bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissolved-Cl2 triggered redox reaction enables high-performance perovskite solar cells
Authors: Luo Yujie , Liu Kaikai , Yang Liu , Feng Wenjing , Zheng Lingfang , Shen Lina , Jin Yongbin , Fang Zheng , Song Peiquan , Tian Wanjia , Xu Peng , Li Yuqing , Tian Chengbo , Xie Liqiang , Wei Zhanhua
Published: June 2023

Constructing 2D/3D perovskite heterojunctions is effective for the surface passivation of perovskite solar cells (PSCs). However, previous reports that studying perovskite post-treatment only physically deposits 2D perovskite on the 3D perovskite, and the bulk 3D perovskite remains defective. Herein, we propose Cl2-dissolved chloroform as a multifunctional solvent for concurrently constructing 2D/3D perovskite heterojunction and inducing the secondary growth of the bulk grains. The mechanism of how Cl2 affects the performance of PSCs is clarified. Specifically, the dissolved Cl2 reacts with the 3D perovskite, leading to Cl/I ionic exchange and Ostwald ripening of the bulk grains. The generated Cl− further diffuses to passivate the bulk crystal and buried interface of PSCs. Hexylammonium bromide dissolved in the solvent reacts with the residual PbI2 to form 2D/3D heterojunctions on the surface. As a result, we achieved high-performance PSCs with a champion efficiency of 24.21% and substantially improved thermal, ambient, and operational stability.
NBEAL2 deficiency in humans leads to low CTLA-4 expression in activated conventional T cells
Authors: Delage Laure , Carbone Francesco , Riller Quentin , Zachayus Jean-Luc , Kerbellec Erwan , Buzy Armelle , Stolzenberg Marie-Claude , Luka Marine , de Cevins Camille , Kalouche Georges , Favier Rémi , Michel Alizée , Meynier Sonia , Corneau Aurélien , Evrard Caroline , Neveux Nathalie , Roudières Sébastien , Pérot Brieuc P. , Fusaro Mathieu , Lenoir Christelle , Pellé Olivier , Parisot Mélanie , Bras Marc , Héritier Sébastien , Leverger Guy , Korganow Anne-Sophie , Picard Capucine , Latour Sylvain , Collet Bénédicte , Fischer Alain , Neven Bénédicte , Magérus Aude , Ménager Mickaël , Pasquier Benoit , Rieux-Laucat Frédéric
Published: June 2023

Loss of NBEAL2 function leads to grey platelet syndrome (GPS), a bleeding disorder characterized by macro-thrombocytopenia and α-granule-deficient platelets. A proportion of patients with GPS develop autoimmunity through an unknown mechanism, which might be related to the proteins NBEAL2 interacts with, specifically in immune cells. Here we show a comprehensive interactome of NBEAL2 in primary T cells, based on mass spectrometry identification of altogether 74 protein association partners. These include LRBA, a member of the same BEACH domain family as NBEAL2, recessive mutations of which cause autoimmunity and lymphocytic infiltration through defective CTLA-4 trafficking. Investigating the potential association between NBEAL2 and CTLA-4 signalling suggested by the mass spectrometry results, we confirm by co-immunoprecipitation that CTLA-4 and NBEAL2 interact with each other. Interestingly, NBEAL2 deficiency leads to low CTLA-4 expression in patient-derived effector T cells, while their regulatory T cells appear unaffected. Knocking-down NBEAL2 in healthy primary T cells recapitulates the low CTLA-4 expression observed in the T cells of GPS patients. Our results thus show that NBEAL2 is involved in the regulation of CTLA-4 expression in conventional T cells and provide a rationale for considering CTLA-4-immunoglobulin therapy in patients with GPS and autoimmune disease.
The turbulent future brings a breath of fresh air
Authors: Stjern Camilla W. , Hodnebrog Øivind , Myhre Gunnar , Pisso Ignacio
Published: June 2023

Ventilation of health hazardous aerosol pollution within the planetary boundary layer (PBL) – the lowest layer of the atmosphere – is dependent upon turbulent mixing, which again is closely linked to the height of the PBL. Here we show that emissions of both CO2 and absorbing aerosols such as black carbon influence the number of severe air pollution episodes through impacts on turbulence and PBL height. While absorbing aerosols cause increased boundary layer stability and reduced turbulence through atmospheric heating, CO2 has the opposite effect over land through surface warming. In future scenarios with increasing CO2 concentrations and reduced aerosol emissions, we find that around 10% of the world’s population currently living in regions with high pollution levels are likely to experience a particularly strong increase in turbulence and PBL height, and thus a reduction in intense pollution events. Our results highlight how these boundary layer processes provide an added positive impact of black carbon mitigation to human health.
Carbon neutral hydrogen storage and release cycles based on dual-functional roles of formamides
Authors: Wei Duo , Shi Xinzhe , Junge Henrik , Du Chunyu , Beller Matthias
Published: June 2023

The development of alternative clean energy carriers is a key challenge for our society. Carbon-based hydrogen storage materials are well-suited to undergo reversible (de)hydrogenation reactions and the development of catalysts for the individual process steps is crucial. In the current state, noble metal-based catalysts still dominate this field. Here, a system for partially reversible and carbon-neutral hydrogen storage and release is reported. It is based on the dual-functional roles of formamides and uses a small molecule Fe-pincer complex as the catalyst, showing good stability and reusability with high productivity. Starting from formamides, quantitative production of CO-free hydrogen is achieved at high selectivity ( > 99.9%). This system works at modest temperatures of 90 °C, which can be easily supplied by the waste heat from e.g., proton-exchange membrane fuel cells. Employing such system, we achieve >70% H2 evolution efficiency and >99% H2 selectivity in 10 charge-discharge cycles, avoiding undesired carbon emission between cycles.
Mitochondrial aconitase suppresses immunity by modulating oxaloacetate and the mitochondrial unfolded protein response
Authors: Kim Eunah , Annibal Andrea , Lee Yujin , Park Hae-Eun H. , Ham Seokjin , Jeong Dae-Eun , Kim Younghun , Park Sangsoon , Kwon Sujeong , Jung Yoonji , Park JiSoo , Kim Sieun S. , Antebi Adam , Lee Seung-Jae V.
Published: June 2023

Accumulating evidence indicates that mitochondria play crucial roles in immunity. However, the role of the mitochondrial Krebs cycle in immunity remains largely unknown, in particular at the organism level. Here we show that mitochondrial aconitase, ACO-2, a Krebs cycle enzyme that catalyzes the conversion of citrate to isocitrate, inhibits immunity against pathogenic bacteria in C. elegans. We find that the genetic inhibition of aco-2 decreases the level of oxaloacetate. This increases the mitochondrial unfolded protein response, subsequently upregulating the transcription factor ATFS-1, which contributes to enhanced immunity against pathogenic bacteria. We show that the genetic inhibition of mammalian ACO2 increases immunity against pathogenic bacteria by modulating the mitochondrial unfolded protein response and oxaloacetate levels in cultured cells. Because mitochondrial aconitase is highly conserved across phyla, a therapeutic strategy targeting ACO2 may eventually help properly control immunity in humans.
Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees
Authors: Luo Xiang Ge , Kuipers Jack , Beerenwinkel Niko
Published: June 2023

Cancer progression is an evolutionary process shaped by both deterministic and stochastic forces. Multi-region and single-cell sequencing of tumors enable high-resolution reconstruction of the mutational history of each tumor and highlight the extensive diversity across tumors and patients. Resolving the interactions among mutations and recovering recurrent evolutionary processes may offer greater opportunities for successful therapeutic strategies. To this end, we present a novel probabilistic framework, called TreeMHN, for the joint inference of exclusivity patterns and recurrent trajectories from a cohort of intra-tumor phylogenetic trees. Through simulations, we show that TreeMHN outperforms existing alternatives that can only focus on one aspect of the task. By analyzing datasets of blood, lung, and breast cancers, we find the most likely evolutionary trajectories and mutational patterns, consistent with and enriching our current understanding of tumorigenesis. Moreover, TreeMHN facilitates the prediction of tumor evolution and provides probabilistic measures on the next mutational events given a tumor tree, a prerequisite for evolution-guided treatment strategies.
Mutagenesis and structural studies reveal the basis for the specific binding of SARS-CoV-2 SL3 RNA element with human TIA1 protein
Authors: Zhang Dong , Qiao Lulu , Lei Xiaobo , Dong Xiaojing , Tong Yunguang , Wang Jianwei , Wang Zhiye , Zhou Ruhong
Published: June 2023

Viral RNA-host protein interactions are indispensable during RNA virus transcription and replication, but their detailed structural and dynamical features remain largely elusive. Here, we characterize the binding interface for the SARS-CoV-2 stem-loop 3 (SL3) cis-acting element to human TIA1 protein with a combined theoretical and experimental approaches. The highly structured SARS-CoV-2 SL3 has a high binding affinity to TIA1 protein, in which the aromatic stacking, hydrogen bonds, and hydrophobic interactions collectively direct this specific binding. Further mutagenesis studies validate our proposed 3D binding model and reveal two SL3 variants have enhanced binding affinities to TIA1. And disruptions of the identified RNA-protein interactions with designed antisense oligonucleotides dramatically reduce SARS-CoV-2 infection in cells. Finally, TIA1 protein could interact with conserved SL3 RNA elements within other betacoronavirus lineages. These findings open an avenue to explore the viral RNA-host protein interactions and provide a pioneering structural basis for RNA-targeting antiviral drug design.
Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania
Authors: Holzschuh Aurel , Lerch Anita , Gerlovina Inna , Fakih Bakar S. , Al-mafazy Abdul-wahid H. , Reaves Erik J. , Ali Abdullah , Abbas Faiza , Ali Mohamed Haji , Ali Mohamed Ali , Hetzel Manuel W. , Yukich Joshua , Koepfli Cristian
Published: June 2023

Zanzibar has made significant progress toward malaria elimination, but recent stagnation requires novel approaches. We developed a highly multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug-resistance loci, and successfully sequenced 290 samples from five districts covering both main islands. Here, we elucidate fine-scale Plasmodium falciparum population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. Despite high genetic diversity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of near-clonal infections on Pemba indicate persistent local transmission with limited parasite importation, presenting an opportunity for local elimination efforts. Furthermore, we observe an admixed parasite population on Unguja and detect a substantial fraction (2.9%) of significantly related infection pairs between Zanzibar and the mainland, suggesting recent importation. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts.
Surges in volcanic activity on the Moon about two billion years ago
Authors: Tian Heng-Ci , Zhang Chi , Yang Wei , Du Jun , Chen Yi , Xiao Zhiyong , Mitchell Ross N. , Hui Hejiu , Changela Hitesh G. , Zhang Tian-Xin , Tang Xu , Zhang Di , Lin Yangting , Li Xianhua , Wu Fuyuan
Published: June 2023

The history of mare volcanism critically informs the thermal evolution of the Moon. However, young volcanic eruptions are poorly constrained by remote observations and limited samples, hindering an understanding of mare eruption flux over time. The Chang’e-5 mission returned the youngest lunar basalts thus far, offering a window into the Moon’s late-stage evolution. Here, we investigate the mineralogy and geochemistry of 42 olivine and pyroxene crystals from the Chang’e-5 basalts. We find that almost all of them are normally zoned, suggesting limited magma recharge or shallow-level assimilation. Most olivine grains record a short timescale of cooling. Thermal modeling used to estimate the thickness and volume of the volcanism sampled by Chang’e-5 reveals enhanced magmatic flux ~2 billion years ago, suggesting that while overall lunar volcanic activity may decrease over time, episodic eruptions at the final stage could exhibit above average eruptive fluxes, thus revising models of lunar thermal evolution.
The narrowing gap in developed and developing country emission intensities reduces global trade’s carbon leakage
Authors: Meng Jing , Huo Jingwen , Zhang Zengkai , Liu Yu , Mi Zhifu , Guan Dabo , Feng Kuishuang
Published: June 2023

International trade affects CO2emissions by redistributing production activities to places where the emission intensities are different from the place of consumption. This study focuses on the net emission change as the result of the narrowing gap in emission intensities between the exporter and importer. Here we show that the relocation of production activities from the global North (developed countries) to the global South (developing countries) in the early 2000s leads to an increase in global emissions due to the higher emission intensities in China and India. The related net emissions are about one-third of the total emissions embodied in the South-North trade. However, the narrowing emission intensities between South-North and the changing trade patterns results in declining net emissions in trade in the past decade. The convergence of emission intensities in the global South alleviates concerns that increasing South-South trade would lead to increased carbon leakage and carbon emissions. The mitigation opportunity to green the supply chain lies in sectors such as electricity, mineral products and chemical products, but calls for a universal assessment of emission intensities and concerted effort.
Plant community stability is associated with a decoupling of prokaryote and fungal soil networks
Authors: in ‘t Zandt Dina , Kolaříková Zuzana , Cajthaml Tomáš , Münzbergová Zuzana
Published: June 2023

Soil microbial networks play a crucial role in plant community stability. However, we lack knowledge on the network topologies associated with stability and the pathways shaping these networks. In a 13-year mesocosm experiment, we determined links between plant community stability and soil microbial networks. We found that plant communities on soil abandoned from agricultural practices 60 years prior to the experiment promoted destabilising properties and were associated with coupled prokaryote and fungal soil networks. This coupling was mediated by strong interactions of plants and microbiota with soil resource cycling. Conversely, plant communities on natural grassland soil exhibited a high stability, which was associated with decoupled prokaryote and fungal soil networks. This decoupling was mediated by a large variety of past plant community pathways shaping especially fungal networks. We conclude that plant community stability is associated with a decoupling of prokaryote and fungal soil networks and mediated by plant-soil interactions.
Predicting in-hospital outcomes of patients with acute kidney injury
Authors: Wu Changwei , Zhang Yun , Nie Sheng , Hong Daqing , Zhu Jiajing , Chen Zhi , Liu Bicheng , Liu Huafeng , Yang Qiongqiong , Li Hua , Xu Gang , Weng Jianping , Kong Yaozhong , Wan Qijun , Zha Yan , Chen Chunbo , Xu Hong , Hu Ying , Shi Yongjun , Zhou Yilun , Su Guobin , Tang Ying , Gong Mengchun , Wang Li , Hou Fanfan , Liu Yongguo , Li Guisen
Published: June 2023

Acute kidney injury (AKI) is prevalent and a leading cause of in-hospital death worldwide. Early prediction of AKI-related clinical events and timely intervention for high-risk patients could improve outcomes. We develop a deep learning model based on a nationwide multicenter cooperative network across China that includes 7,084,339 hospitalized patients, to dynamically predict the risk of in-hospital death (primary outcome) and dialysis (secondary outcome) for patients who developed AKI during hospitalization. A total of 137,084 eligible patients with AKI constitute the analysis set. In the derivation cohort, the area under the receiver operator curve (AUROC) for 24-h, 48-h, 72-h, and 7-day death are 95·05%, 94·23%, 93·53%, and 93·09%, respectively. For dialysis outcome, the AUROC of each time span are 88·32%, 83·31%, 83·20%, and 77·99%, respectively. The predictive performance is consistent in both internal and external validation cohorts. The model can predict important outcomes of patients with AKI, which could be helpful for the early management of AKI.
A randomized non-inferiority trial of therapeutic strategy with immunosuppressants versus biologics for Vogt-Koyanagi-Harada disease
Authors: Zhong Zhenyu , Dai Lingyu , Wu Qiuying , Gao Yu , Pu Yanlin , Su Guannan , Lu Xiaorong , Zhang Fuxiang , Tang Chong , Wang Yao , Zhou Chunjiang , Yang Peizeng
Published: June 2023

Biologics are increasingly used to treat Vogt-Koyanagi-Harada disease, but head-to-head comparisons with conventional immunosuppressants are lacking. Here in this randomized trial (Chinese Clinical Trial Registry, ChiCTR2100043061), we assigned 110 patients (27 early-phase and 83 late-phase) to cyclosporine-based immunosuppressant strategy (N = 56) or adalimumab-based biologic strategy (N = 54), each combined with a modified corticosteroid regimen. The primary outcome is change from baseline in best-corrected visual acuity at week 26. The margin of non-inferiority for cyclosporine is −7 letters. The primary outcome is 11.2 letters (95% CI, 7.5 to 14.9) in the cyclosporine group and 6.3 letters (95% CI, 3.1 to 9.6) in the adalimumab group (difference, 4.9; 95% CI, 0.2 to 9.5; P < 0.001 for non-inferiority). The between-group difference is −0.8 letters (95% CI, −6.1 to 4.5) in early-phase disease and 5.7 letters (95% CI, 0.2 to 11.2) in late-phase. Serious adverse events are reported less frequently in the cyclosporine group than in the adalimumab group (0.70 vs. 1.21 events per patient-year). Here, we report that combined with a non-standard corticosteroid regimen, cyclosporine-based immunosuppressant strategy is non-inferior to adalimumab-based biologic strategy by 26 weeks for visual improvement in a cohort of patients with Vogt-Koyanagi-Harada disease, 75% of whom have a late-phase disease.
Direct observation of hot-electron-enhanced thermoelectric effects in silicon nanodevices
Authors: Xue Huanyi , Qian Ruijie , Lu Weikang , Gong Xue , Qin Ludi , Zhong Zhenyang , An Zhenghua , Chen Lidong , Lu Wei
Published: June 2023

The study of thermoelectric behaviors in miniatured transistors is of fundamental importance for developing bottom-level thermal management. Recent experimental progress in nanothermetry has enabled studies of the microscopic temperature profiles of nanostructured metals, semiconductors, two-dimensional material, and molecular junctions. However, observations of thermoelectric (such as nonequilibrium Peltier and Thomson) effect in prevailing silicon (Si)—a critical step for on-chip refrigeration using Si itself—have not been addressed so far. Here, we carry out nanothermometric imaging of both electron temperature (Te) and lattice temperature (TL) of a Si nanoconstriction device and find obvious thermoelectric effect in the vicinity of the electron hotspots: When the electrical current passes through the nanoconstriction channel generating electron hotspots (withTe~1500 K being much higher thanTL~320 K), prominent thermoelectric effect is directly visualized attributable to the extremely large electron temperature gradient (~1 K/nm). The quantitative measurement shows a distinctive third-power dependence of the observed thermoelectric on the electrical current, which is consistent with the theoretically predicted nonequilibrium thermoelectric effects. Our work suggests that the nonequilibrium hot carriers may be potentially utilized for enhancing the thermoelectric performance and therefore sheds new light on the nanoscale thermal management of post-Moore nanoelectronics.
Pre-aged terrigenous organic carbon biases ocean ventilation-age reconstructions in the North Atlantic
Authors: Liu Jingyu , Wang Yipeng , Jaccard Samuel L. , Wang Nan , Gong Xun , Fang Nianqiao , Bao Rui
Published: June 2023

Changes in ocean ventilation have been pivotal in regulating carbon sequestration and release on centennial to millennial timescales. However, paleoceanographic reconstructions documenting changes in deep-ocean ventilation using 14C dating, may bear multidimensional explanations, obfuscating the roles of ocean ventilation played on climate evolution. Here, we show that previously inferred poorly ventilated conditions in the North Atlantic were linked to enhanced pre-aged organic carbon (OC) input during Heinrich Stadial 1 (HS1). The 14C age of sedimentary OC was approximately 13,345 ± 692 years older than the coeval foraminifera in the central North Atlantic during HS1, which is coupled to a ventilation age of 5,169 ± 660 years. Old OC was mainly of terrigenous origin and exported to the North Atlantic by ice-rafting. Remineralization of old terrigenous OC in the ocean may have contributed to, at least in part, the anomalously old ventilation ages reported for the high-latitude North Atlantic during HS1.
Industrial source identification of polyhalogenated carbazoles and preliminary assessment of their global emissions
Authors: Sun Yuxiang , Yang Lili , Zheng Minghui , Weber Roland , Falandysz Jerzy , Lammel Gerhard , Zhao Chenyan , Chen Changzhi , Yang Qiuting , Liu Guorui
Published: June 2023

Polyhalogenated carbazoles (PHCZs) are emerging global pollutants found in environmental matrices, e.g., 3000 tonnes of PHCZs have been detected in the sediments of the Great Lakes. Recognition of PHCZ emissions from ongoing industrial activities worldwide is still lacking. Here, we identify and quantify PHCZ emissions from 13 large-scale industries, 12 of which previously have no data. Congener profiles of PHCZs from investigated industrial sources are clarified, which enables apportioning of PHCZ sources. Annual PHCZ emissions from major industries are estimated on the basis of derived emission factors and then mapped globally. Coke production is a prime PHCZ emitter of 9229 g/yr, followed by iron ore sintering with a PHCZ emission of 3237 g/yr. China, Australia, Japan, India, USA, and Russia are found to be significant emitters through these industrial activities. PHCZ pollution is potentially a global human health and environmental issue.
Asymmetric dinitrogen-coordinated nickel single-atomic sites for efficient CO2 electroreduction
Authors: Zhou Yuzhu , Zhou Quan , Liu Hengjie , Xu Wenjie , Wang Zhouxin , Qiao Sicong , Ding Honghe , Chen Dongliang , Zhu Junfa , Qi Zeming , Wu Xiaojun , He Qun , Song Li
Published: June 2023

Developing highly efficient, selective and low-overpotential electrocatalysts for carbon dioxide (CO2) reduction is crucial. This study reports an efficient Ni single-atom catalyst coordinated with pyrrolic nitrogen and pyridinic nitrogen for CO2 reduction to carbon monoxide (CO). In flow cell experiments, the catalyst achieves a CO partial current density of 20.1 mA cmgeo−2 at −0.15 V vs. reversible hydrogen electrode (VRHE). It exhibits a high turnover frequency of over 274,000 site−1 h−1 at −1.0 VRHE and maintains high Faradaic efficiency of CO (FECO) exceeding 90% within −0.15 to −0.9 VRHE. Operando synchrotron-based infrared and X-ray absorption spectra, and theoretical calculations reveal that mono CO-adsorbed Ni single sites formed during electrochemical processes contribute to the balance between key intermediates formation and CO desorption, providing insights into the catalyst’s origin of catalytic activity. Overall, this work presents a Ni single-atom catalyst with good selectivity and activity for CO2 reduction while shedding light on its underlying mechanism.
Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield
Authors: Lopez-Fernandez Margarita , Westmeijer George , Turner Stephanie , Broman Elias , Ståhle Magnus , Bertilsson Stefan , Dopson Mark
Published: June 2023

Biofilm formation is a common adaptation for microbes in energy-limited conditions such as those prevalent in the vast deep terrestrial biosphere. However, due to the low biomass and the inaccessible nature of subsurface groundwaters, the microbial populations and genes involved in its formation are understudied. Here, a flow-cell system was designed to investigate biofilm formation under in situ conditions in two groundwaters of contrasting age and geochemistry at the Äspö Hard Rock Laboratory, Sweden. Metatranscriptomes showed Thiobacillus, Sideroxydans, and Desulforegula to be abundant and together accounted for 31% of the transcripts in the biofilm communities. Differential expression analysis highlighted Thiobacillus to have a principal role in biofilm formation in these oligotrophic groundwaters by being involved in relevant processes such as the formation of extracellular matrix, quorum sensing, and cell motility. The findings revealed an active biofilm community with sulfur cycling as a prominent mode of energy conservation in the deep biosphere.
Center-environment deep transfer machine learning across crystal structures: from spinel oxides to perovskite oxides
Authors: Li Yihang , Zhu Ruijie , Wang Yuanqing , Feng Lingyan , Liu Yi
Published: June 2023

In data-driven materials design where the target materials have limited data, the transfer machine learning from large known source materials, becomes a demanding strategy especially across different crystal structures. In this work, we proposed a deep transfer learning approach to predict thermodynamically stable perovskite oxides based on a large computational dataset of spinel oxides. The deep neural network (DNN) source domain model with “Center-Environment” (CE) features was first developed using the formation energy of 5329 spinel oxide structures and then was fine-tuned by learning a small dataset of 855 perovskite oxide structures, leading to a transfer learning model with good transferability in the target domain of perovskite oxides. Based on the transferred model, we further predicted the formation energy of potential 5329 perovskite structures with combination of 73 elements. Combining the criteria of formation energy and structure factors including tolerance factor (0.7 < t ≤ 1.1) and octahedron factor (0.45 < μ < 0.7), we predicted 1314 thermodynamically stable perovskite oxides, among which 144 oxides were reported to be synthesized experimentally, 10 oxides were predicted computationally by other literatures, 301 oxides were recorded in the Materials Project database, and 859 oxides have been first reported. Combing with the structure-informed features the transfer machine learning approach in this work takes the advantage of existing data to predict new structures at a lower cost, providing an effective acceleration strategy for the expensive high-throughput computational screening in materials design. The predicted stable novel perovskite oxides serve as a rich platform for exploring potential renewable energy and electronic materials applications.
Globally invariant behavior of oncogenes and random genes at population but not at single cell level
Authors: Sirbu Olga , Helmy Mohamed , Giuliani Alessandro , Selvarajoo Kumar
Published: June 2023

Cancer is widely considered a genetic disease. Notably, recent works have highlighted that every human gene may possibly be associated with cancer. Thus, the distinction between genes that drive oncogenesis and those that are associated to the disease, but do not play a role, requires attention. Here we investigated single cells and bulk (cell-population) datasets of several cancer transcriptomes and proteomes in relation to their healthy counterparts. When analyzed by machine learning and statistical approaches in bulk datasets, both general and cancer-specific oncogenes, as defined by the Cancer Genes Census, show invariant behavior to randomly selected gene sets of the same size for all cancers. However, when protein–protein interaction analyses were performed, the oncogenes-derived networks show higher connectivity than those relative to random genes. Moreover, at single-cell scale, we observe variant behavior in a subset of oncogenes for each considered cancer type. Moving forward, we concur that the role of oncogenes needs to be further scrutinized by adopting protein causality and higher-resolution single-cell analyses.
Ultrastable Co-NC membrane for sterilization of Escherichia coli in flowing water
Authors: Li Chao , Li Jiale , Huang Niu , Kong Xin Ying , Xiao Qingyi , Huang Yingping , Wong Po Keung , Ye Liqun
Published: June 2023

Advanced oxidation technology based on peroxonosulfate (PMS) has attracted extensive attention in water treatment research due to its fast reaction speed and wide pH range adaptability. Cobalt-based catalysts are considered to be one of the most effective reagents for PMS activation in various PMS activation methods. However, Co-ion leaching and difficulty in recovery have greatly hindered its practical applications. Herein, we developed a robust membrane constructed by nitrogen-doped carbon nanotubes embedded with cobalt nanoparticles (Co-NC) to concurrently address the Co-ion leaching and recovery issues. Based on our customization, continuous water flow reactor, the Co-NC membrane exhibited excellent catalytic activity and stability, in which it demonstrated a remarkable sterilization efficiency of 99.9999% againstE. coli, and it retained a superior stability of 96.29% after 40 repeated cycles. Fewer attempts to put such efficient heterogeneous advanced oxidation processes (AOPs) into practical application, to mimic real-life applications, the performance of the Co-NC/PMS system was extended to the water taken from Qiuxi River. Remarkably, there is no deterioration in performance over 12 h of continuous real sewage processing. Mechanistic studies revealed that abundant high-valence metals (CoIV=O) were generated in the system, which can attack and penetrate into the cell membrane to destroy its intracellular defense system. This work provides useful insights into designing robust membranes with superior efficiency and stability for PMS-based advanced oxidation technology.
Electron cooling in graphene enhanced by plasmon–hydron resonance
Authors: Yu Xiaoqing , Principi Alessandro , Tielrooij Klaas-Jan , Bonn Mischa , Kavokine Nikita
Published: June 2023

Evidence is accumulating for the crucial role of a solid’s free electrons in the dynamics of solid–liquid interfaces. Liquids induce electronic polarization and drive electric currents as they flow; electronic excitations, in turn, participate in hydrodynamic friction. Yet, the underlying solid–liquid interactions have been lacking a direct experimental probe. Here we study the energy transfer across liquid–graphene interfaces using ultrafast spectroscopy. The graphene electrons are heated up quasi-instantaneously by a visible excitation pulse, and the time evolution of the electronic temperature is then monitored with a terahertz pulse. We observe that water accelerates the cooling of the graphene electrons, whereas other polar liquids leave the cooling dynamics largely unaffected. A quantum theory of solid–liquid heat transfer accounts for the water-specific cooling enhancement through a resonance between the graphene surface plasmon mode and the so-called hydrons—water charge fluctuations—particularly the water libration modes, which allows for efficient energy transfer. Our results provide direct experimental evidence of a solid–liquid interaction mediated by collective modes and support the theoretically proposed mechanism for quantum friction. They further reveal a particularly large thermal boundary conductance for the water–graphene interface and suggest strategies for enhancing the thermal conductivity in graphene-based nanostructures.
Characterisation of physical and mechanical properties of seven particulate materials proposed as traction enhancers
Authors: Maramizonouz Sadaf , Nadimi Sadegh , Skipper William , Lewis Roger
Published: June 2023

Particulate materials are utilised in many applications to manipulate the friction between surfaces. This dataset provides the characteristics of particulates used as rail sand in the train’s wheel/rail interface (via an on-board system) to facilitate the train’s acceleration and deceleration. Seven materials are studied including Austrian rail sand, standard Great British rail sand, waste glass beads, recycled crushed glass, non-coated alumina, coated alumina, and dolomite. The main objective of this research is to provide a physical and mechanical characterisation of these granular materials in terms of their density, bulk behaviour, particle size, particle shape, hardness, reduced modulus, and mineralogical properties. In particular, three-dimensional raw and post-processed micro-computed tomography images of more than 1200 particles are shared. The results provide a detailed dataset which can be used in ongoing and future experimental and numerical investigations studying the role of particulates in the wheel/rail interface.
Prediction of prostate cancer biochemical recurrence by using discretization supports the critical contribution of the extra-cellular matrix genes
Authors: Marin Laura , Casado Fanny
Published: June 2023

Due to its complexity, much effort has been devoted to the development of biomarkers for prostate cancer that have acquired the utmost clinical relevance for diagnosis and grading. However, all of these advances are limited due to the relatively large percentage of biochemical recurrence (BCR) and the limited strategies for follow up. This work proposes a methodology that uses discretization to predict prostate cancer BCR while optimizing the necessary variables. We used discretization of RNA-seq data to increase the prediction of biochemical recurrence and retrieve a subset of ten genes functionally known to be related to the tissue structure. Equal width and equal frequency data discretization methods were compared to isolate the contribution of the genes and their interval of action, simultaneously. Adding a robust clinical biomarker such as prostate specific antigen (PSA) improved the prediction of BCR. Discretization allowed classifying the cancer patients with an accuracy of 82% on testing datasets, and 75% on a validation dataset when a five-bin discretization by equal width was used. After data pre-processing, feature selection and classification, our predictions had a precision of 71% (testing dataset: MSKCC and GSE54460) and 69% (Validation dataset: GSE70769) should the patients present BCR up to 24 months after their final treatment. These results emphasize the use of equal width discretization as a pre-processing step to improve classification for a limited number of genes in the signature. Functionally, many of these genes have a direct or expected role in tissue structure and extracellular matrix organization. The processing steps presented in this study are also applicable to other cancer types to increase the speed and accuracy of the models in diverse datasets.
Proteomic-based identification of APCS as candidate protein for diagnosis of patients exhibiting anti-tubercular drug induced liver injury
Authors: Kaur Bhavneet , Dixit Ravi , Bakshi Shikha , Konar Monidipa , Sinha Saroj K. , Duseja Ajay Kumar , Sharma Sadhna
Published: June 2023

Traditional markers evaluate anti-tubercular drug-induced liver injury (AT-DILI). However, these markers have certain limitations and studies are in progress to characterize AT-DILI at an early stage. In the present study, 40 patients were categorized and equally distributed into healthy controls, newly diagnosed tuberculosis (TB), TB without hepatotoxicity and TB with hepatotoxicity groups based on their conventional liver function tests. Relative protein quantification was performed on depleted pooled serum samples of each representative group by LC–MS/MS, and validation of shortlisted protein was done by ELISA. Levels of all analysed biochemical parameters showed a statistical increment in the hepatotoxicity group compared to the other three groups, representing AT-DILI. Comparative proteomic analysis between TB with hepatotoxicity versus TB without hepatotoxicity groups highlighted 24 significant differentially expressed proteins, including PROS1, KNG1, CFH, LCAT, APCS and ADIPOQ. Identified proteins were involved in complement activation, triglyceride-rich lipoprotein particle remodelling and pathways comprising complement, coagulation cascades and cholesterol metabolism. Based on functional relevance, the serum amyloid P component (APCS) was shortlisted for validation, and it showed a similar trend as observed in the discovery phase with 100% sensitivity and 87% specificity; however, findings need exploration in larger cohorts.
Prevalence and factors associated with severe undernutrition among under-5 children in Bangladesh, Pakistan, and Nepal: a comparative study using multilevel analysis
Authors: Chowdhury Mohammad Rocky Khan , Rahman Md Shafiur , Billah Baki , Rashid Mamunur , Almroth Melody , Kader Manzur
Published: June 2023

Despite economic growth and poverty reduction, under-5 child undernutrition is still rampant in South Asian countries. This study explored the prevalence and risk factors of severe undernutrition among under-5 children in Bangladesh, Pakistan, and Nepal for comparison using the Composite Index of Severe Anthropometric Failure. We utilised information on under-5 children from recent Demographic Health Surveys. We used multilevel logistic regression models for data analysis. The prevalence of severe undernutrition among under-5 children was around 11.5%, 19.8%, and 12.6% in Bangladesh, Pakistan, and Nepal, respectively. Children from the lowest socioeconomic quintile, and children born with low birth weight were key factors associated with severe undernutrition in these countries. The factors, parental education, maternal nutritional status, antenatal and postnatal care, and birth order were not homogeneous in explaining the determinants of child severe undernutrition across the countries. Our results suggest that the poorest households, and low birth weight of children have significant effects on severe undernutrition among under-5 children in these countries, which should be considered to formulate an evidence-based strategy to reduce severe undernutrition in South Asia.
Numerical simulation of deposition of drifts and salt from multiple super-large seawater cooling towers
Authors: Liang Ziqi , Li Lujun , Yang Jie , Zhu Qing
Published: June 2023

A three-dimensional CFD simulation model was established to study the characteristics of flow, drifts and salt deposition from 6 super-large seawater cooling towers in a power station. In the model, site meteorological data, design parameters of cooling tower, general layout, environmental characteristics, are considered. The results show that: (1) when the wind direction is parallel to the towers, the streams overlap, reducing deposition of drifts and salt onto the ground. (2) The drifts with particle size greater than 550 μm cannot float out of cooling towers. (3) In normal operation of 6 such cooling towers, the resulting salt deposition will not cause serious damage to plants.
Early maturation of sound duration processing in the infant’s brain
Authors: Polver Silvia , Háden Gábor P. , Bulf Hermann , Winkler István , Tóth Brigitta
Published: June 2023

The ability to process sound duration is crucial already at a very early age for laying the foundation for the main functions of auditory perception, such as object perception and music and language acquisition. With the availability of age-appropriate structural anatomical templates, we can reconstruct EEG source activity with much-improved reliability. The current study capitalized on this possibility by reconstructing the sources of event-related potential (ERP) waveforms sensitive to sound duration in 4- and 9-month-old infants. Infants were presented with short (200 ms) and long (300 ms) sounds equiprobable delivered in random order. Two temporally separate ERP waveforms were found to be modulated by sound duration. Generators of these waveforms were mainly located in the primary and secondary auditory areas and other language-related regions. The results show marked developmental changes between 4 and 9 months, partly reflected by scalp-recorded ERPs, but appearing in the underlying generators in a far more nuanced way. The results also confirm the feasibility of the application of anatomical templates in developmental populations.
Interaction between retinol intake and ISX rs5755368 polymorphism in colorectal cancer risk: a case–control study in a Korean population
Authors: Bui Anh Quynh , Gunathilake Madhawa , Lee Jeonghee , Oh Jae Hwan , Chang Hee Jin , Sohn Dae Kyung , Shin Aesun , Kim Jeongseon
Published: June 2023

This study aimed to examine whether the ISX rs5755368 genotypes are associated with the effect of dietary retinol consumption on CRC risk. We recruited 923 CRC patients and 1846 controls to identify the association between dietary retinol and CRC risk. Dietary retinol intake was assessed using a semiquantitative food frequency questionnaire. Genotype data were available for 1419 patients (600 cases and 819 controls) of the total study population. Genotyping was performed using an Illumina MEGA Expanded Array. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated using unconditional logistic regression models. Retinol intake was inversely associated with CRC (OR = 0.49; 95% CI = 0.37–0.63). Participants with AA genotype showed lower CRC risk than subjects carrying the G allele (AG + GG) (OR = 0.76; 95% CI = 0.58–0.99). A 68% reduced risk of CRC was related to subjects who had the highest retinol intake and carrying AA genotype compared to the risk of participants consumed the lowest retinol intake and carrying the G allele (OR = 0.32; 95% CI = 0.20–0.53; P interaction = 0.026). Retinol intake could be a protective factor for CRC risk while this association could be strengthened among individuals carrying the homozygous AA genotype.
Intracerebral gadolinium deposition following blood–brain barrier disturbance in two different mouse models
Authors: Kromrey M. L. , Oswald S. , Becher D. , Bartel J. , Schulze J. , Paland H. , Ittermann T. , Hadlich S. , Kühn J. P. , Mouchantat S.
Published: June 2023

To evaluate the influence of the blood–brain barrier on neuronal gadolinium deposition in a mouse model after multiple intravenous applications of the linear contrast agent gadodiamide. The prospective study held 54 mice divided into three groups: healthy mice (A), mice with iatrogenic induced disturbance of the blood–brain barrier by glioblastoma (B) or cerebral infarction (C). In each group 9 animals received 10 iv-injections of gadodiamide (1.2 mmol/kg) every 48 h followed by plain T1-weighted brain MRI. A final MRI was performed 5 days after the last contrast injection. Remaining mice underwent MRI in the same time intervals without contrast application (control group). Signal intensities of thalamus, pallidum, pons, dentate nucleus, and globus pallidus-to-thalamus and dentate nucleus-to-pons ratios, were determined. Gadodiamide complex and total gadolinium amount were quantified after the last MR examination via LC–MS/MS and ICP-MS. Dentate nucleus-to-pons and globus pallidus-to-thalamus SI ratios showed no significant increase over time within all mice groups receiving gadodiamide, as well as compared to the control groups at last MR examination. Comparing healthy mice with group B and C after repetitive contrast administration, a significant SI increase could only be detected for glioblastoma mice in globus pallidus-to-thalamus ratio (p = 0.033), infarction mice showed no significant SI alteration. Tissue analysis revealed significantly higher gadolinium levels in glioblastoma group compared to healthy (p = 0.013) and infarction mice (p = 0.029). Multiple application of the linear contrast agent gadodiamide leads to cerebral gadolinium deposition without imaging correlate in MRI.
Cross-reactivity trends when selecting scFv antibodies against snake toxins using a phage display-based cross-panning strategy
Authors: Sørensen Christoffer V. , Ledsgaard Line , Wildenauer Helen H. K. , Dahl Camilla H. , Ebersole Tasja W. , Bohn Markus-Frederik , Ljungars Anne , Jenkins Timothy P. , Laustsen Andreas H.
Published: June 2023

Antibodies with cross-reactive binding and broad toxin-neutralizing capabilities are advantageous for treating indications such as infectious diseases and animal envenomings. Such antibodies have been successfully selected against closely related antigens using phage display technology. However, the mechanisms driving antibody cross-reactivity typically remain to be elucidated. Therefore, we sought to explore how a previously reported phage display-based cross-panning strategy drives the selection of cross-reactive antibodies using seven different snake toxins belonging to three protein (sub-)families: phospholipases A2, long-chain α-neurotoxins, and short-chain α-neurotoxins. We showcase how cross-panning can increase the chances of discovering cross-reactive single-chain variable fragments (scFvs) from phage display campaigns. Further, we find that the feasibility of discovering cross-reactive antibodies using cross-panning cannot easily be predicted by analyzing the sequence, structural, or surface similarity of the antigens alone. However, when antigens share the (exact) same functions, this seems to increase the chances of selecting cross-reactive antibodies, which may possibly be due to the existence of structurally similar motifs on the antigens.
The histone H2B Arg95 residue efficiently recruits the transcription factor Spt16 to mediate Ste5 expression of the pheromone response pathway
Authors: Sulaiman Abdallah Alhaj , Ali Reem , Ramotar Dindial
Published: June 2023

In yeast Saccharomyces cerevisiae, the immunosuppressant rapamycin inhibits the TORC1 kinase causing rapid alteration in gene expression and leading to G1 arrest. We recently reported the isolation and characterization from the histone mutant collection of a histone H2B R95A mutant that displays resistance to rapamycin. This mutant is defective in the expression of several genes belonging to the pheromone response pathway including STE5 encoding a scaffold protein that promotes the activation of downstream MAP kinases. Cells lacking Ste5 cannot arrest the cell cycle in response to rapamycin and as a consequence exhibit similar resistance to rapamycin as the H2B R95A mutant. Herein, we show that the H2B R95A mutation weakens the association of H2B with Spt16 a component of the FACT complex (FAcilitates Chromatin Transcription), and an essential factor that interacts with the histone H2A-H2B dimer to promote transcription and preserve chromatin integrity. From a collection of spt16 mutants, spt16 E857K and spt16-11 showed striking sensitivity to rapamycin as compared to the parent strain. spt16 E857K and spt16-11 expressed distinct forms of Ste5, while a suppressor mutation H2B A84D of the spt16-11 mutant prevents the expression of Ste5 and confers marked resistance to rapamycin. We interpret these findings to suggest that the Arg95 residue of histone H2B is required to recruit Spt16 to maintain the expression of STE5, which performs a role to arrest cells in the G1 phase in response to rapamycin.