bluuebunny/crossref_metadata_2025 huggingface dataset:
Graph deep learning accelerated efficient crystal structure search and feature extraction
Authors: Li Chuan-Nan , Liang Han-Pu , Zhang Xie , Lin Zijing , Wei Su-Huai
Published: September 2023

Structural search and feature extraction are a central subject in modern materials design, the efficiency of which is currently limited, but can be potentially boosted by machine learning (ML). Here, we develop an ML-based prediction-analysis framework, which includes a symmetry-based combinatorial crystal optimization program (SCCOP) and a feature additive attribution model, to significantly reduce computational costs and to extract property-related structural features. Our method is highly accurate and predictive, and extracts structural features from desired structures to guide materials design. We first test SCCOP on 35 typical compounds to demonstrate its generality. As a case study, we apply our approach to a two-dimensional B-C-N system, which identifies 28 previously undiscovered stable structures out of 82 compositions; our analysis further establishes the structural features that contribute most to energy and bandgap. Compared to conventional approaches, SCCOP is about 10 times faster while maintaining a comparable accuracy. Our framework is generally applicable to all types of systems for precise and efficient structural search, providing insights into the relationship between ML-extracted structural features and physical properties.
A Continuous Action Space Tree search for INverse desiGn (CASTING) framework for materials discovery
Authors: Banik Suvo , Loefller Troy , Manna Sukriti , Chan Henry , Srinivasan Srilok , Darancet Pierre , Hexemer Alexander , Sankaranarayanan Subramanian K. R. S.
Published: September 2023

Material properties share an intrinsic relationship with their structural attributes, making inverse design approaches crucial for discovering new materials with desired functionalities. Reinforcement Learning (RL) approaches are emerging as powerful inverse design tools, often functioning in discrete action spaces. This constrains their application in materials design problems, which involve continuous search spaces. Here, we introduce an RL-based framework CASTING (Continuous Action Space Tree Search for inverse design), that employs a decision tree-based Monte Carlo Tree Search (MCTS) algorithm with continuous space adaptation through modified policies and sampling. Using representative examples like Silver (Ag) for metals, Carbon (C) for covalent systems, and multicomponent systems such as graphane, boron nitride, and complex correlated oxides, we showcase its accuracy, convergence speed, and scalability in materials discovery and design. Furthermore, with the inverse design of super-hard Carbon phases, we demonstrate CASTING’s utility in discovering metastable phases tailored to user-defined target properties and preferences.
Mapping microstructure to shock-induced temperature fields using deep learning
Authors: Li Chunyu , Verduzco Juan Carlos , Lee Brian H. , Appleton Robert J. , Strachan Alejandro
Published: September 2023

The response of materials to shock loading is important to planetary science, aerospace engineering, and energetic materials. Thermally activated processes, including chemical reactions and phase transitions, are significantly accelerated by energy localization into hotspots. These result from the interaction of the shockwave with the materials’ microstructure and are governed by complex, coupled processes, including the collapse of porosity, interfacial friction, and localized plastic deformation. These mechanisms are not fully understood and the lack of models limits our ability to predict shock to detonation transition from chemistry and microstructure alone. We demonstrate that deep learning can be used to predict the resulting shock-induced temperature fields in composite materials obtained from large-scale molecular dynamics simulations with the initial microstructure as the only input. The accuracy of the Microstructure-Informed Shock-induced Temperature net (MISTnet) model is higher than the current state of the art and its evaluation requires a fraction of the computation cost.
A biomass map of the Brazilian Amazon from multisource remote sensing
Authors: Ometto Jean Pierre , Gorgens Eric Bastos , de Souza Pereira Francisca Rocha , Sato Luciane , de Assis Mauro Lúcio Rodrigures , Cantinho Roberta , Longo Marcos , Jacon Aline Daniele , Keller Michael
Published: September 2023

The Amazon Forest, the largest contiguous tropical forest in the world, stores a significant fraction of the carbon on land. Changes in climate and land use affect total carbon stocks, making it critical to continuously update and revise the best estimates for the region, particularly considering changes in forest dynamics. Forest inventory data cover only a tiny fraction of the Amazon region, and the coverage is not sufficient to ensure reliable data interpolation and validation. This paper presents a new forest above-ground biomass map for the Brazilian Amazon and the associated uncertainty both with a resolution of 250 meters and baseline for the satellite dataset the year of 2016 (i.e., the year of the satellite observation). A significant increase in data availability from forest inventories and remote sensing has enabled progress towards high-resolution biomass estimates. This work uses the largest airborne LiDAR database ever collected in the Amazon, mapping 360,000 km2 through transects distributed in all vegetation categories in the region. The map uses airborne laser scanning (ALS) data calibrated by field forest inventories that are extrapolated to the region using a machine learning approach with inputs from Synthetic Aperture Radar (PALSAR), vegetation indices obtained from the Moderate-Resolution Imaging Spectroradiometer (MODIS) satellite, and precipitation information from the Tropical Rainfall Measuring Mission (TRMM). A total of 174 field inventories geolocated using a Differential Global Positioning System (DGPS) were used to validate the biomass estimations. The experimental design allowed for a comprehensive representation of several vegetation types, producing an above-ground biomass map varying from a maximum value of 518 Mg ha−1, a mean of 174 Mg ha−1, and a standard deviation of 102 Mg ha−1. This unique dataset enabled a better representation of the regional distribution of the forest biomass and structure, providing further studies and critical information for decision-making concerning forest conservation, planning, carbon emissions estimate, and mechanisms for supporting carbon emissions reductions.
A Global Feature-Rich Network Dataset of Cities and Dashboard for Comprehensive Urban Analyses
Authors: Yap Winston , Biljecki Filip
Published: September 2023

Urban network analytics has become an essential tool for understanding and modeling the intricate complexity of cities. We introduce the Urbanity data repository to nurture this growing research field, offering a comprehensive, open spatial network resource spanning 50 major cities in 29 countries worldwide. Our workflow enhances OpenStreetMap networks with 40 + high-resolution indicators from open global sources such as street view imagery, building morphology, urban population, and points of interest, catering to a diverse range of applications across multiple fields. We extract streetscape semantic features from more than four million street view images using computer vision. The dataset’s strength lies in its thorough processing and validation at every stage, ensuring data quality and consistency through automated and manual checks. Accompanying the dataset is an interactive, web-based dashboard we developed which facilitates data access to even non-technical stakeholders. Urbanity aids various GeoAI and city comparative analyses, underscoring the growing importance of urban network analytics research.
Effect of recombination on genetic diversity of Caenorhabditis elegans
Authors: Hwang Ho-Yon , Wang Jiou
Published: September 2023

Greater molecular divergence and genetic diversity are present in regions of high recombination in many species. Studies describing the correlation between variant abundance and recombination rate have long focused on recombination in the context of linked selection models, whereby interference between linked sites under positive or negative selection reduces genetic diversity in regions of low recombination. Here, we show that indels, especially those of intermediate sizes, are enriched relative to single nucleotide polymorphisms in regions of high recombination in C. elegans. To explain this phenomenon, we reintroduce an alternative model that emphasizes the mutagenic effect of recombination. To extend the analysis, we examine the variants with a phylogenetic context and discuss how different models could be examined together. The number of variants generated by recombination in natural populations could be substantial including possibly the majority of some indel subtypes. Our work highlights the potential importance of a mutagenic effect of recombination, which could have a significant role in the shaping of natural genetic diversity.
Simultaneous LC–MS/MS method for the quantitation of Azithromycin, Hydroxychloroquine and its metabolites in SARS-CoV-2(−/ +) populations using dried blood spots
Authors: Chhonker Yashpal S. , Aldhafiri Wafaa N. , Soni Dhruvkumar , Trivedi Neerja , Steinbronn Claire , Johnson Christine , Karita Helen C. Stankiewicz , Paasche-Orlow Michael K. , Barnabas Ruanne , Arnold Samuel L. , Murry Daryl J.
Published: September 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to a global pandemic of coronavirus disease 2019 (COVID-19). Early in the pandemic, efforts were made to test the SARS-CoV-2 antiviral efficacy of repurposed medications that were already approved and available for other indications, including hydroxychloroquine (HCQ) and azithromycin (AZI). To reduce the risk of SARS-CoV-2 exposure for clinical-trial study participants and to conform with lockdowns and social distancing guidelines, biospecimen collection for HCQ and AZI included at-home dried blood spot (DBS) collection rather than standard venipuncture by trained clinicians. In this study, we developed and validated the first sensitive and selective simultaneous LC–MS/MS method to accurately quantitate the concentration of HCQ, HCQ metabolites (Desethylchloroquine [DCQ], Bisdesethylchloroquine [BDCQ], Monodesethylhydroxychloroquine [DHCQ]) and AZI extracted from DBS. The validated method was successfully applied for the quantification of over 2000 DBS specimens to evaluate the pharmacokinetic profile of AZI, HQC, and its metabolites. This new method has a small sample volume requirement (~ 10 µL), results in high sensitivity (1 ng/mL), and would facilitate remotely conducted therapeutic drug monitoring.
Neither sulfoxaflor, Crithidia bombi, nor their combination impact bumble bee colony development or field bean pollination
Authors: Straw Edward A. , Cini Elena , Gold Harriet , Linguadoca Alberto , Mayne Chloe , Rockx Joris , Brown Mark J. F. , Garratt Michael P. D. , Potts Simon G. , Senapathi Deepa
Published: September 2023

Many pollinators, including bumble bees, are in decline. Such declines are known to be driven by a number of interacting factors. Decreases in bee populations may also negatively impact the key ecosystem service, pollination, that they provide. Pesticides and parasites are often cited as two of the drivers of bee declines, particularly as they have previously been found to interact with one another to the detriment of bee health. Here we test the effects of an insecticide, sulfoxaflor, and a highly prevalent bumble bee parasite, Crithidia bombi, on the bumble bee Bombus terrestris. After exposing colonies to realistic doses of either sulfoxaflor and/or Crithidia bombi in a fully crossed experiment, colonies were allowed to forage on field beans in outdoor exclusion cages. Foraging performance was monitored, and the impacts on fruit set were recorded. We found no effect of either stressor, or their interaction, on the pollination services they provide to field beans, either at an individual level or a whole colony level. Further, there was no impact of any treatment, in any metric, on colony development. Our results contrast with prior findings that similar insecticides (neonicotinoids) impact pollination services, and that sulfoxaflor impacts colony development, potentially suggesting that sulfoxaflor is a less harmful compound to bee health than neonicotinoids insecticides.
Repurposing disulfiram, an alcohol-abuse drug, in neuroblastoma causes KAT2A downregulation and in vivo activity with a water/oil emulsion
Authors: Beaudry Annie , Jacques-Ricard Simon , Darracq Anaïs , Sgarioto Nicolas , Garcia Araceli , García Teresita Rode , Lemieux William , Béland Kathie , Haddad Elie , Cordeiro Paulo , Duval Michel , McGraw Serge , Richer Chantal , Caron Maxime , Marois François , St-Onge Pascal , Sinnett Daniel , Banquy Xavier , Raynal Noël J.-M.
Published: September 2023

Neuroblastoma, the most common type of pediatric extracranial solid tumor, causes 10% of childhood cancer deaths. Despite intensive multimodal treatment, the outcomes of high-risk neuroblastoma remain poor. We urgently need to develop new therapies with safe long-term toxicity profiles for rapid testing in clinical trials. Drug repurposing is a promising approach to meet these needs. Here, we investigated disulfiram, a safe and successful chronic alcoholism treatment with known anticancer and epigenetic effects. Disulfiram efficiently induced cell cycle arrest and decreased the viability of six human neuroblastoma cell lines at half-maximal inhibitory concentrations up to 20 times lower than its peak clinical plasma level in patients treated for chronic alcoholism. Disulfiram shifted neuroblastoma transcriptome, decreasing MYCN levels and activating neuronal differentiation. Consistently, disulfiram significantly reduced the protein level of lysine acetyltransferase 2A (KAT2A), drastically reducing acetylation of its target residues on histone H3. To investigate disulfiram’s anticancer effects in an in vivo model of high-risk neuroblastoma, we developed a disulfiram-loaded emulsion to deliver the highly liposoluble drug. Treatment with the emulsion significantly delayed neuroblastoma progression in mice. These results identify KAT2A as a novel target of disulfiram, which directly impacts neuroblastoma epigenetics and is a promising candidate for repurposing to treat pediatric neuroblastoma.
Jahn–Teller distortion in Sr2FeO4: group-theoretical analysis and hybrid DFT calculations
Authors: Zvejnieks Guntars , Mastrikov Yuri , Gryaznov Denis
Published: September 2023

We present theoretical justification for distorted Ruddlesden–Popper (RP) phases of the first-order by using hybrid density functional theory (DFT) calculations and group-theoretical analysis. We, thus, demonstrate the existence of the Jahn–Teller effect around an Fe$$^{4\texttt {+}}$$

4
+

ion in Sr$$_{2}$$

2

FeO$$_{4}$$

4

. On the calculation side, we have established a combination of Wu–Cohen (WC) exchange and Perdew-Wang (PW) correlation in a three-parameter functional WC3PW, giving the most accurate description of Sr$$_{2}$$

2

FeO$$_{4}$$

4

from the comparison of three hybrid DFT functionals. Self-consistently obtained Hartree–Fock exact exchange of 0.16 demonstrates consistent results with the experimental literature data. Importantly, we explain conditions for co-existing proper and pseudo-Jahn–Teller effects from the crystalline orbitals, symmetry-mode analysis and irreps products. Moreover, phonon frequency calculations support and confirm the results of symmetry-mode analysis. In particular, the symmetry-mode analysis identifies a dominating irreducible representation of the Jahn-Teller mode (X2) and corresponding space group (SG) of ground state structure (SG Cmce model). Therefore, the usually suggested high-symmetry tetragonal crystal structure (SG I4/mmm model) is higher in energy by 121 meV/f.u. (equivalent to the Jahn-Teller stabilization energy) compared with the distorted low-symmetry structure (SG Cmce model). We also present diffraction patterns for the two crystal symmetries to discuss the differences. Therefore, our results shed light on the existence of low-symmetry RP phases and make possible direct comparisons with future experiments.
Innate immune dysregulation in multisystem inflammatory syndrome in children (MIS-C)
Authors: Isaza-Correa Johana , Ryan Laura , Kelly Lynne , Allen John , Melo Ashanty , Jones Jennifer , Huggard Dean , Ryan Emer , Ó Maoldomhnaigh Cilian , Geoghehan Sarah , Gavin Patrick , Leahy Timothy Ronan , Butler Karina , Freyne Bridget , Molloy Eleanor J.
Published: September 2023

MIS-C is a systemic inflammation disorder with poorly characterised immunopathological mechanisms. We compared changes in the systemic immune response in children with MIS-C (n = 12, 5–13 years) to healthy controls (n = 14, 5–15 years). Analysis was done in whole blood treated with LPS. Expression of CD11b and Toll-like receptor-4 (TLR4) in neutrophils and monocytes were analysed by flow cytometry. Serum cytokines (IL-1β, IL-2, IL-6, IL-8, IL-10, IL-Ira, TNF-α, TNF-β, IFN-Υ, VEGF, EPO and GM-CSF) and mRNA levels of inflammasome molecules (NLRP3, ASC and IL-1β) were evaluated. Subpopulations of lymphocytes (CD3+, CD19+, CD56+, CD4+, CD8+, TCR Vδ1+, TCR Vδ2+) were assessed at basal levels. Absolute counts of neutrophils and NLR were high in children with MIS-C while absolute counts of lymphocytes were low. Children with MIS-C had increased levels of IL-6, IL-10, TNF-β and VEGF serum cytokines at the basal level, and significantly increased TNF-β post-LPS, compared to controls. IL-1RA and EPO decreased at baseline and post-LPS in MIS-C patients compared to controls. The percentage of CD3+ cells, NK cells and Vδ1 was lower while B cells were higher in children with MIS-C than in controls. Dysregulated immune response in children with MIS-C was evident and may be amenable to immunomodulation.
The simplified Kirchhoff network model (SKNM): a cell-based reaction–diffusion model of excitable tissue
Authors: Jæger Karoline Horgmo , Tveito Aslak
Published: September 2023

Cell-based models of excitable tissues offer the advantage of cell-level precision, which cannot be achieved using traditional homogenized electrophysiological models. However, this enhanced accuracy comes at the cost of increased computational demands, necessitating the development of efficient cell-based models. The widely-accepted bidomain model serves as the standard in computational cardiac electrophysiology, and under certain anisotropy ratio conditions, it is well known that it can be reduced to the simpler monodomain model. Recently, the Kirchhoff Network Model (KNM) was developed as a cell-based counterpart to the bidomain model. In this paper, we aim to demonstrate that KNM can be simplified using the same steps employed to derive the monodomain model from the bidomain model. We present the cell-based Simplified Kirchhoff Network Model (SKNM), which produces results closely aligned with those of KNM while requiring significantly less computational resources.
Origin of mysterious geothermal gas emissions in the middle of the Western Desert, stable shelf area, Dakhla Oasis, Egypt
Authors: Abdel Zaher Mohamed , El-Hadidy Mahmoud , El-Qady Gad , Rabeh Taha , Atya Magdy , El-hady Sherif , Tantawy Abdel Aziz , El-Hemaly Ibrahim , Al Deep Mohamed , Awad Ahmed , Salama Hamada , Khalifa Mohamed Mostafa , Leila Mahmoud
Published: September 2023

This work responds to what was reported in various audio-visual media channels and to queries and explanations from individuals and local residents on the causes of gaseous and thermal emissions from the Earth near the vicinity of the village of Al-Hindaw in Dakhla city, New Valley Governorate, Egypt. At the location of the fume exit area, magnetic, seismic, and electromagnetic geophysical investigations were carried out to identify the factor(s) responsible for the event in question. Rock samples were collected and studied geochemically and radiographically to assess their chemical compositions, as well as the quantity of organic chemicals that may have contributed to the burning and temperature increase. In light of the results of the geochemical and geophysical research, it is believed that the self-ignitions are the result of near-surface reactions and oxidation instead of volcanic activity, such as the presence of magma or other comparable phenomena.
Ecological effect life cycle assessment of house buildings based on emergy footprint model
Authors: He Mengyang , Wang Yang , Ma Haotian
Published: September 2023

Construction is an important sector for climate action. The construction, operation and maintenance, demolition and disposal stages of house buildings consume many resources and have a significant impact on society, the economy and the environment. To assess such efforts, we propose the emergy footprint model of house buildings, which can quantitatively analyse the ecological effect in the house buildings life cycle. The research shows the following. China’s ecological efficiency of the housing sector is characterized by improvement. In the house building fifty-year life cycle, the emergy footprint of the operation and maintenance stage is the largest (75.92%), followed by the construction stage (21.95%), but the emergy footprint intensity of the latter is 4.82 times that of the former. Reducing energy consumption and carbon dioxide emissions in the operation and maintenance stage is the key to reducing the life cycle emergy footprint of house buildings. The ecological impact coefficient of house buildings is negatively exponentially correlated with their service life. It reaches ecological break-even when the service period of the house building is equal to 36.73 years. If the house building is demolished after less than nine years of service, the impact is extremely unfavourable.
Fuzzy interactions between the auto-phosphorylated C-terminus and the kinase domain of CK1δ inhibits activation of TAp63α
Authors: Lambert Mahil , Gebel Jakob , Trejtnar Charlotte , Wesch Nicole , Bozkurt Süleyman , Adrian-Allgood Martin , Löhr Frank , Münch Christian , Dötsch Volker
Published: September 2023

The p53 family member TAp63α plays an important role in maintaining the genetic integrity in oocytes. DNA damage, in particular DNA double strand breaks, lead to the transformation of the inhibited, only dimeric conformation into the active tetrameric one that results in the initiation of an apoptotic program. Activation requires phosphorylation by the kinase CK1 which phosphorylates TAp63α at four positions. The third phosphorylation event is the decisive step that transforms TAp63α into the active state. This third phosphorylation, however, is ~ 20 times slower than the first two phosphorylation events. This difference in the phosphorylation kinetics constitutes a safety mechanism that allows oocytes with a low degree of DNA damage to survive. So far these kinetic investigations of the phosphorylation steps have been performed with the isolated CK1 kinase domain. However, all CK1 enzymes contain C-terminal extensions that become auto-phosphorylated and inhibit the activity of the kinase. Here we have investigated the effect of auto-phosphorylation of the C-terminus in the kinase CK1δ and show that it slows down phosphorylation of the first two sites in TAp63α but basically inhibits the phosphorylation of the third site. We have identified up to ten auto-phosphorylation sites in the CK1δ C-terminal domain and show that all of them interact with the kinase domain in a “fuzzy” way in which not a single site is particularly important. Through mutation analysis we further show that hydrophobic amino acids following the phosphorylation site are important for a substrate to be able to successfully compete with the auto-inhibitory effect of the C-terminal domain. This auto-phosphorylation adds a new layer to the regulation of apoptosis in oocytes.
Discovery of a cystathionine γ-lyase (CSE) selective inhibitor targeting active-site pyridoxal 5′-phosphate (PLP) via Schiff base formation
Authors: Echizen Honami , Hanaoka Kenjiro , Shimamoto Kazuhito , Hibi Ryota , Toma-Fukai Sachiko , Ohno Hisashi , Sasaki Eita , Komatsu Toru , Ueno Tasuku , Tsuchiya Yukihiro , Watanabe Yasuo , Otsuka Takao , Saito Hiroaki , Nagatoishi Satoru , Tsumoto Kouhei , Kojima Hirotatsu , Okabe Takayoshi , Shimizu Toshiyuki , Urano Yasuteru
Published: September 2023

D,L-Propargylglycine (PAG) has been widely used as a selective inhibitor to investigate the biological functions of cystathionine γ-lyase (CSE), which catalyzes the formation of reactive sulfur species (RSS). However, PAG also inhibits other PLP (pyridoxal-5′-phosphate)-dependent enzymes such as methionine γ-lyase (MGL) and L-alanine transaminase (ALT), so highly selective CSE inhibitors are still required. Here, we performed high-throughput screening (HTS) of a large chemical library and identified oxamic hydrazide 1 as a potent inhibitor of CSE (IC50 = 13 ± 1 μM (mean ± S.E.)) with high selectivity over other PLP-dependent enzymes and RSS-generating enzymes. Inhibitor 1 inhibited the enzymatic activity of human CSE in living cells, indicating that it is sufficiently membrane-permeable. X-Ray crystal structure analysis of the complex of rat CSE (rCSE) with 1 revealed that 1 forms a Schiff base linkage with the cofactor PLP in the active site of rCSE. PLP in the active site may be a promising target for development of selective inhibitors of PLP-dependent enzymes, including RSS-generating enzymes such as cystathionine β-synthase (CBS) and cysteinyl-tRNA synthetase 2 (CARS2), which have unique substrate binding pocket structures.
Concomitant dual-site tDCS and dark chocolate improve cognitive and endurance performance following cognitive effort under hypoxia: a randomized controlled trial
Authors: Banaei Parisa , Tadibi Vahid , Amiri Ehsan , Machado Daniel Gomes da Silva
Published: September 2023

Ten male cyclists were randomized into four experimental conditions in this randomized, cross-over, double-blind, and sham-controlled study to test the combined effect of acute dark chocolate (DC) ingestion and anodal concurrent dual-site transcranial direct current stimulation (a-tDCS) targeting M1 and left DLPFC on cognitive and whole-body endurance performance in hypoxia after performing a cognitive task. Two hours before the sessions, chocolate was consumed. After arriving at the lab, participants completed an incongruent Stroop task for 30 min in hypoxia (O2 = 13%) to induce mental fatigue, followed by 20 min of tDCS (2 mA) in hypoxia. Then, in hypoxia, they performed a time-to-exhaustion task (TTE) while measuring physiological and psychophysiological responses. Cognitive performance was measured at baseline, after the Stroop task, and during and after TTE. TTE in ‘DC + a-tDCS’ was significantly longer than in ‘white chocolate (WC) + a-tDCS’ and WC + sham-tDCS’. The vastus medialis muscle electromyography amplitude was significantly higher in ‘DC + a-tDCS’ and ‘DC + sham-tDCS’ than in ‘WC + sh-tDCS’. During and after the TTE, choice reaction time was significantly lower in ‘DC + a-tDCS’ compared to ‘WC + sh-tDCS’. Other physiological or psychophysiological variables showed no significant differences. The concurrent use of acute DC consumption and dual-site a-tDCS might improve cognitive and endurance performance in hypoxia.
Morphological analysis of descending tracts in mouse spinal cord using tissue clearing, tissue expansion and tiling light sheet microscopy techniques
Authors: Xie Jiongfang , Feng Ruili , Chen Yanlu , Gao Liang
Published: September 2023

Descending tracts carry motor signals from the brain to spinal cord. However, few previous studies show the full view of the long tracts from a 3D perspective. In this study, we have followed five less well-known tracts that project from midbrain, hindbrain, and cerebellum to the mouse spinal cord, using the tissue clearing method in combination with tiling light sheet microscopy. By tracing axons in spinal cord, we found several notable features: among the five tracts the collateral "sister" branches occurred only in the axons originating from the cerebellospinal tracts; the axons from the spinal trigeminal nucleus crossed the midline of spinal cord to the contralateral side; those arising in the medullary reticular formation ventral part gave many branches in both cervical and lumbar segments; the axons from superior colliculus terminated only at upper cervical but with abundant branches in the hindbrain. Furthermore, we investigated the monosynaptic connections between the tracts and motor neurons in the spinal cord through hydrogel-based tissue expansion, and found several monosynaptic connections between the medullary reticular formation ventral part axons and spinal motor neurons. We believe that this is the first study to show the full 3D scope of the projection patterns and axonal morphologies of these five descending tracts to the mouse spinal cord. In addition, we have developed a new method for future study of descending tracts by three-dimensional imaging.
Genetic contributions to brain serotonin transporter levels in healthy adults
Authors: Bruzzone Silvia Elisabetta Portis , Nasser Arafat , Aripaka Sagar Sanjay , Spies Marie , Ozenne Brice , Jensen Peter Steen , Knudsen Gitte Moos , Frokjaer Vibe Gedsoe , Fisher Patrick MacDonald
Published: September 2023

The serotonin transporter (5-HTT) critically shapes serotonin neurotransmission by regulating extracellular brain serotonin levels; it remains unclear to what extent 5-HTT levels in the human brain are genetically determined. Here we applied [11C]DASB positron emission tomography to image brain 5-HTT levels and evaluated associations with five common serotonin-related genetic variants that might indirectly regulate 5-HTT levels (BDNF rs6265, SLC6A4 5-HTTLPR, HTR1A rs6295, HTR2A rs7333412, and MAOA rs1137070) in 140 healthy volunteers. In addition, we explored whether these variants could predict in vivo 5-HTT levels using a five-fold cross-validation random forest framework. MAOA rs1137070 T-carriers showed significantly higher brain 5-HTT levels compared to C-homozygotes (2–11% across caudate, putamen, midbrain, thalamus, hippocampus, amygdala and neocortex). We did not observe significant associations for the HTR1A rs6295 and HTR2A rs7333412 genotypes. Our previously observed lower subcortical 5-HTT availability for rs6265 met-carriers remained in the presence of these additional variants. Despite this significant association, our prediction models showed that genotype moderately improved prediction of 5-HTT in caudate, but effects were not statistically significant after adjustment for multiple comparisons. Our observations provide additional evidence that serotonin-related genetic variants modulate adult human brain serotonin neurotransmission.
Feasibility and safety of uniportal thoracoscopy for chronic pulmonary aspergillosis
Authors: Wang Bing , Yao Li , Sheng Jian , Liu Xiaoyu , Jiang Yuhui , Shen Lei , Xu Feng , Liu Qibin , Gao Chao , Dai Xiyong
Published: September 2023

Surgery plays a crucial role in the treatment of patients with chronic pulmonary aspergillosis (CPA). However, there is currently limited information available regarding the use of uniportal thoracoscopy (Uni-VATS) in CPA patients. To address this gap, we conducted a retrospective analysis of surgical procedures performed at a single center, aiming to demonstrate the feasibility and safety of Uni-VATS for patients with CPA. We collected basic information and surgical data from patients who underwent surgery for CPA at our hospital between January 2018 and June 2022. All patients received voriconazole antifungal medication for 3–6 months post-surgery and were monitored for a minimum of 6 months. A total of 110 patients, comprising 59 cases in the traditional open chest incision group and 51 cases in the Uni-VATS group, met the inclusion criteria. Among those who underwent surgery, 70% were male (77/110). The median age (IQR) of all enrolled patients was 55 (46–62) years. There were no statistically significant differences in general information, such as age, sex, comorbidities, BMI, FEV1, FVC, clinical symptoms, location of the disease, and duration of voriconazole antifungal medication, between the OS group and the Uni-VATS group (p > 0.05). The postoperative complication rates were 40.7% (24/59) for the traditional open chest incision group and 17.6% (9/51) for the Uni-VATS group. Through univariate analysis, we identified sex and operative approach as risk factors for postoperative complications. Multivariate logistic analysis confirmed that male and OS procedures were the independent risk factors for postoperative complications. There were statistically significant differences in operative time, intraoperative blood loss volume, postoperative drainage volume, pain scores, postoperative drainage tube removal time, postoperative hospital stay time between the OS group and the Uni-VATS group (p < 0.05). Uni-VATS is a feasible and safe surgical procedure for patients with CPA, and we recommend it as a preferred option for selected patients with CPA.
Estimating residual undifferentiated cells in human chemically induced pluripotent stem cell derived islets using lncRNA as biomarkers
Authors: Wu Yandan , Zhang Zhenzhen , Wu Shuangshuang , Chen Zhaolong , Pu Yue
Published: September 2023

Human pluripotent stem cells (hPSCs) can generate insulin-producing beta cells for diabetes treatment, but residual undifferentiated cells may cause tumors. We developed a highly sensitive assay to detect these cells in islet cells derived from human chemically induced pluripotent stem cells (hCiPSCs), which are transgene-free and safer. We used RNA-seq data to find protein-coding and non-coding RNAs that were only expressed in hCiPSCs, not in islet cells. We confirmed these biomarkers by RT-qPCR and ddPCR. We chose long non-coding RNA (lncRNA) markers, which performed better than protein-coding RNA markers. We found that LNCPRESS2, LINC00678 and LOC105370482 could detect 1, 1 and 3 hCiPSCs in 106 islet cells by ddPCR, respectively. We tested our method on several hCiPSC lines, which could quantify 0.0001% undifferentiated cell in 106 islet cells by targeting hCiPSCs-specific lncRNA transcripts, ensuring the safety and quality of hCiPSC-derived islet cells for clinical use.
Highly efficient visible light active ZnO/Cu-DPA composite photocatalysts for the treatment of wastewater contaminated with organic dye
Authors: Berehe Biniyam Abdu , Assen Ayalew H. , Kumar A. Santhana Krishna , Ulla Hidayath , Duma Alemayehu Dubale , Chang Jia-Yaw , Gedda Gangaraju , Girma Wubshet Mekonnen
Published: September 2023

Industrial effluents are a leading major threat for water contamination, subsequently which results in severe health associated risks. Hence, purifying wastewater before releasing into the water resources is essential to avoid contamination. In this study, ZnO/Cu-DPA nano-composites were prepared by altering the percentage of Cu-DPA (20%, 30%, 40%, and 50% which are denoted to be ZnO/20%Cu-DPA, ZnO/30%Cu-DPA, ZnO/40%Cu-DPA and ZnO/50%Cu-DPA) using a simple mechanical grinding process. Several spectroscopic studies were employed such as electron paramagnetic analysis (EPR), powdered X-ray diffractometer (PXRD), UV–Vis absorbance spectroscopy, Fourier transform infrared (FT-IR) spectroscopy and scanning electron microscope to characterize these nano-composites. The photo-catalytic activities of the prepared nano-composites were studied by degrading MB under visible light irradiation. ZnO, ZnO/20%Cu-DPA, ZnO/30%Cu-DPA, ZnO/40%Cu-DPA and ZnO/50%Cu-DPA degradation efficiencies were determined to be 71.8, 78.5, 77.1, and 66.1%, respectively. Among the composite catalysts, the ZnO/20%Cu-DPA coupled system are demonstrated the best efficiency (87%) for photo-degradation of MB within 80 min when exposed to visible light. The ZnO/Cu-DPA nano-composites had a greater MB photodegradation efficiency than pristine ZnO owing to p-n heterojunction in the linked system. Under visible light irradiation, the ZnO/20%Cu-DPA catalysed the conversion of dissolved O2 to hydroxyl radicals (OH·), triggering the reduction of MB. This suggests that ·OH is the primary specific active radical involved in the photo-catalytic decomposition of MB. Furthermore, EPR analysis indicates the existence of ·OH in the photo-catalytic system. The proposed nano-composites (ZnO/20%Cu-DPA) reusability was investigated across three cycles as the most efficient photo-catalyst. The results show that, the ZnO/Cu-DPA nano-catalyst is a potential candidate for the remediation of dirty water.
A possible role for proinflammatory activation via cGAS-STING pathway in atherosclerosis induced by accumulation of DNA double-strand breaks
Authors: Sakai Chiemi , Ueda Keitaro , Goda Kohei , Fujita Rikuto , Maeda Junji , Nakayama Shinya , Sotomaru Yusuke , Tashiro Satoshi , Yoshizumi Masao , Ishida Takafumi , Ishida Mari
Published: September 2023

DNA damage contributes to atherosclerosis. However, causative links between DNA double-strand breaks (DSBs) and atherosclerosis have yet to be established. Here, we investigated the role of DSBs in atherosclerosis using mice and vascular cells deficient in Ku80, a DSB repair protein. After 4 weeks of a high-fat diet, Ku80-deficient apolipoprotein E knockout mice (Ku80+/−ApoE−/−) displayed increased plaque size and DSBs in the aorta compared to those of ApoE−/− control. In the preatherosclerotic stages (two-week high-fat diet), the plaque size was similar in both the Ku80+/−ApoE−/− and ApoE−/− control mice, but the number of DSBs and mRNA levels of inflammatory cytokines such as IL-6 and MCP-1 were significantly increased in the Ku80+/−ApoE−/− aortas. We further investigated molecular links between DSBs and inflammatory responses using vascular smooth muscle cells isolated from Ku80 wild-type and Ku80+/− mice. The Ku80+/− cells displayed senescent features and elevated levels of inflammatory cytokine mRNAs. Moreover, the cytosolic DNA-sensing cGAS-STING pathway was activated in the Ku80+/− cells. Inhibiting the cGAS-STING pathway reduced IL-6 mRNA level. Notably, interferon regulatory factor 3 (IRF3), a downstream effector of the cGAS-STING pathway, was activated, and the depletion of IRF3 also reduced IL-6 mRNA levels in the Ku80+/− cells. Finally, DSBs accumulation in normal cells also activated the cGAS-STING-IRF3 pathway. In addition, cGAS inhibition attenuated DNA damage-induced IL-6 expression and cellular senescence in these cells. These results suggest that DSBs accumulation promoted atherosclerosis by upregulating proinflammatory responses and cellular senescence via the cGAS-STING (-IRF3) pathway.
Key to ENSO phase-locking simulation: effects of sea surface temperature diurnal amplitude
Authors: Yang Xiaodan , Bao Ying , Song Zhenya , Shu Qi , Song Yajuan , Wang Xin , Qiao Fangli
Published: September 2023

The tendency of El Niño/Southern Oscillation (ENSO) events to peak during boreal winter is known as ENSO phase-locking, whose accurate simulation is essential for ENSO prediction. However, the simulated peaks of ENSO events usually occur outside boreal winter in state-of-the-art climate models. Based on the Coupled Model Intercomparison Project Phase 6 (CMIP6) models, the model with a more reasonable diurnal amplitude (DA) in the sea surface temperature (SST) had a better simulation ability for ENSO phase-locking compared with other models. Further experiments based on the earth system model revealed that the DA is vital for ENSO phase-locking simulation primarily due to the spatial inhomogeneities in seasonal DA anomaly variations in ENSO years with positive/negative DA anomalies in the central equatorial Pacific and negative/positive in the western or eastern Pacific during El Niño/La Niña. Our findings indicate that DA simulation in climate models is crucial for resolving the long-standing failure associated with the ENSO phase-locking simulation accuracy.
Downscaling and bias-correction contribute considerable uncertainty to local climate projections in CMIP6
Authors: Lafferty David C. , Sriver Ryan L.
Published: September 2023

Efforts to diagnose the risks of a changing climate often rely on downscaled and bias-corrected climate information, making it important to understand the uncertainties and potential biases of this approach. Here, we perform a variance decomposition to partition uncertainty in global climate projections and quantify the relative importance of downscaling and bias-correction. We analyze simple climate metrics such as annual temperature and precipitation averages, as well as several indices of climate extremes. We find that downscaling and bias-correction often contribute substantial uncertainty to local decision-relevant climate outcomes, though our results are strongly heterogeneous across space, time, and climate metrics. Our results can provide guidance to impact modelers and decision-makers regarding the uncertainties associated with downscaling and bias-correction when performing local-scale analyses, as neglecting to account for these uncertainties may risk overconfidence relative to the full range of possible climate futures.
Slow magnetic relaxation in 8-coordinate Mn(ii) compounds
Authors: Wang Li-Xin , Wu Xiao-Fan , Jin Xin-Xin , Li Jia-Yi , Wang Bing-Wu , Liu Ji-Yan , Xiang Jing , Gao Song
Published: September 2023

Four mononuclear 8-coordinate Mn(ii) compounds have been obtained and all the compounds show field-induced slow magnetic relaxation (SMR) behaviors.
Using slow sand filter for organic matter and suspended solids removal as post-treatment unit for wastewater effluent
Authors: Alnahhal Samir Y. , Elfari Amany A. , Afifi Samir A. , Aljubb Alaa Edden R.
Published: September 2023

Certain applications of wastewater after treatment necessitate the implementation of a post-treatment system (PTS) to elevate effluent quality, especially in cases where human exposure, such as irrigation, is a possibility.
Comparison of different coagulants to improve membrane distillation performance for landfill leachate concentrate treatment
Authors: Xia Ruohan , Liu Wancen , Cao Dingge , Wang Ning , Li Guoxue , Nghiem Long D. , Luo Wenhai
Published: September 2023

This study investigated the impacts of different coagulants on the performance of membrane distillation (MD) for landfill leachate concentrate treatment.
Assessing weight loss control strategies in pomegranate (Punica granatum L.) fruit: plastic packaging and surface waxing
Authors: Lufu Robert , Ambaw Alemayehu , Opara Umezuruike Linus
Published: September 2023

Covering fresh fruit with sustainable edible coating, even by dipping at the top end or bottom end alone, provided significant reduction of weight loss.
Covalent organic frameworks confining ultra-dense hydrated hydrogen-bond networks for efficient intrinsic proton conduction
Authors: Zhu Ruo-Meng , Fu Jia-Xing , Chen Liang-Hui , Feng Jing-Dong , Gu Zhi-Guo
Published: September 2023

Preinstalling proton donor groups in covalent organic frameworks to confine dense hydrated hydrogen-bond networks enables efficient intrinsic proton conduction.
Fundamental difference between simple arenes and PAHs found in o-PAH-connected porphyrins
Authors: Ko Min-Sung , Hong Jung-Ho , Desale Pradeep P. , Roh Tae-Ho , Cho Dong-Gyu
Published: September 2023

Simple arenes and PAHs are distinguishable, but identifying their unique differences poses a challenge. This manuscript reveals, for the first time, how these differences manifest in global aromaticity within porphyrinoids.
Nitrenium ions as new versatile reagents for electrophilic amination
Authors: Avigdori Idan , Singh Kuldeep , Fridman Natalia , Gandelman Mark
Published: September 2023

Bench-stable N-heterocyclic nitrenium ions were used for the efficient electrophilic amination of organometallic nucleophiles. The previously unexplored N-alkyl/aryl triazane intermediates were reduced to produce a diverse scope of primary amines.
3D flower-like CuO@NiAl-LDH microspheres with enhanced removal affinity to organic dyes: mechanistic insights, DFT calculations and toxicity assessment
Authors: Chen Yao , Lian Honglin , Wang Hao , Qin Jun , Chen Xiaolang , Lu Zongcheng
Published: September 2023

Highly efficient removal of organic dyes in wastewater is attracting more and more attention.
Recent advances in the construction and application of stretchable PEDOT smart electronic membranes
Authors: Chen Jiahua , Ye Chunfa , Cang Tianyu , Gao Rui , Li Xiaoyan
Published: September 2023

A comprehensive overview of stretchable PEDOT membranes for smart electronics, including stretchable structures, preparation strategies and recent applications.
Platinum-adsorbed defective 2D monolayer boron nitride: a promising electrocatalyst for O2 reduction reaction
Authors: Yadav Lokesh , Pakhira Srimanta
Published: September 2023

Hexagonal boron nitride (hBN) has long been thought to be chemically inert due to its wide bandgap and strong covalent bonds.
Probing cosmic ray escape from η Carinae
Authors: Steinmassl S. , Breuhaus M. , White R. , Reville B. , Hinton J. A.
Published: September 2023

The binary stellar system η Carinae is one of very few established astrophysical hadron accelerators. It seems likely that at least some fraction of the particles accelerated by η Carinae escape from the system. Copious target material for hadronic interactions and associated γ-ray emission exist on a wide range of spatial scales outside the binary system. This material creates a unique opportunity to trace the propagation of particles into the interstellar medium. In this work, we analyse γ-ray data from Fermi-LAT of η Carinae and surrounding molecular clouds and investigate the many different scales on which escaping particles may interact and produce γ-rays. We find that interactions of escaping cosmic rays from η Carinae in the wind region and the Homunculus Nebula could produce a significant contribution to the γ-ray emission associated with the system. Furthermore, we detect excess emission from the surrounding molecular clouds. The derived radial cosmic-ray excess profile is consistent with a steady injection of cosmic rays by a central source. However, this would require a higher flux of escaping cosmic rays from η Carinae than provided by our model. Therefore, it is likely that additional cosmic ray sources contribute to the hadronic γ-ray emission from the clouds.
ChatGPT and the rise of semi-humans
Authors: Al Lily Abdulrahman Essa , Ismail Abdelrahim Fathy , Abunaser Fathi M. , Al-Lami Firass , Abdullatif Ali Khalifa Atwa
Published: September 2023

This article explores the research question: ‘What are ChatGPT’s human-like traits as perceived by society?’ Thematic analyses of insights from 452 individuals worldwide yielded two categories of traits. Category 1 entails social traits, where ChatGPT embodies the social roles of ‘author’ (imitating human phrasing and paraphrasing practices) and ‘interactor’ (simulating human collaboration and emotion). Category 2 encompasses political traits, with ChatGPT assuming the political roles of ‘agent’ (emulating human cognition and identity) and ‘influencer’ (mimicking human diplomacy and consultation). When asked, ChatGPT confirmed the possession of these human-like traits (except for one trait). Thus, ChatGPT displays human-like qualities, humanising itself through the ‘game of algorithms’. It transcends its inherent technical essence and machine-based origins to manifest as a ‘semi-human’ living actor within human society, showcasing the emergence of semi-humans. Therefore, researchers should redirect their attention towards the ‘sociology of semi-humans’ (studying their socio-political traits) beyond the ‘biology of semi-humans’ (examining their technical traits). While medieval society was captivated by mythical semi-human beings (e.g. mermaids), modern society finds itself increasingly captivated by computational semi-human beings like ChatGPT. Ethical concerns arise as semi-humans impersonate human traits without consent or genuine human existence, blurring the boundaries between what is authentically and artificially ‘human’.