authors: Silva Mónica C. , Catry Paulo , Bried Joël , Kawakami Kazuto , Flint Elizabeth , Granadeiro José P. 
Published: February 2023

AbstractThe patterns of population divergence of mid-latitude marine birds are impacted by only a few biogeographic barriers to dispersal and the effect of intrinsic factors, such as fidelity to natal colonies or wintering grounds, may become more conspicuous. Here we describe, for the first time, the phylogeographic patterns and historical demography of Bulwer’s petrel Bulweria bulwerii and provide new insights regarding the drivers of species diversification in the marine environment. We sampled Bulwer’s petrels from the main breeding colonies and used a statistical phylogeography approach based on surveying nuclear and mitochondrial loci (~ 9100 bp) to study its mechanisms of global diversification. We uncovered three highly differentiated groups including the Western Pacific, the Central Pacific and the Atlantic. The older divergence occurred within the Pacific Ocean, ca. 850,000 ya, and since then the W Pacific group has been evolving in isolation. Conversely, divergence between the Central Pacific and Atlantic populations occurred within the last 200,000 years. While the Isthmus of Panama is important in restricting gene flow between oceans in Bulwer’s petrels, the deepest phylogeographic break is within the Pacific Ocean, where oceanographic barriers are key in driving and maintaining the remarkable structure found in this highly mobile seabird. This is in contrast with the Atlantic, where no structure was detected. Further data will provide insights regarding the extent of lineage divergence of Bulwer’s petrels in the Western Pacific.
Heterogeneity of interaction strengths and its consequences on ecological systems
Authors: Jackson Zachary , Xue BingKan 
Published: February 2023

AbstractEcosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among individual organisms even within the same species, causing heterogeneity in their interaction strengths with other species. The consequences of such heterogeneous interactions for the ecosystem have not been studied systematically. As a theoretical exploration, we analyze a simple ecosystem with trophic interactions between two predators and a shared prey, which would exhibit competitive exclusion in models with homogeneous interactions. We consider several scenarios where individuals of the prey species differentiate into subpopulations with different interaction strengths. We show that in all these cases, whether the heterogeneity is inherent, reversible, or adaptive, the ecosystem can stabilize at a new equilibrium where all three species coexist. Moreover, the prey population that has heterogeneous interactions with its predators reaches a higher density than it would without heterogeneity, and can even reach a higher density in the presence of two predators than with just one. Our results suggest that heterogeneity may be a naturally selected feature of ecological interactions that have important consequences for the stability and diversity of ecosystems.
Designing plant–transparent agrivoltaics
Authors: Stallknecht Eric J. , Herrera Christopher K. , Yang Chenchen , King Isaac , Sharkey Thomas D. , Lunt Richard R. , Runkle Erik S. 
Published: February 2023

AbstractCovering greenhouses and agricultural fields with photovoltaics has the potential to create multipurpose agricultural systems that generate revenue through conventional crop production as well as sustainable electrical energy. In this work, we evaluate the effects of wavelength-selective cutoffs of visible and near-infrared (biologically active) radiation using transparent photovoltaic (TPV) absorbers on the growth of three diverse, representative, and economically important crops: petunia, basil, and tomato. Despite the differences in TPV harvester absorption spectra, photon transmission of photosynthetically active radiation (PAR; 400–700 nm) is the most dominant predictor of crop yield and quality. This indicates that different wavebands of blue, red, and green are essentially equally important to these plants. When the average photosynthetic daily light integral is > 12 mol m–2 d–1, basil and petunia yield and quality is acceptable for commercial production. However, even modest decreases in TPV transmission of PAR reduces tomato growth and fruit yield. These results identify crop-specific design requirements that exist for TPV harvester transmission and the necessity to maximize transmission of PAR to create the most broadly applicable TPV greenhouse harvesters for diverse crops and geographic locations. We determine that the deployment of 10% power conversion efficiency (PCE) plant-optimized TPVs over approximately 10% of total agricultural and pasture land in the U.S. would generate 7 TW, nearly double the entire energy demand of the U.S.
Reynolds nano fluid model for Casson fluid flow conveying exponential nanoparticles through a slandering sheet
Authors: Nadeem Sohail , Ishtiaq Bushra , Ben Hamida Mohamed Bechir , Almutairi Shahah , Ghazwani Hassan Ali , Eldin Sayed M. , Al-Shafay A. S. 
Published: February 2023

AbstractNanofluids with their augmented thermal characteristics exhibit numerous implementations in engineering and industrial fields such as heat exchangers, microelectronics, chiller, pharmaceutical procedures, etc. Due to such properties of nanofluids, a mathematical model of non-Newtonian Casson nanofluid is analyzed in this current study to explore the steady flow mechanism with the contribution of water-based Aluminum oxide nanoparticles. A stretchable surface incorporating variable thickness is considered to be the source of the concerning fluid flow in two-dimension. An exponential viscosity of the nanofluid is proposed to observe the fluid flow phenomenon. Different models of viscosity including Brinkman and Einstein are also incorporated in the flow analysis and compared with the present exponential model. The physical flow problem is organized in the boundary layer equations which are further tackled by the execution of the relevant similarity transformations and appear in the form of ordinary nonlinear differential equations. The different three models of nanofluid viscosity exhibit strong graphical and tabulated relations with each other relative to the various aspects of the flow problem. In all concerned models of the viscosity, the deteriorating nature of the velocity field corresponding to the Casson fluid and surface thickness parameters is observed.
Multimodal single-cell analyses of peripheral blood mononuclear cells of COVID-19 patients in Japan
Authors: Kashima Yukie , Mizutani Taketoshi , Nakayama-Hosoya Kaori , Moriyama Saya , Matsumura Takayuki , Yoshimura Yoshihiro , Sasaki Hiroaki , Horiuchi Hiroshi , Miyata Nobuyuki , Miyazaki Kazuhito , Tachikawa Natsuo , Takahashi Yoshimasa , Suzuki Tadaki , Sugano Sumio , Matano Tetsuro , Kawana-Tachikawa Ai , Suzuki Yutaka 
Published: February 2023

AbstractSARS-CoV-2 continues to spread worldwide. Patients with COVID-19 show distinct clinical symptoms. Although many studies have reported various causes for the diversity of symptoms, the underlying mechanisms are not fully understood. Peripheral blood mononuclear cells from COVID-19 patients were collected longitudinally, and single-cell transcriptome and T cell receptor repertoire analysis was performed. Comparison of molecular features and patients’ clinical information revealed that the proportions of cells present, and gene expression profiles differed significantly between mild and severe cases; although even among severe cases, substantial differences were observed among the patients. In one severely-infected elderly patient, an effective antibody response seemed to have failed, which may have caused prolonged viral clearance. Naïve T cell depletion, low T cell receptor repertoire diversity, and aberrant hyperactivation of most immune cell subsets were observed during the acute phase in this patient. Through this study, we provided a better understanding of the diversity of immune landscapes and responses. The information obtained from this study can help medical professionals develop personalized optimal clinical treatment strategies for COVID-19.
A mechanistic understanding of the effects of polyethylene terephthalate nanoplastics in the zebrafish (Danio rerio) embryo
Authors: Bashirova Narmin , Poppitz David , Klüver Nils , Scholz Stefan , Matysik Jörg , Alia A. 
Published: February 2023

AbstractPlastic pollution, especially by nanoplastics (NPs), has become an emerging topic due to the widespread existence and accumulation in the environment. The research on bioaccumulation and toxicity mechanism of NPs from polyethylene terephthalate (PET), which is widely used for packaging material, have been poorly investigated. Herein, we report the first use of high-resolution magic-angle spinning (HRMAS) NMR based metabolomics in combination with toxicity assay and behavioural end points to get systems-level understanding of toxicity mechanism of PET NPs in intact zebrafish embryos. PET NPs exhibited significant alterations on hatching and survival rate. Accumulation of PET NPs in larvae were observed in liver, intestine, and kidney, which coincide with localization of reactive oxygen species in these areas. HRMAS NMR data reveal that PET NPs cause: (1) significant alteration of metabolites related to targeting of the liver and pathways associated with detoxification and oxidative stress; (2) impairment of mitochondrial membrane integrity as reflected by elevated levels of polar head groups of phospholipids; (3) cellular bioenergetics as evidenced by changes in numerous metabolites associated with interrelated pathways of energy metabolism. Taken together, this work provides for the first time a comprehensive system level understanding of toxicity mechanism of PET NPs exposure in intact larvae.
Characterisation of a cyclic peptide that binds to the RAS binding domain of phosphoinositide 3-kinase p110α
Authors: Ismail Mohamed , Martin Stephen R. , George Roger , Houghton Francesca , Kelly Geoff , Chaleil Raphaël A. G. , Anastasiou Panayiotis , Wang Xinyue , O’Reilly Nicola , Federico Stefania , Joshi Dhira , Nagaraj Hemavathi , Cooley Rachel , Hui Ning Sze , Molina-Arcas Miriam , Hancock David C. , Tavassoli Ali , Downward Julian 
Published: February 2023

AbstractP110α is a member of the phosphoinositide 3-kinase (PI3K) enzyme family that functions downstream of RAS. RAS proteins contribute to the activation of p110α by interacting directly with its RAS binding domain (RBD), resulting in the promotion of many cellular functions such as cell growth, proliferation and survival. Previous work from our lab has highlighted the importance of the p110α/RAS interaction in tumour initiation and growth. Here we report the discovery and characterisation of a cyclic peptide inhibitor (cyclo-CRVLIR) that interacts with the p110α-RBD and blocks its interaction with KRAS. cyclo-CRVLIR was discovered by screening a “split-intein cyclisation of peptides and proteins” (SICLOPPS) cyclic peptide library. The primary cyclic peptide hit from the screen initially showed a weak affinity for the p110α-RBD (Kd about 360 µM). However, two rounds of amino acid substitution led to cyclo-CRVLIR, with an improved affinity for p110α-RBD in the low µM (Kd 3 µM). We show that cyclo-CRVLIR binds selectively to the p110α-RBD but not to KRAS or the structurally-related RAF-RBD. Further, using biophysical, biochemical and cellular assays, we show that cyclo-CRVLIR effectively blocks the p110α/KRAS interaction in a dose dependent manner and reduces phospho-AKT levels in several oncogenic KRAS cell lines.
Design, development and application of a compact robotic transplanter with automatic seedling picking mechanism for plug-type seedlings
Authors: Khadatkar Abhijit , Pandirwar A. P. , Paradkar V. 
Published: February 2023

AbstractAutomation of agricultural operation such as seedling transplanting is needed to ensure efficient as well as timely operation. Robotics is the area that needs to be focused for the future of automatic seedling transplanter. This paper presents the design, development as well as working of the robotic transplanter (RT) for plug seedlings. The developed RT consists of three systems: (1) robot initiation; (2) seedling picking mechanism (SPM); and (3) vehicle movement system (VMS). The SPM consists of a main frame, manipulator, end-effector and control unit. Whereas, the VMS is having photoelectric sensor, robot controller and DC motor. The stepper motors were mounted on the main frame for movement in XY direction. The manipulator was on the crossbar that used to move the end-effector in Z-axis. The pick-up mechanism consists of an end-effector having jaw-type gripper controlled by servo motor. The control unit consists of microchip 16F877 and the system is controlled with computer programming. The gripper moves to each seedling in the pro-tray, grasp and pick-up the seedling, moves to the delivery point and then release the seedling. The manipulator was tested and analyzed for pickup and releasing of 96 seedlings with soil base from pro-tray. The initial experimental result showed that the seedling success rate, leakage rate and successful transplanting of 30 days old chilli seedling was 95.1%, 7.6% and 90.3%, respectively. Robotic technology seems to be expensive but the scope lies in the non-availability or high cost of manual labour and to ensure timeliness of repetitive field operations.
Extra-viral DNA in adeno-associated viral vector preparations induces TLR9-dependent innate immune responses in human plasmacytoid dendritic cells
Authors: Bucher Kirsten , Rodríguez-Bocanegra Eduardo , Wissinger Bernd , Strasser Torsten , Clark Simon J. , Birkenfeld Andreas L. , Siegel-Axel Dorothea , Fischer M. Dominik 
Published: February 2023

AbstractAdeno-associated viral (AAV) vector suspensions produced in either human derived HEK cells or in Spodoptera frugiperda (Sf9) insect cells differ in terms of residual host cell components as well as species-specific post-translational modifications displayed on the AAV capsid proteins. Here we analysed the impact of these differences on the immunogenic properties of the vector. We stimulated human plasmacytoid dendritic cells with various lots of HEK cell-produced and Sf9 cell-produced AAV-CMV-eGFP vectors derived from different manufacturers. We found that AAV8-CMV-eGFP as well as AAV2-CMV-eGFP vectors induced lot-specific but not production platform-specific or manufacturer-specific inflammatory cytokine responses. These could be reduced or abolished by blocking toll-like receptor 9 signalling or by enzymatically reducing DNA in the vector lots using DNase. Successful HEK cell transduction by DNase-treated AAV lots and DNA analyses demonstrated that DNase did not affect the integrity of the vector but degraded extra-viral DNA. We conclude that both HEK- and Sf9-cell derived AAV preparations can contain immunogenic extra-viral DNA components which can trigger lot-specific inflammatory immune responses. This suggests that improved strategies to remove extra-viral DNA impurities may be instrumental in reducing the immunogenic properties of AAV vector preparations.