bluuebunny/crossref_metadata_2025 huggingface dataset:
THRONCAT: metabolic labeling of newly synthesized proteins using a bioorthogonal threonine analog
Authors: Ignacio Bob J. , Dijkstra Jelmer , Mora Natalia , Slot Erik F. J. , van Weijsten Margot J. , Storkebaum Erik , Vermeulen Michiel , Bonger Kimberly M.
Published: June 2023

Profiling the nascent cellular proteome and capturing early proteomic changes in response to external stimuli provides valuable insights into cellular physiology. Existing metabolic protein labeling approaches based on bioorthogonal methionine- or puromycin analogs allow for the selective visualization and enrichment of newly synthesized proteins. However, their applications are limited as they often require methionine-free conditions, auxotrophic cells and/or are toxic to cells. Here, we introduce THRONCAT, a threonine-derived non-canonical amino acid tagging method based on the bioorthogonal threonine analog β-ethynylserine (βES) that enables efficient labeling of the nascent proteome in complete growth media within minutes. We use THRONCAT for the visualization and enrichment of nascent proteins in bacteria, mammalian cells and Drosophila melanogaster. We profile immediate proteome dynamics of B-cells in response to B-cell receptor activation simply by adding βES to the culture medium, demonstrating the ease-of-use of the method and its potential to address diverse biological questions. In addition, using a Drosophila model of Charcot-Marie-Tooth peripheral neuropathy, we show that THRONCAT enables visualization and quantification of relative protein synthesis rates in specific cell types in vivo.
NO at low concentration can enhance the formation of highly oxygenated biogenic molecules in the atmosphere
Authors: Nie Wei , Yan Chao , Yang Liwen , Roldin Pontus , Liu Yuliang , Vogel Alexander L. , Molteni Ugo , Stolzenburg Dominik , Finkenzeller Henning , Amorim Antonio , Bianchi Federico , Curtius Joachim , Dada Lubna , Draper Danielle C. , Duplissy Jonathan , Hansel Armin , He Xu-Cheng , Hofbauer Victoria , Jokinen Tuija , Kim Changhyuk , Lehtipalo Katrianne , Nichman Leonid , Mauldin Roy L. , Makhmutov Vladimir , Mentler Bernhard , Mizelli-Ojdanic Andrea , Petäjä Tuukka , Quéléver Lauriane L. J. , Schallhart Simon , Simon Mario , Tauber Christian , Tomé António , Volkamer Rainer , Wagner Andrea C. , Wagner Robert , Wang Mingyi , Ye Penglin , Li Haiyan , Huang Wei , Qi Ximeng , Lou Sijia , Liu Tengyu , Chi Xuguang , Dommen Josef , Baltensperger Urs , El Haddad Imad , Kirkby Jasper , Worsnop Douglas , Kulmala Markku , Donahue Neil M. , Ehn Mikael , Ding Aijun
Published: June 2023

The interaction between nitrogen monoxide (NO) and organic peroxy radicals (RO2) greatly impacts the formation of highly oxygenated organic molecules (HOM), the key precursors of secondary organic aerosols. It has been thought that HOM production can be significantly suppressed by NO even at low concentrations. Here, we perform dedicated experiments focusing on HOM formation from monoterpenes at low NO concentrations (0 – 82 pptv). We demonstrate that such low NO can enhance HOM production by modulating the RO2loss and favoring the formation of alkoxy radicals that can continue to autoxidize through isomerization. These insights suggest that HOM yields from typical boreal forest emissions can vary between 2.5%-6.5%, and HOM formation will not be completely inhibited even at high NO concentrations. Our findings challenge the notion that NO monotonically reduces HOM yields by extending the knowledge of RO2-NO interactions to the low-NO regime. This represents a major advance towards an accurate assessment of HOM budgets, especially in low-NO environments, which prevails in the pre-industrial atmosphere, pristine areas, and the upper boundary layer.
Northern expansion is not compensating for southern declines in North American boreal forests
Authors: Rotbarth Ronny , Van Nes Egbert H. , Scheffer Marten , Jepsen Jane Uhd , Vindstad Ole Petter Laksforsmo , Xu Chi , Holmgren Milena
Published: June 2023

Climate change is expected to shift the boreal biome northward through expansion at the northern and contraction at the southern boundary respectively. However, biome-scale evidence of such a shift is rare. Here, we used remotely-sensed tree cover data to quantify temporal changes across the North American boreal biome from 2000 to 2019. We reveal a strong north-south asymmetry in tree cover change, coupled with a range shrinkage of tree cover distributions. We found no evidence for tree cover expansion in the northern biome, while tree cover increased markedly in the core of the biome range. By contrast, tree cover declined along the southern biome boundary, where losses were related largely to wildfires and timber logging. We show that these contrasting trends are structural indicators for a possible onset of a biome contraction which may lead to long-term carbon declines.
Single-gene resolution of diversity-driven overyielding in plant genotype mixtures
Authors: Wuest Samuel E. , Schulz Lukas , Rana Surbhi , Frommelt Julia , Ehmig Merten , Pires Nuno D. , Grossniklaus Ueli , Hardtke Christian S. , Hammes Ulrich Z. , Schmid Bernhard , Niklaus Pascal A.
Published: June 2023

In plant communities, diversity often increases productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute positive diversity effects to complementary niches occupied by different species or genotypes. However, the specific nature of niche complementarity often remains unclear, including how it is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to study positive diversity effects in mixtures of natural Arabidopsis thaliana genotypes. Using two orthogonal genetic mapping approaches, we find that between-plant allelic differences at the AtSUC8 locus are strongly associated with mixture overyielding. AtSUC8 encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation in AtSUC8 affects the biochemical activities of protein variants and natural variation at this locus is associated with different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying genes important for ecosystem functioning may ultimately allow linking ecological processes to evolutionary drivers, help identify traits underlying positive diversity effects, and facilitate the development of high-performance crop variety mixtures.
Sensitive near-infrared circularly polarized light detection via non-fullerene acceptor blends
Authors: Wan Li , Zhang Rui , Cho Eunkyung , Li Hongxiang , Coropceanu Veaceslav , Brédas Jean-Luc , Gao Feng
Published: June 2023

Circularly polarized light (CPL) is widely used for various applications in sensing and imaging1–3. An ongoing challenge is to realize high-quality CPL detection using chiral organic semiconductors, especially in the near-infrared (NIR) region4. Chiral molecules tend to rely on twisted stereogenic moieties; however, conventional approaches to reduce the bandgap of organic semiconductors are based on the use of co-planar backbones that commonly lead to molecular symmetries preventing chirality. Here we report a widely applicable strategy to directly induce chiroptical activity in planar non-fullerene acceptors5–7, which are widely used for high-performance organic photovoltaics and provide a wealth of opportunities to fill the spectral gap of CPL detection in the NIR regime. We demonstrate proof-of-concept circularly polarized organic photodiodes using chiroptically active non-fullerene acceptor blends, which exhibit strong circular dichroism and hence great sensitivity to CPL in the NIR region. Importantly, this strategy is found to be effective in a wide series of state-of-the-art non-fullerene acceptor families including ITIC5, o-IDTBR6 and Y6 analogues7, which substantially broadens the range of materials applicable to NIR CPL detection.
Population, land use and economic exposure estimates for Europe at 100 m resolution from 1870 to 2020
Authors: Paprotny Dominik , Mengel Matthias
Published: June 2023

Understanding the influence of climate change on past extreme weather impacts is a vital research task. However, the effects of climate change are obscured in the observed impact data series due to the rapid evolution of the social and economic circumstances in which the events occurred. The HANZE v2.0 (Historical Analysis of Natural HaZards in Europe) dataset presented in this study quantifies the evolution of key socioeconomic drivers in Europe since 1870, namely land use, population, economic activity and assets. It consists of algorithms to reallocate baseline (2011) land use and population for any given year based on a large collection of historical subnational- and national-level statistics, and then disaggregate data on production and tangible assets by economic sector into a high-resolution grid. Raster datasets generated by the model enable reconstructing exposure within the footprint of any extreme event both at the time of occurrence and anytime between 1870 and 2020. This allows the separation of the effects of climate change from the effects of exposure change.
Impacts of spaceflight experience on human brain structure
Authors: McGregor Heather R. , Hupfeld Kathleen E. , Pasternak Ofer , Beltran Nichole E. , De Dios Yiri E. , Bloomberg Jacob J. , Wood Scott J. , Mulavara Ajitkumar P. , Riascos Roy F. , Reuter-Lorenz Patricia A. , Seidler Rachael D.
Published: June 2023

Spaceflight induces widespread changes in human brain morphology. It is unclear if these brain changes differ with varying mission duration or spaceflight experience history (i.e., novice or experienced, number of prior missions, time between missions). Here we addressed this issue by quantifying regional voxelwise changes in brain gray matter volume, white matter microstructure, extracellular free water (FW) distribution, and ventricular volume from pre- to post-flight in a sample of 30 astronauts. We found that longer missions were associated with greater expansion of the right lateral and third ventricles, with the majority of expansion occurring during the first 6 months in space then appearing to taper off for longer missions. Longer inter-mission intervals were associated with greater expansion of the ventricles following flight; crew with less than 3 years of time to recover between successive flights showed little to no enlargement of the lateral and third ventricles. These findings demonstrate that ventricle expansion continues with spaceflight with increasing mission duration, and inter-mission intervals less than 3 years may not allow sufficient time for the ventricles to fully recover their compensatory capacity. These findings illustrate some potential plateaus in and boundaries of human brain changes with spaceflight.
Underpinning the use of indium as a neutron absorbing additive in zirconolite by X-ray absorption spectroscopy
Authors: Blackburn Lewis R. , Townsend Luke T. , Dixon Wilkins Malin C. , Ina Toshiaki , Kuman Merve , Sun Shi-Kuan , Mason Amber R. , Gardner Laura J. , Stennett Martin C. , Corkhill Claire L. , Hyatt Neil C.
Published: June 2023

Indium (In) is a neutron absorbing additive that could feasibly be used to mitigate criticality in ceramic wasteforms containing Pu in the immobilised form, for which zirconolite (nominally CaZrTi2O7) is a candidate host phase. Herein, the solid solutions Ca1-xZr1-xIn2xTi2O7 (0.10 ≤ x ≤ 1.00; air synthesis) and Ca1-xUxZrTi2-2xIn2xO7 (x = 0.05, 0.10; air and argon synthesis) were investigated by conventional solid state sintering at a temperature of 1350 °C maintained for 20 h, with a view to characterise In3+ substitution behaviour in the zirconolite phase across the Ca2+, Zr4+ and Ti4+ sites. When targeting Ca1-xZr1-xIn2xTi2O7, single phase zirconolite-2M was formed at In concentrations of 0.10 ≤ x ≤ 0.20; beyond x ≥ 0.20, a number of secondary In-containing phases were stabilised. Zirconolite-2M remained a constituent of the phase assemblage up to a concentration of x = 0.80, albeit at relatively low concentration beyond x ≥ 0.40. It was not possible to synthesise the In2Ti2O7 end member compound using a solid state route. Analysis of the In K-edge XANES spectra in the single phase zirconolite-2M compounds confirmed that the In inventory was speciated as trivalent In3+, consistent with targeted oxidation state. However, fitting of the EXAFS region using the zirconolite-2M structural model was consistent with In3+ cations accommodated within the Ti4+ site, contrary to the targeted substitution scheme. When deploying U as a surrogate for immobilised Pu in the Ca1-xUxZrTi2-2xIn2xO7 solid solution, it was demonstrated that, for both x = 0.05 and 0.10, In3+ was successfully able to stabilise zirconolite-2M when U was distributed predominantly as both U4+ and average U5+, when synthesised under argon and air, respectively, determined by U L3-edge XANES analysis.
Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein–protein interactions
Authors: Kaur Gurjeet , Prajapat Manisha , Singh Harvinder , sarma Phulen , Bhadada Sanjay kumar , Shekhar Nishant , Sharma Saurabh , Sinha Shweta , kumar Subodh , Prakash Ajay , Medhi Bikash
Published: June 2023

Protein–protein interactions (PPIs) play a critical role in all biological processes. Menin is tumor suppressor protein, mutated in multiple endocrine neoplasia type 1 syndrome and has been shown to interact with multiple transcription factors including (RPA2) subunit of replication protein A (RPA). RPA2, heterotrimeric protein required for DNA repair, recombination and replication. However, it’s still remains unclear the specific amino acid residues that have been involved in Menin-RPA2 interaction. Thus, accurately predicting the specific amino acid involved in interaction and effects of MEN1 mutations on biological systems is of great interests. The experimental approaches for identifying amino acids in menin-RPA2 interactions are expensive, time-consuming, and challenging. This study leverages computational tools, free energy decomposition and configurational entropy scheme to annotate the menin-RPA2 interaction and effect on menin point mutation, thereby proposing a viable model of menin-RPA2 interaction. The menin–RPA2 interaction pattern was calculated on the basis of different 3D structures of menin and RPA2 complexes, constructed using homology modeling and docking strategy, generating three best-fit models: Model 8 (− 74.89 kJ/mol), Model 28 (− 92.04 kJ/mol) and Model 9 (− 100.4 kJ/mol). The molecular dynamic (MD) was performed for 200 ns and binding free energies and energy decomposition analysis were calculated using Molecular Mechanics Poisson–Boltzmann Surface Area (MM/PBSA) in GROMACS. From binding free energy change, model 8 of Menin-RPA2 exhibited most negative binding energy of − 205.624 kJ/mol, followed by model 28 of Menin-RPA2 with − 177.382 kJ/mol. After S606F point mutation in Menin, increase of BFE (ΔGbind) by − 34.09 kJ/mol in Model 8 of mutant Menin-RPA2 occurs. Interestingly, we found a significant reduction of BFE (ΔGbind) and configurational entropy by − 97.54 kJ/mol and − 2618 kJ/mol in mutant model 28 as compared the o wild type. Collectively, this is the first study to highlight the configurational entropy of protein–protein interactions thereby strengthening the prediction of two significant important interaction sites in menin for the binding of RPA2. These predicted sites could be vulnerable for structural alternation in terms of binding free energy and configurational entropy after missense mutation in menin.
Climatic niche convergence through space and time for a potential archaeophyte (Acacia caven) in South America
Authors: Velasco Nicolás , Andrade Nicolás , Smit Christian , Bustamante Ramiro
Published: June 2023

Based on the niche conservatism hypothesis, i.e. the idea that niches remain unchanged over space and time, climatic niche modelling (CNM) is a useful tool for predicting the spread of introduced taxa. Recent advances have extended such predictions deeper in time for plant species dispersed by humans before the modern era. The latest CNMs successfully evaluate niche differentiation and estimate potential source areas for intriguing taxa such as archaeophytes (i.e., species introduced before 1492 AD). Here, we performed CNMs forAcacia caven, a common Fabaceae tree in South America, considered an archaeophyte west of the Andes, in Central Chile. Accounting for the infraspecific delimitation of the species, our results showed that even when climates are different, climatic spaces used by the species overlap largely between the eastern and western ranges. Despite slight variation, results were consistent when considering one, two, or even three-environmental dimensions, and in accordance with the niche conservatism hypothesis. Specific distribution models calibrated for each region (east vs west) and projected to the past, indicate a common area of occupancy available in southern Bolivia—northwest Argentina since the late Pleistocene, which could have acted as a source-area, and this signal becomes stronger through the Holocene. Then, in accordance with a taxon introduced in the past, and comparing regional vs continental distribution models calibrated at the infraspecific or species level, the western populations showed their spread status to be mostly in equilibrium with the environment. Our study thus indicates how niche and species distribution models are useful to improve our knowledge related to taxa introduced before the modern era.
HighAltitudeOmicsDB, an integrated resource for high-altitude associated genes and proteins, networks and semantic-similarities
Authors: Gupta Apoorv , Pathak Sandhya , Varshney Rajeev , Ahmad Yasmin , Khurana Pankaj
Published: June 2023

Millions of people worldwide visit, live or work in the hypoxic environment encountered at high altitudes and it is important to understand the biomolecular responses to this stress. This would help design mitigation strategies for high altitude illnesses. In spite of a number of studies spanning over 100 years, still the complex mechanisms controlling acclimatization to hypoxia remain largely unknown. To identify potential diagnostic, therapeutic and predictive markers for HA stress, it is important to comprehensively compare and analyse these studies. Towards this goal, HighAltitudeOmicsDB is a unique resource that provides a comprehensive, curated, user-friendly and detailed compilation of various genes/proteins which have been experimentally validated to be associated with various HA conditions, their protein–protein interactions (PPIs) and gene ontology (GO) semantic similarities. For each database entry, HighAltitudeOmicsDB additionally stores the level of regulation (up/down-regulation), fold change, study control group, duration and altitude of exposure, tissue of expression, source organism, level of hypoxia, method of experimental validation, place/country of study, ethnicity, geographical location etc. The database also collates information on disease and drug association, tissue-specific expression level, GO and KEGG pathway associations. The web resource is a unique server platform that offers interactive PPI networks and GO semantic similarity matrices among the interactors.These unique features help to offer mechanistic insights into the disease pathology. Hence, HighAltitudeOmicsDBis a unique platform for researchers working in this area to explore, fetch, compare and analyse HA-associated genes/proteins, their PPI networks, and GO semantic similarities. The database is available at http://www.altitudeomicsdb.in.
Single-machine scheduling with periodic maintenance and learning effect
Authors: Wu Hui , Zheng Hongmei
Published: June 2023

This paper discusses a single-machine scheduling problem with periodic maintenance activities and position-based learning effect to minimize the makespan. To obtain exact solutions of small-scale problems, one new two-stage binary integer programming model is formulated. In addition, a branch and bound algorithm combining boundary method and pruning rules is also proposed. According to the property of the optimal solution, a special search neighborhood is constructed. A hybrid genetic-tabu search algorithm based on genetic mechanism with tabu technique as an operator is proposed to solve medium-scale and large-scale problems. Moreover, to improve the efficiency of genetic algorithm and hybrid genetic-tabu search algorithm, Taguchi method is used for parameter tuning. Furthermore, computational experiments are carried out to compare the efficiency and performance of these algorithms.
Agricultural adaptations to mid-late Holocene climate change in western Türkiye
Authors: Maltas Tom , Şahoğlu Vasıf , Erkanal Hayat
Published: June 2023

The period around the mid-late Holocene transition (c. 2200bc) saw major societal developments across the eastern Mediterranean. At the same time, the region experienced a shift to more arid climatic conditions. This included punctuated episodes of rapid climate change such as the ‘4.2 ka event’, which has been implicated in widespread societal ‘collapse’ at the end of the Early Bronze Age. The ways in which societies adapted agricultural production to cope with a drying climate are poorly understood. We begin to rectify this through stable isotope analysis of archaeobotanical remains from the Aegean region of western Türkiye, conducted to reveal changes in agricultural decision making across the mid-late Holocene transition. We find that Bronze Age farmers adapted agricultural production strategies by investing in drought-tolerant cereals cultivated on drier fields with water management strategies redirected towards pulses. Despite this, we find no evidence for pronounced drought stress in cereals grown during the period of the 4.2 ka event. This raises the potential for alternative explanations for societal disruptions visible across the Anatolian Plateau during this time, such as the breakdown of long-distance trade networks.
Design of phononic crystal using open resonators as harmful gases sensor
Authors: Zaky Zaky A. , Mohaseb M. A. , Hendy Ahmed S. , Aly Arafa H.
Published: June 2023

This paper investigates the ability to use a finite one-dimensional phononic crystal composed of branched open resonators with a horizontal defect to detect the concentration of harmful gases such as CO2. This research investigates the impact of periodic open resonators, defect duct at the center of the structure, and geometrical parameters such as cross-sections and length of the primary waveguide and resonators on the model's performance. As far as we know, this research is unique in the sensing field. Furthermore, these simulations show that the investigated finite one-dimensional phononic crystal composed of branched open resonators with a horizontal defect is a promising sensor.
A set of vectors and strains for chromosomal integration in fission yeast
Authors: Matsuyama Akihisa , Hashimoto Atsushi , Nishimura Shinichi , Yoshida Minoru
Published: June 2023

The expression of heterologous genes is an important technique in yeast genetics. In fission yeast, the leu1 and ura4 genes have been used mainly as selectable markers for heterologous expression. To expand the repertoire of selection markers available for heterologous expression of genes, here we developed new host-vector systems employing lys1 and arg3. By employing genome editing with the CRISPR/Cas9 system, we isolated several alleles of lys1 and arg3, each having a critical mutation in the ORF region. In parallel, we developed a set of vectors that complement the amino acid auxotrophy of lys1 and arg3 mutants when integrated into each locus. Using these vectors in combination with the previously developed integration vector pDUAL, we successfully observed the localization of three proteins in a cell simultaneously by fusing them with different fluorescent proteins. Thus, these vectors enable combinatorial expression of heterologous genes, which addresses increasingly diverse experimental challenges.
Assessing the impacts of dam/weir operation on streamflow predictions using LSTM across South Korea
Authors: Kwon Yongsung , Cha YoonKyung , Park Yeonjeong , Lee Sangchul
Published: June 2023

Recently, weather data have been applied to one of deep learning techniques known as “long short-term memory (LSTM)” to predict streamflow in rainfall-runoff relationships. However, this approach may not be suitable for regions with artificial water management structures such as dams and weirs. Therefore, this study aims to evaluate the prediction accuracy of LSTM for streamflow depending on the availability of dam/weir operational data across South Korea. Four scenarios were prepared for 25 streamflow stations. Scenarios #1 and #2 used weather data and weather and dam/weir operational data, respectively, with the same LSTM model conditions for all stations. Scenarios #3 and #4 used weather data and weather and dam/weir operational data, respectively, with the different LSTM models for individual stations. The Nash–Sutcliffe efficiency (NSE) and the root mean squared error (RMSE) were adopted to assess the LSTM’s performance. The results indicated that the mean values of NSE and RMSE were 0.277 and 292.6 (Scenario #1), 0.482 and 214.3 (Scenario #2), 0.410 and 260.7 (Scenario #3), and 0.592 and 181.1 (Scenario #4), respectively. Overall, the model performance was improved by the addition of dam/weir operational data, with an increase in NSE values of 0.182–0.206 and a decrease in RMSE values of 78.2–79.6. Surprisingly, the degree of performance improvement varied according to the operational characteristics of the dam/weir, and the performance tended to increase when the dam/weir with high frequency and great amount of water discharge was included. Our findings showed that the overall LSTM prediction of streamflow was improved by the inclusion of dam/weir operational data. When using dam/weir operational data to predict streamflow using LSTM, understanding of their operational characteristics is important to obtain reliable streamflow predictions.
All green sulfolane-based solvent enhanced electrical conductivity and rigidity of perovskite crystalline layer
Authors: Siripraparat Akarapitch , Mittanonsakul Pimolrat , Pansa-Ngat Pimsuda , Seriwattanachai Chaowaphat , Kumnorkaew Pisist , Kaewprajak Anusit , Kanjanaboos Pongsakorn , Pakawatpanurut Pasit
Published: June 2023

Industrial commercialization of perovskite solar cells not only depends on sufficient device performance, but also requires complete elimination of hazardous solvents in the fabrication process to enable sustainable development of the technology. This work reports a new solvent system based on sulfolane,$$\gamma$$γ-butyrolactone (GBL), and acetic acid (AcOH) as a significantly greener alternative to common but more hazardous solvents. Interestingly, this solvent system not only resulted in densely-packed perovskite layer of bigger crystal size and better crystallinity, the grain boundaries were found to be more rigid and highly conductive to electrical current. The physical changes at the grain boundaries were due to the sulfolane-infused crystal interfaces, which were expected to facilitate better charge transfer and provide stronger barrier to moisture within the perovskite layer, yielding higher current density and longer performance of the device as a result. In fact, by using a mixed solvent system consisting of sulfolane, GBL, and AcOH in the volume ratio of 70.0:27.5:2.5, the device stability was better and the photovoltaic performance was statistically comparable with those prepared using DMSO-based solvent. Our report reflects unprecedented findings of enhanced electrical conductivity and rigidity of the perovskite layer simply by using an appropriate choice of the all-green solvent.
A comparative multi-level toxicity assessment of carbon-based Gd-free dots and Gd-doped nanohybrids from coffee waste: hematology, biochemistry, histopathology and neurobiology study
Authors: Kuznietsova Halyna , Dziubenko Natalia , Paliienko Konstantin , Pozdnyakova Natalia , Krisanova Natalia , Pastukhov Artem , Lysenko Tetiana , Dudarenko Marina , Skryshevsky Valeriy , Lysenko Vladimir , Borisova Tatiana
Published: June 2023

Here, a comparative toxicity assessment of precursor carbon dots from coffee waste (cofCDs) obtained using green chemistry principles and Gd-doped nanohybrids (cofNHs) was performed using hematological, biochemical, histopathological assays in vivo (CD1 mice, intraperitoneal administration, 14 days), and neurochemical approach in vitro (rat cortex nerve terminals, synaptosomes). Serum biochemistry data revealed similar changes in cofCDs and cofNHs-treated groups, i.e. no changes in liver enzymes' activities and creatinine, but decreased urea and total protein values. Hematology data demonstrated increased lymphocytes and concomitantly decreased granulocytes in both groups, which could evidence inflammatory processes in the organism and was confirmed by liver histopathology; decreased red blood cell-associated parameters and platelet count, and increased mean platelet volume, which might indicate concerns with platelet maturation and was confirmed by spleen histopathology. So, relative safety of both cofCDs and cofNHs for kidney, liver and spleen was shown, whereas there were concerns about platelet maturation and erythropoiesis. In acute neurotoxicity study, cofCDs and cofNHs (0.01 mg/ml) did not affect the extracellular level of L-[14C]glutamate and [3H]GABA in nerve terminal preparations. Therefore, cofNHs demonstrated minimal changes in serum biochemistry and hematology assays, had no acute neurotoxicity signs, and can be considered as perspective biocompatible non-toxic theragnostic agent.
Using pressure to unravel the structure–dynamic-disorder relationship in metal halide perovskites
Authors: Xu Kai , Pérez-Fidalgo Luis , Charles Bethan L. , Weller Mark T. , Alonso M. Isabel , Goñi Alejandro R.
Published: June 2023

The exceptional optoelectronic properties of metal halide perovskites (MHPs) are presumed to arise, at least in part, from the peculiar interplay between the inorganic metal-halide sublattice and the atomic or molecular cations enclosed in the cage voids. The latter can exhibit a roto-translative dynamics, which is shown here to be at the origin of the structural behavior of MHPs as a function of temperature, pressure and composition. The application of high hydrostatic pressure allows for unraveling the nature of the interaction between both sublattices, characterized by the simultaneous action of hydrogen bonding and steric hindrance. In particular, we find that under the conditions of unleashed cation dynamics, the key factor that determines the structural stability of MHPs is the repulsive steric interaction rather than hydrogen bonding. Taking as example the results from pressure and temperature-dependent photoluminescence and Raman experiments on MAPbBr$$_3$$3but also considering the pertinent MHP literature, we provide a general picture about the relationship between the crystal structure and the presence or absence of cationic dynamic disorder. The reason for the structural sequences observed in MHPs with increasing temperature, pressure, A-site cation size or decreasing halide ionic radius is found principally in the strengthening of the dynamic steric interaction with the increase of the dynamic disorder. In this way, we have deepened our fundamental understanding of MHPs; knowledge that could be coined to improve performance in future optoelectronic devices based on this promising class of semiconductors.
Thickness of hydrogel for nitrifying biomass entrapment determines the free ammonia susceptibility differently in batch and continuous modes
Authors: Song Minsu , Yuan Meng , Jeong Sanghyun , Bae Hyokwan
Published: June 2023

Hydrogels immobilizing nitrifying bacteria with different thicknesses of 0.55 and 1.13 cm (HG-0.55 and HG-1.13, respectively) were produced. It was recognized that the thickness of media is a crucial parameter that affects both the stability and efficiency of wastewater treatment. Batch mode experiments were conducted to quantify specific oxygen uptake rate (SOUR) values at various total ammonium nitrogen (TAN) concentrations and pH levels. In the batch test, HG-0.55 exhibited 2.4 times higher nitrifying activity than HG-1.13, with corresponding SOUR values of 0.00768 and 0.00317 mg-O2/L mL-PVA min, respectively. However, HG-0.55 was more susceptible to free ammonia (FA) toxicity than HG-1.13, resulting in a reduction of 80% and 50% in SOUR values for HG-0.55 and -1.13, respectively, upon increasing the FA concentration from 15.73 to 118.12 mg-FA/L. Continuous mode experiments were conducted to assess the partial nitritation (PN) efficiency in practical applications, where continuous wastewater inflow maintains low FA toxicity through high ammonia-oxidizing rates. With step-wise TAN concentration increases, HG-0.55 experienced a gentler increase in FA concentration compared to HG-1.13. At a nitrogen loading rate of 0.78–0.95 kg-N/m3 day, the FA increase rate for HG-0.55 was 0.0179 kg-FA/m3 day, while that of HG-1.13 was 0.0516 kg-FA/m3 day. In the batch mode, where wastewater is introduced all at once, the high accumulation of FA posed a disadvantage for the FA-susceptible HG-0.55, which made it unsuitable for application. However, in the continuous mode, the thinner HG-0.55, with its larger surface area and high ammonia oxidation activity, proved to be suitable and demonstrated its effectiveness. This study provides valuable insights and a framework for the utilization strategy of immobilized gels in addressing the toxic effects of FA in practical processes.
Primary mouse myoblast metabotropic purinoceptor profiles and calcium signalling differ with their muscle origin and are altered in mdx dystrophinopathy
Authors: Róg Justyna , Oksiejuk Aleksandra , Górecki Dariusz C. , Zabłocki Krzysztof
Published: June 2023

Mortality of Duchenne Muscular Dystrophy (DMD) is a consequence of progressive wasting of skeletal and cardiac muscle, where dystrophinopathy affects not only muscle fibres but also myogenic cells. Elevated activity of P2X7 receptors and increased store-operated calcium entry have been identified in myoblasts from the mdx mouse model of DMD. Moreover, in immortalized mdx myoblasts, increased metabotropic purinergic receptor response was found. Here, to exclude any potential effects of cell immortalization, we investigated the metabotropic response in primary mdx and wild-type myoblasts. Overall, analyses of receptor transcript and protein levels, antagonist sensitivity, and cellular localization in these primary myoblasts confirmed the previous data from immortalised cells. However, we identified significant differences in the pattern of expression and activity of P2Y receptors and the levels of the “calcium signalling toolkit” proteins between mdx and wild-type myoblasts isolated from different muscles. These results not only extend the earlier findings on the phenotypic effects of dystrophinopathy in undifferentiated muscle but, importantly, also reveal that these changes are muscle type-dependent and endure in isolated cells. This muscle-specific cellular impact of DMD may not be limited to the purinergic abnormality in mice and needs to be taken into consideration in human studies.
Retreatment of oval-shaped root canals filled with TotalFill bioceramic or AH plus sealer
Authors: Jamleh Ahmed , Nassar Mohannad , Alfadley Abdulmohsen , Alanazi Azhar , Alotiabi Hadeel , Alghilan Maryam , Alfouzan Khalid
Published: June 2023

This study investigated retreatment of oval canals filled with gutta-percha and different sealers using WaveOne Gold (WOG). Single oval canals were prepared to size 30, 0.04 and obturated with gutta percha and AH Plus (AHP) or TotalFill bioceramic (TFBC) sealer. After 6-month incubation, the canals were retreated with WOG Primary (25, 0.07) under simulated body temperature, and the developed load and torque were simultaneously measured. The time and regaining the apical patency were checked. Micro-computed tomography scanning was performed to calculate the remaining obturating materials. An independent t-test and chi-square test were performed at a 95% confidence level. A shorter retreatment time was needed in TFBC than in AHP (P = 0.003). However, a higher maximum apical load was reported with AHP (P = 0.000). Meanwhile, comparable maximum coronal load and maximum torque values were observed. Apical patency was regained in all TFBC roots and only 75% of the AHP samples (P = 0.217). The remaining obturating materials were comparable in TFBC (13.02 ± 8.12%) and AHP (10.11 ± 8.46%) (P = 0.398). WOG was able to remove 89.89% and 86.98% of obturating materials in TFBC and AHP, respectively. The TFBC presented lower apical loads and faster retreatment compared to AHP.
Exceptional response to lorlatinib and cabozantinib in ROS1-rearranged NSCLC with acquired F2004V and L2086F resistance
Authors: Sakamoto Mandy , Patil Tejas
Published: June 2023

Patients with ROS1-rearranged NSCLC demonstrate excellent disease control with ROS1-targeted therapy, but acquired resistance is inevitable. Of particular interest is the ROS1 L2086F kinase domain mutation which is refractory to all currently available ROS1 TKIs apart from cabozantinib. We present a case of a patient with metastatic ROS1-rearranged NSCLC with dual ROS1 F2004V and L2086F resistance mutations who radiographically responded to the combination of lorlatinib and cabozantinib in a patient with metastatic NSCLC. Furthermore, the patient experienced exceptional clinical improvement and tolerance with the combined use of lorlatinib and cabozantinib. This case builds the case for cabozantinib as an agent to overcome ROS1 L2086F resistance. It also highlights the efficacy and safety of using combination of ROS1 TKIs to overcome complex resistance patterns.
Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition
Authors: Wang Hanwen , Arulraj Theinmozhi , Kimko Holly , Popel Aleksander S.
Published: June 2023

Generating realistic virtual patients from a limited amount of patient data is one of the major challenges for quantitative systems pharmacology modeling in immuno-oncology. Quantitative systems pharmacology (QSP) is a mathematical modeling methodology that integrates mechanistic knowledge of biological systems to investigate dynamics in a whole system during disease progression and drug treatment. In the present analysis, we parameterized our previously published QSP model of the cancer-immunity cycle to non-small cell lung cancer (NSCLC) and generated a virtual patient cohort to predict clinical response to PD-L1 inhibition in NSCLC. The virtual patient generation was guided by immunogenomic data from iAtlas portal and population pharmacokinetic data of durvalumab, a PD-L1 inhibitor. With virtual patients generated following the immunogenomic data distribution, our model predicted a response rate of 18.6% (95% bootstrap confidence interval: 13.3-24.2%) and identified CD8/Treg ratio as a potential predictive biomarker in addition to PD-L1 expression and tumor mutational burden. We demonstrated that omics data served as a reliable resource for virtual patient generation techniques in immuno-oncology using QSP models.
Progress towards the Sustainable Development Goals has been slowed by indirect effects of the COVID-19 pandemic
Authors: Yuan Haixia , Wang Xiaoming , Gao Lei , Wang Tao , Liu Bingsheng , Fang Dongping , Gao Yi
Published: June 2023

The COVID-19 pandemic has undermined the ability of many countries to achieve the Sustainable Developments Goals (SDGs) by 2030. Here, we systematically assess the likely impacts of the pandemic on progress towards each SDG by 2030 at global, regional and national scales. In our analysis, we account for the social and economic shocks triggered by COVID-19 and their relative impacts on the SDGs. We also analyze the interconnections between SDG indicators during the pandemic to assess the indirect cascading effects of COVID-19 on the SDGs. We find that these indirect effects slowed progress much more than the direct initial disruptions. Globally, poverty eradication (SDG 1) is most affected by the pandemic. Regionally, SDG progress has been set back most in Latin America and the Caribbean, South Asia, the Middle East and North Africa and Sub-Saharan Africa. We suggest that for high and upper-middle-income countries a focus on reducing inequality (SDG 10) would be most beneficial, whereas for low-income and lower-middle-income countries industry, innovation, and infrastructure (SDG 9) are a priority in the post-COVID-19 phase.
Projected increases in emissions of high global warming potential fluorinated gases in China
Authors: Guo Liya , Yang Yang , Fraser Paul J. , Velders Guus J. M. , Liu Zhu , Cui Duo , Quan Jiayu , Cai Zhouxiang , Yao Bo , Hu Jianxin , Fang Xuekun
Published: June 2023

China is the largest greenhouse gas emitter in the world and has committed to mitigating global warming through achieving carbon neutrality by 2060. However, detailed information on China’s historical and projected emissions of fluorinated greenhouse gases, with high global warming potentials, is lacking. Here we establish a comprehensive and up-to-date inventory of China’s fluorinated greenhouse gas emissions and find that they show an accelerating growth rate, increasing from 5.5 to 221 million tons CO2-equivalent per year from 1990 to 2019. China has become the world’s largest emitter of fluorinated greenhouse gases and contributed 93% of the global emission increase during the period 1990−2019. We find that total emissions of fluorinated greenhouse gases from China are projected to increase to 506–1356 million tons CO2-equivalent per year in 2060 if there is no regulation, which is larger than the projected CO2 emissions under China’s carbon neutrality commitment for 2060.
Targeting lymphoid-derived IL-17 signaling to delay skin aging
Authors: Solá Paloma , Mereu Elisabetta , Bonjoch Júlia , Casado-Peláez Marta , Prats Neus , Aguilera Mònica , Reina Oscar , Blanco Enrique , Esteller Manel , Di Croce Luciano , Heyn Holger , Solanas Guiomar , Benitah Salvador Aznar
Published: June 2023

Skin aging is characterized by structural and functional changes that contribute to age-associated frailty. This probably depends on synergy between alterations in the local niche and stem cell-intrinsic changes, underscored by proinflammatory microenvironments that drive pleotropic changes. The nature of these age-associated inflammatory cues, or how they affect tissue aging, is unknown. Based on single-cell RNA sequencing of the dermal compartment of mouse skin, we show a skew towards an IL-17-expressing phenotype of T helper cells, γδ T cells and innate lymphoid cells in aged skin. Importantly, in vivo blockade of IL-17 signaling during aging reduces the proinflammatory state of the skin, delaying the appearance of age-related traits. Mechanistically, aberrant IL-17 signals through NF-κB in epidermal cells to impair homeostatic functions while promoting an inflammatory state. Our results indicate that aged skin shows signs of chronic inflammation and that increased IL-17 signaling could be targeted to prevent age-associated skin ailments.
Supramolecular assembly guided by photolytic redox cycling
Authors: Roth Patrick , Meyer Raphael , Harley Iain , Landfester Katharina , Lieberwirth Ingo , Wagner Manfred , Ng David Y. W. , Weil Tanja
Published: June 2023

In living systems, the formation of structures relies on balancing kinetic and thermodynamic influences powered by reversible covalent bond chemistry. Although synthetic efforts have replicated these processes to some extent, elucidating their combination is necessary to identify mechanisms that confer nature’s structural precision and flexibility within a complex environment. Here we design a photolytic reaction cascade where competing redox pathways control the transience, interconversion and production rates of thiol/disulfide supramolecular monomers in situ. In contrast to direct assembly by dissolution, cascade generation of the same monomers formed hierarchical assemblies with different structural order. Redox-induced cycling between thiol–disulfide formation led to the emergence of new secondary structures and chirality within the final assemblies. These multiple structural states found within the same molecular system demonstrate the concept of assembly plasticity engaged frequently in biology. We demonstrate the importance of reaction complexity in controlling supramolecular propagation and in expanding the library of nanoarchitectures that can be created.
The elusive active species in nickel(ii)-mediated oxidations of hydrocarbons by peracids: a NiII–oxyl species, an aroyloxy radical, or a NiII–peracid complex?
Authors: Wu Zhimin , Sun Dongru , Lee Yong-Min , Zhao Yufen , Nam Wonwoo , Wang Yong
Published: June 2023

A multiple-oxidant mechanism, in which a mCBA· radical, a NiIII–OH species and a NiII–mCPBA complex act as the oxdiants, works in Ni(ii)-mediated oxidation of cyclohexane with mCPBA.
The regulatory effects of fucoidan and laminarin on functional dyspepsia mice induced by loperamide
Authors: Liu Tianxu , Zhang Mengting , Asif Ismail Muhammad , Wu Yonglin , Li Bin , Wang Ling
Published: June 2023

Gastrointestinal dysmotility is a common cause of functional dyspepsia. Both fucoidan and laminarin relieve the gastrointestinal symptoms induced by loperamide. The machanisms include restoring the rhythm of the migrating motor complex and regulating gut microecology.
Ultralow-iridium content NiIr alloy derivative nanochain arrays as bifunctional electrocatalysts for overall water splitting
Authors: Cai Zhengyang , Wang Ping , Zhao Xianglong , Bu Xiuming , Zhang Jiajia , Chen Yuhao , Xu Jingcheng , Yan Ya , Chen Aiying , Wang Xianying
Published: June 2023

An ultralow-iridium content nickel–iridium alloy derivative nanochain array with a self-supported three-dimensional core–shell structure for efficient and durable overall water splitting.
NIR squaraine dyes for dual colorimetric and fluorescent determination of Fe3+, Cu2+, and Hg2+ ions
Authors: Li Huifang , Tang Yiru , Shen Kunrong , Lu Ji , Zhang Zhijie , Yi Dong , Hao Na , Fu Qiang , Ye Zi , Wei Jun , Wang Jun , Pan Xianchao , Wei Siping , Yang Lin
Published: June 2023

Squaraine dyes were synthesized and exhibited NIR intense absorption and fluorescent emission and showed significant selectivity in the recognition of Fe3+, Cu2+ and Hg2+ through binding the O atom, N atom and olefin π bond with Fe3+, Cu2+ and Hg2+.
Catalyst-free thiazolidine formation chemistry enables the facile construction of peptide/protein–cell conjugates (PCCs) at physiological pH
Authors: Liu Xiangquan , Wang Youyu , Ye Bangce , Bi Xiaobao
Published: June 2023

A novel methodology is presented to synthesize peptide/protein–cell conjugates (PCCs) under physiological conditions by leveraging thiazolidine ring formation chemistry while retaining cell viability and function.
Monolithically integrated flexible sensing systems with multi-dimensional printable MXene electrodes
Authors: Liu Shuiren , Meng Qi , Gao Yadong , Zhang Juzhong , Li Jiarong , Yang Youwei , Zhang Xiaomeng , Li Hongpeng , Liu Xuying
Published: June 2023

Bottlebrush-like BPEI is introduced to promote the gelation of MXene to develop printable aqueous inks. Flexible integrated sensing systems with excellent sensitivity were demonstrated by utilization of multifunctional printable MXene electrodes.
Partially H-bonded covalent organic frameworks for photocatalytic hydrogen evolution
Authors: Dong Wenbo , Xiao Yueyuan , Qin Zhiying , Qiao Bo , Li Longyu
Published: June 2023

Oligo(phenylenevinylene) based covalent organic frameworks (COFs) with different extents of hydrogen bonding were prepared. The effects of the extent of hydrogen bonding of these COFs were evaluated by photocatalytic hydrogen evolution.