bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the Deep Carbon Release in an Active Volcanic Field Using Hydrochemistry, δ13CDIC and Δ14CDIC
Authors: Zhong Jun , Wang Linan , Caracausi Antonio , Galy Albert , Li Si‐Liang , Wang Wanfa , Zhang Maoliang , Liu Cong‐Qiang , Liu Guo‐Ming , Xu Sheng
Published: April 2023

Volcanic activities have great implications on the geological carbon cycle, and ascertaining the deep carbon contribution in the Earth's surface that runs along the volcanic edifices is important to understand the relationship between solid Earth degassing and global climate change. This study reports analytical results of major dissolved ions concentrations, carbon isotopic compositions (δ13CDIC and Δ14CDIC) of dissolved inorganic carbon (DIC) of rivers, cold springs, and hot springs from Changbaishan volcanic area, Northeast China. The hydrothermal fluids had a significant impact on solutes budgets, as well as carbon isotopes for the rivers. The changes in concentrations of major ions are mainly controlled by mixing of high‐temperature water/rock interaction and low‐temperature water/rock interaction, and low‐temperature water/rock interaction can be explained by the change of chemical composition between volcanic cone (trachyte) and basaltic shield. Because Δ14CDIC is conservative to CO2 outgassing, we used Δ14CDIC to figure out the contributions of deep carbon and surface carbon. While δ13CDIC is sensitive to CO2 outgassing, we thus estimated the minimum deep CO2 outgassing yield (1.24 × 104 t C yr−1) based on DIC flux corrected for outgassing by a Rayleigh model. In the Changbaishan volcanic area, deep carbon release flux was higher than CO2 consumption flux by silicate weathering, while the deep CO2 outgassing flux was an underestimate, consistent with the hypothesis that deep CO2 release regulates climate on geological timescales. This study calls for a better understanding of the effects of volcanic activities on Earth's surface carbon cycling, which has great implications on studying global climate change.
The KMT2A recombinome of acute leukemias in 2023
Authors: Meyer C. , Larghero P. , Almeida Lopes B. , Burmeister T. , Gröger D. , Sutton R. , Venn N. C. , Cazzaniga G. , Corral Abascal L. , Tsaur G. , Fechina L. , Emerenciano M. , Pombo-de-Oliveira M. S. , Lund-Aho T. , Lundán T. , Montonen M. , Juvonen V. , Zuna J. , Trka J. , Ballerini P. , Lapillonne H. , Van der Velden V. H. J. , Sonneveld E. , Delabesse E. , de Matos R. R. C. , Silva M. L. M. , Bomken S. , Katsibardi K. , Keernik M. , Grardel N. , Mason J. , Price R. , Kim J. , Eckert C. , Lo Nigro L. , Bueno C. , Menendez P. , zur Stadt U. , Gameiro P. , Sedék L. , Szczepański T. , Bidet A. , Marcu V. , Shichrur K. , Izraeli S. , Madsen H. O. , Schäfer B. W. , Kubetzko S. , Kim R. , Clappier E. , Trautmann H. , Brüggemann M. , Archer P. , Hancock J. , Alten J. , Möricke A. , Stanulla M. , Lentes J. , Bergmann A. K. , Strehl S. , Köhrer S. , Nebral K. , Dworzak M. N. , Haas O. A. , Arfeuille C. , Caye-Eude A. , Cavé H. , Marschalek R.
Published: April 2023

Chromosomal rearrangements of the human KMT2A/MLL gene are associated with de novo as well as therapy-induced infant, pediatric, and adult acute leukemias. Here, we present the data obtained from 3401 acute leukemia patients that have been analyzed between 2003 and 2022. Genomic breakpoints within the KMT2A gene and the involved translocation partner genes (TPGs) and KMT2A-partial tandem duplications (PTDs) were determined. Including the published data from the literature, a total of 107 in-frame KMT2A gene fusions have been identified so far. Further 16 rearrangements were out-of-frame fusions, 18 patients had no partner gene fused to 5’-KMT2A, two patients had a 5’-KMT2A deletion, and one ETV6::RUNX1 patient had an KMT2A insertion at the breakpoint. The seven most frequent TPGs and PTDs account for more than 90% of all recombinations of the KMT2A, 37 occur recurrently and 63 were identified so far only once. This study provides a comprehensive analysis of the KMT2A recombinome in acute leukemia patients. Besides the scientific gain of information, genomic breakpoint sequences of these patients were used to monitor minimal residual disease (MRD). Thus, this work may be directly translated from the bench to the bedside of patients and meet the clinical needs to improve patient survival.
RAF1 contributes to cell proliferation and STAT3 activation in colorectal cancer independently of microsatellite and KRAS status
Authors: Dorard Coralie , Madry Claire , Buhard Olivier , Toifl Stefanie , Didusch Sebastian , Ratovomanana Toky , Letourneur Quentin , Dolznig Helmut , Garnett Mathew J. , Duval Alex , Baccarini Manuela
Published: April 2023

More than 30% of all human cancers are driven by RAS mutations and activating KRAS mutations are present in 40% of colorectal cancer (CRC) in the two main CRC subgroups, MSS (Microsatellite Stable) and MSI (Microsatellite Instable). Studies in RAS-driven tumors have shown essential roles of the RAS effectors RAF and specifically of RAF1, which can be dependent or independent of RAF’s ability to activate the MEK/ERK module. In this study, we demonstrate that RAF1, but not its kinase activity, plays a crucial role in the proliferation of both MSI and MSS CRC cell line-derived spheroids and patient-derived organoids, and independently of KRAS mutation status. Moreover, we could define a RAF1 transcriptomic signature which includes genes that contribute to STAT3 activation, and could demonstrate that RAF1 ablation decreases STAT3 phosphorylation in all CRC spheroids tested. The genes involved in STAT3 activation as well as STAT3 targets promoting angiogenesis were also downregulated in human primary tumors expressing low levels of RAF1. These results indicate that RAF1 could be an attractive therapeutic target in both MSI and MSS CRC regardless of their KRAS status and support the development of selective RAF1 degraders rather than RAF1 inhibitors for clinical use in combination therapies.
The MEF2A transcription factor interactome in cardiomyocytes
Authors: Moustafa Amira , Hashemi Sara , Brar Gurnoor , Grigull Jörg , Ng Siemon H. S. , Williams Declan , Schmitt-Ulms Gerold , McDermott John C.
Published: April 2023

Transcriptional regulators encoded by the Myocyte Enhancer Factor 2 (MEF2) gene family play a fundamental role in cardiac development, homeostasis and pathology. Previous studies indicate that MEF2A protein-protein interactions serve as a network hub in several cardiomyocyte cellular processes. Based on the idea that interactions with regulatory protein partners underly the diverse roles of MEF2A in cardiomyocyte gene expression, we undertook a systematic unbiased screen of the MEF2A protein interactome in primary cardiomyocytes using an affinity purification-based quantitative mass spectrometry approach. Bioinformatic processing of the MEF2A interactome revealed protein networks involved in the regulation of programmed cell death, inflammatory responses, actin dynamics and stress signaling in primary cardiomyocytes. Further biochemical and functional confirmation of specific protein-protein interactions documented a dynamic interaction between MEF2A and STAT3 proteins. Integration of transcriptome level data from MEF2A and STAT3-depleted cardiomyocytes reveals that the balance between MEF2A and STAT3 activity exerts a level of executive control over the inflammatory response and cardiomyocyte cell survival and experimentally ameliorates Phenylephrine induced cardiomyocyte hypertrophy. Lastly, we identified several MEF2A/STAT3 co-regulated genes, including the MMP9 gene. Herein, we document the cardiomyocyte MEF2A interactome, which furthers our understanding of protein networks involved in the hierarchical control of normal and pathophysiological cardiomyocyte gene expression in the mammalian heart.
Aberrant RNA m6A modification in gastrointestinal malignancies: versatile regulators of cancer hallmarks and novel therapeutic opportunities
Authors: Shen Li-Ting , Che Lin-Rong , He Zongsheng , Lu Qian , Chen Dong-Feng , Qin Zhong-yi , Wang Bin
Published: April 2023

Gastrointestinal (GI) cancer is one of the most common malignancies, and a leading cause of cancer-related death worldwide. However, molecular targeted therapies are still lacking, leading to poor treatment efficacies. As an important layer of epigenetic regulation, RNA N6-Methyladenosine (m6A) modification is recently linked to various biological hallmarks of cancer by orchestrating RNA metabolism, including RNA splicing, export, translation, and decay, which is partially involved in a novel biological process termed phase separation. Through these regulatory mechanisms, m6A dictates gene expression in a dynamic and reversible manner and may play oncogenic, tumor suppressive or context-dependent roles in GI tumorigenesis. Therefore, regulators and effectors of m6A, as well as their modified substrates, represent a novel class of molecular targets for cancer treatments. In this review, we comprehensively summarize recent advances in this field and highlight research findings that documented key roles of RNA m6A modification in governing hallmarks of GI cancers. From a historical perspective, milestone findings in m6A machinery are integrated with a timeline of developing m6A targeting compounds. These available chemical compounds, as well as other approaches that target core components of the RNA m6A pathway hold promises for clinical translational to treat human GI cancers. Further investigation on several outstanding issues, e.g. how oncogenic insults may disrupt m6A homeostasis, and how m6A modification impacts on the tumor microenvironment, may dissect novel mechanisms underlying human tumorigenesis and identifies next-generation anti-cancer therapeutics.
Well-TEMP-seq as a microwell-based strategy for massively parallel profiling of single-cell temporal RNA dynamics
Authors: Lin Shichao , Yin Kun , Zhang Yingkun , Lin Fanghe , Chen Xiaoyong , Zeng Xi , Guo Xiaoxu , Zhang Huimin , Song Jia , Yang Chaoyong
Published: April 2023

Single-cell RNA sequencing (scRNA-seq) reveals the transcriptional heterogeneity of cells, but the static snapshots fail to reveal the time-resolved dynamics of transcription. Herein, we develop Well-TEMP-seq, a high-throughput, cost-effective, accurate, and efficient method for massively parallel profiling the temporal dynamics of single-cell gene expression. Well-TEMP-seq combines metabolic RNA labeling with scRNA-seq method Well-paired-seq to distinguish newly transcribed RNAs marked by T-to-C substitutions from pre-existing RNAs in each of thousands of single cells. The Well-paired-seq chip ensures a high single cell/barcoded bead pairing rate (~80%) and the improved alkylation chemistry on beads greatly alleviates chemical conversion-induced cell loss (~67.5% recovery). We further apply Well-TEMP-seq to profile the transcriptional dynamics of colorectal cancer cells exposed to 5-AZA-CdR, a DNA-demethylating drug. Well-TEMP-seq unbiasedly captures the RNA dynamics and outperforms the splicing-based RNA velocity method. We anticipate that Well-TEMP-seq will be broadly applicable to unveil the dynamics of single-cell gene expression in diverse biological processes.
Structural mechanism of a drug-binding process involving a large conformational change of the protein target
Authors: Ayaz Pelin , Lyczek Agatha , Paung YiTing , Mingione Victoria R. , Iacob Roxana E. , de Waal Parker W. , Engen John R. , Seeliger Markus A. , Shan Yibing , Shaw David E.
Published: April 2023

Proteins often undergo large conformational changes when binding small molecules, but atomic-level descriptions of such events have been elusive. Here, we report unguided molecular dynamics simulations of Abl kinase binding to the cancer drug imatinib. In the simulations, imatinib first selectively engages Abl kinase in its autoinhibitory conformation. Consistent with inferences drawn from previous experimental studies, imatinib then induces a large conformational change of the protein to reach a bound complex that closely resembles published crystal structures. Moreover, the simulations reveal a surprising local structural instability in the C-terminal lobe of Abl kinase during binding. The unstable region includes a number of residues that, when mutated, confer imatinib resistance by an unknown mechanism. Based on the simulations, NMR spectra, hydrogen-deuterium exchange measurements, and thermostability measurements and estimates, we suggest that these mutations confer imatinib resistance by exacerbating structural instability in the C-terminal lobe, rendering the imatinib-bound state energetically unfavorable.
Localized nuclear reaction breaks boron drug capsules loaded with immune adjuvants for cancer immunotherapy
Authors: Shi Yaxin , Guo Zhibin , Fu Qiang , Shen Xinyuan , Zhang Zhongming , Sun Wenjia , Wang Jinqiang , Sun Junliang , Zhang Zizhu , Liu Tong , Gu Zhen , Liu Zhibo
Published: April 2023

Boron neutron capture therapy (BNCT) was clinically approved in 2020 and exhibits remarkable tumour rejection in preclinical and clinical studies. It is binary radiotherapy that may selectively deposit two deadly high-energy particles (4He and 7Li) within a cancer cell. As a radiotherapy induced by localized nuclear reaction, few studies have reported its abscopal anti-tumour effect, which has limited its further clinical applications. Here, we engineer a neutron-activated boron capsule that synergizes BNCT and controlled immune adjuvants release to provoke a potent anti-tumour immune response. This study demonstrates that boron neutron capture nuclear reaction forms considerable defects in boron capsule that augments the drug release. The following single-cell sequencing unveils the fact and mechanism that BNCT heats anti-tumour immunity. In female mice tumour models, BNCT and the controlled drug release triggered by localized nuclear reaction causes nearly complete regression of both primary and distant tumour grafts.
Selection and adaptive introgression guided the complex evolutionary history of the European common bean
Authors: Bellucci Elisa , Benazzo Andrea , Xu Chunming , Bitocchi Elena , Rodriguez Monica , Alseekh Saleh , Di Vittori Valerio , Gioia Tania , Neumann Kerstin , Cortinovis Gaia , Frascarelli Giulia , Murube Ester , Trucchi Emiliano , Nanni Laura , Ariani Andrea , Logozzo Giuseppina , Shin Jin Hee , Liu Chaochih , Jiang Liang , Ferreira Juan José , Campa Ana , Attene Giovanna , Morrell Peter L. , Bertorelle Giorgio , Graner Andreas , Gepts Paul , Fernie Alisdair R. , Jackson Scott A. , Papa Roberto
Published: April 2023

Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro’s expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.
Structure and function of the metagenomic plastic-degrading polyester hydrolase PHL7 bound to its product
Authors: Richter P. Konstantin , Blázquez-Sánchez Paula , Zhao Ziyue , Engelberger Felipe , Wiebeler Christian , Künze Georg , Frank Ronny , Krinke Dana , Frezzotti Emanuele , Lihanova Yuliia , Falkenstein Patricia , Matysik Jörg , Zimmermann Wolfgang , Sträter Norbert , Sonnendecker Christian
Published: April 2023

The recently discovered metagenomic-derived polyester hydrolase PHL7 is able to efficiently degrade amorphous polyethylene terephthalate (PET) in post-consumer plastic waste. We present the cocrystal structure of this hydrolase with its hydrolysis product terephthalic acid and elucidate the influence of 17 single mutations on the PET-hydrolytic activity and thermal stability of PHL7. The substrate-binding mode of terephthalic acid is similar to that of the thermophilic polyester hydrolase LCC and deviates from the mesophilicIsPETase. The subsite I modifications L93F and Q95Y, derived from LCC, increased the thermal stability, while exchange of H185S, derived fromIsPETase, reduced the stability of PHL7. The subsite II residue H130 is suggested to represent an adaptation for high thermal stability, whereas L210 emerged as the main contributor to the observed high PET-hydrolytic activity. Variant L210T showed significantly higher activity, achieving a degradation rate of 20 µm h−1with amorphous PET films.
Lunar eclipses illuminate timing and climate impact of medieval volcanism
Authors: Guillet Sébastien , Corona Christophe , Oppenheimer Clive , Lavigne Franck , Khodri Myriam , Ludlow Francis , Sigl Michael , Toohey Matthew , Atkins Paul S. , Yang Zhen , Muranaka Tomoko , Horikawa Nobuko , Stoffel Markus
Published: April 2023

Explosive volcanism is a key contributor to climate variability on interannual to centennial timescales1. Understanding the far-field societal impacts of eruption-forced climatic changes requires firm event chronologies and reliable estimates of both the burden and altitude (that is, tropospheric versus stratospheric) of volcanic sulfate aerosol2,3. However, despite progress in ice-core dating, uncertainties remain in these key factors4. This particularly hinders investigation of the role of large, temporally clustered eruptions during the High Medieval Period (HMP, 1100–1300 ce), which have been implicated in the transition from the warm Medieval Climate Anomaly to the Little Ice Age5. Here we shed new light on explosive volcanism during the HMP, drawing on analysis of contemporary reports of total lunar eclipses, from which we derive a time series of stratospheric turbidity. By combining this new record with aerosol model simulations and tree-ring-based climate proxies, we refine the estimated dates of five notable eruptions and associate each with stratospheric aerosol veils. Five further eruptions, including one responsible for high sulfur deposition over Greenland circa 1182 ce, affected only the troposphere and had muted climatic consequences. Our findings offer support for further investigation of the decadal-scale to centennial-scale climate response to volcanic eruptions.
mRNA decoding in human is kinetically and structurally distinct from bacteria
Authors: Holm Mikael , Natchiar S. Kundhavai , Rundlet Emily J. , Myasnikov Alexander G. , Watson Zoe L. , Altman Roger B. , Wang Hao-Yuan , Taunton Jack , Blanchard Scott C.
Published: April 2023

In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems1. Although key features are conserved across evolution2, eukaryotes achieve higher-fidelity mRNA decoding than bacteria3. In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment4–6. Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species.
De novo design of modular peptide-binding proteins by superhelical matching
Authors: Wu Kejia , Bai Hua , Chang Ya-Ting , Redler Rachel , McNally Kerrie E. , Sheffler William , Brunette T. J. , Hicks Derrick R. , Morgan Tomos E. , Stevens Tim J. , Broerman Adam , Goreshnik Inna , DeWitt Michelle , Chow Cameron M. , Shen Yihang , Stewart Lance , Derivery Emmanuel , Silva Daniel Adriano , Bhabha Gira , Ekiert Damian C. , Baker David
Published: April 2023

General approaches for designing sequence-specific peptide-binding proteins would have wide utility in proteomics and synthetic biology. However, designing peptide-binding proteins is challenging, as most peptides do not have defined structures in isolation, and hydrogen bonds must be made to the buried polar groups in the peptide backbone1–3. Here, inspired by natural and re-engineered protein–peptide systems4–11, we set out to design proteins made out of repeating units that bind peptides with repeating sequences, with a one-to-one correspondence between the repeat units of the protein and those of the peptide. We use geometric hashing to identify protein backbones and peptide-docking arrangements that are compatible with bidentate hydrogen bonds between the side chains of the protein and the peptide backbone12. The remainder of the protein sequence is then optimized for folding and peptide binding. We design repeat proteins to bind to six different tripeptide-repeat sequences in polyproline II conformations. The proteins are hyperstable and bind to four to six tandem repeats of their tripeptide targets with nanomolar to picomolar affinities in vitro and in living cells. Crystal structures reveal repeating interactions between protein and peptide interactions as designed, including ladders of hydrogen bonds from protein side chains to peptide backbones. By redesigning the binding interfaces of individual repeat units, specificity can be achieved for non-repeating peptide sequences and for disordered regions of native proteins.
Cryo-EM structure of the transposon-associated TnpB enzyme
Authors: Nakagawa Ryoya , Hirano Hisato , Omura Satoshi N. , Nety Suchita , Kannan Soumya , Altae-Tran Han , Yao Xiao , Sakaguchi Yuriko , Ohira Takayuki , Wu Wen Y. , Nakayama Hiroshi , Shuto Yutaro , Tanaka Tatsuki , Sano Fumiya K. , Kusakizako Tsukasa , Kise Yoshiaki , Itoh Yuzuru , Dohmae Naoshi , van der Oost John , Suzuki Tsutomu , Zhang Feng , Nureki Osamu
Published: April 2023

The class 2 type V CRISPR effector Cas12 is thought to have evolved from the IS200/IS605 superfamily of transposon-associated TnpB proteins1. Recent studies have identified TnpB proteins as miniature RNA-guided DNA endonucleases2,3. TnpB associates with a single, long RNA (ωRNA) and cleaves double-stranded DNA targets complementary to the ωRNA guide. However, the RNA-guided DNA cleavage mechanism of TnpB and its evolutionary relationship with Cas12 enzymes remain unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of Deinococcus radiodurans ISDra2 TnpB in complex with its cognate ωRNA and target DNA. In the structure, the ωRNA adopts an unexpected architecture and forms a pseudoknot, which is conserved among all guide RNAs of Cas12 enzymes. Furthermore, the structure, along with our functional analysis, reveals how the compact TnpB recognizes the ωRNA and cleaves target DNA complementary to the guide. A structural comparison of TnpB with Cas12 enzymes suggests that CRISPR–Cas12 effectors acquired an ability to recognize the protospacer-adjacent motif-distal end of the guide RNA–target DNA heteroduplex, by either asymmetric dimer formation or diverse REC2 insertions, enabling engagement in CRISPR–Cas adaptive immunity. Collectively, our findings provide mechanistic insights into TnpB function and advance our understanding of the evolution from transposon-encoded TnpB proteins to CRISPR–Cas12 effectors.
Umbilical cord-derived mesenchymal stromal cell therapy to prevent the development of neurodevelopmental disorders related to low birth weight
Authors: Tsuji Masahiro , Mukai Takeo , Sato Yoshiaki , Azuma Yasue , Yamamoto Saki , Cayetanot Florence , Bodineau Laurence , Onoda Atsuto , Nagamura-Inoue Tokiko , Coq Jacques-Olivier
Published: April 2023

Low birth weight (LBW) increases the risk of neurodevelopmental disorders (NDDs) such as attention-deficit/hyperactive disorder and autism spectrum disorder, as well as cerebral palsy, for which no prophylactic measure exists. Neuroinflammation in fetuses and neonates plays a major pathogenic role in NDDs. Meanwhile, umbilical cord-derived mesenchymal stromal cells (UC-MSCs) exhibit immunomodulatory properties. Therefore, we hypothesized that systemic administration of UC-MSCs in the early postnatal period may attenuate neuroinflammation and thereby prevent the emergence of NDDs. The LBW pups born to dams subjected to mild intrauterine hypoperfusion exhibited a significantly lesser decrease in the monosynaptic response with increased frequency of stimulation to the spinal cord preparation from postnatal day 4 (P4) to P6, suggesting hyperexcitability, which was improved by intravenous administration of human UC-MSCs (1 × 105 cells) on P1. Three-chamber sociability tests at adolescence revealed that only LBW males exhibited disturbed sociability, which tended to be ameliorated by UC-MSC treatment. Other parameters, including those determined via open-field tests, were not significantly improved by UC-MSC treatment. Serum or cerebrospinal fluid levels of pro-inflammatory cytokines were not elevated in the LBW pups, and UC-MSC treatment did not decrease these levels. In conclusion, although UC-MSC treatment prevents hyperexcitability in LBW pups, beneficial effects for NDDs are marginal.
CLUMondo-BNU for simulating land system changes based on many-to-many demand–supply relationships with adaptive conversion orders
Authors: Gao Peichao , Gao Yifan , Zhang Xiaodan , Ye Sijing , Song Changqing
Published: April 2023

Land resources are fundamentally important to human society, and their transition from one macroscopic state to another is a vital driving force of environment and climate change locally and globally. Thus, many efforts have been devoted to the simulations of land changes. Among all spatially explicit simulation models, CLUMondo is the only one that simulates land changes by incorporating the multifunctionality of a land system and allows the establishment of many-to-many demand–supply relationships. In this study, we first investigated the source code of CLUMondo, providing a complete, detailed mechanism of this model. We found that the featured function of CLUMondo—balancing demands and supplies in a many-to-many mode—relies on a parameter called conversion order. The setting of this parameter is a manual process and requires expert knowledge, which is not feasible for users without an understanding of the whole, detailed mechanism. Therefore, the second contribution of this study is the development of an automatic method for adaptively determining conversion orders. Comparative experiments demonstrated the validity and effectiveness of the proposed automated method. We revised the source code of CLUMondo to incorporate the proposed automated method, resulting in CLUMondo-BNU v1.0. This study facilitates the application of CLUMondo and helps to exploit its full potential.
Research on the community electric carbon emission prediction considering the dynamic emission coefficient of power system
Authors: Yu Hui , Yang Yang , Li Bin , Liu Bowen , Guo Yuanhu , Wang Yunqi , Guo Zhongfu , Meng Ronghua
Published: April 2023

Based on the counted power system emission factors of North China Power Grid, a community carbon emissions sample database is constructed. The support vector regression (SVR) model is trained to forecast the power carbon emissions, which is optimized by genetic algorithm (GA). A community carbon emission warning system is designed according the results. The dynamic emission coefficient curve of the power system is obtained by fitting the annual carbon emission coefficients. The time series SVR carbon emission prediction model is constructed, while the GA is improved to optimize its parameters. Taking Beijing Caochang Community as an example, a carbon emission sample database is generated based on the electricity consumption and emission coefficient curve to train and test the SVR model. The results show that the GA–SVR model fits well with the training set and the testing set, and the prediction accuracy of the testing set reaches 86%. In view of the training model in this paper, the carbon emission trend of community electricity consumption in the next month is predicted. The carbon emission warning system of the community is designed, and the specific strategy of community carbon emission reduction is proposed.
Long-term stability of PVDF-SiO2-HDTMS composite hollow fiber membrane for carbon dioxide absorption in gas–liquid contacting process
Authors: Pang Honglei , Qiu Yayu , Sheng Weipeng
Published: April 2023

Hybrid polyvinylidene fluoride-silica-hexadecyltrimethoxysilane (PVDF-SiO2-HDTMS) membranes were fabricated via a non-solvent-induced phase-inversion method to create stable hollow-fiber membranes for use in the membrane contact absorption of carbon dioxide (CO2). The surface properties, performance characteristics, and long-term performance stability of the prepared membranes were compared and analyzed. The outer surfaces of the prepared membranes were superhydrophobic because of the formation of rough nanoscale microstructures on the surfaces and their low surface free energy. The addition of inorganic nanoparticles improved the mechanical strength of the PVDF-SiO2-HDTMS. Long-term stable operation experiments were carried out with a mixed inlet gas (CO2/N2 = 19/81, v/v) at a flow rate of 20 mL/min. The absorbent liquid in these experiments was 1 mol/L diethanolamine (DEA) at a flow rate of 50 mL/min. The mass transfer flux of CO2 through the PVDF-SiO2-HDTMS membrane decreased from an initial value of 2.39 × 10–3 mol/m2s to 2.31 × 10–3 mol/m2s, a decrease of 3% after 20 days. The addition of highly stable and hydrophobic inorganic nanoparticles prevented pore wetting and structural damage to the membrane. The PVDF-SiO2-HDTMS membrane was found to have excellent long-term stable performance in absorbing CO2.
Evaluation of transorbital sonography measures of optic nerve diameter in the context of global and regional brain volume in multiple sclerosis
Authors: Antal Szabolcs István , Kincses Bálint , Veréb Dániel , Király András , Tóth Eszter , Bozsik Bence , Faragó Péter , Szabó Nikoletta , Kocsis Krisztián , Bencsik Krisztina , Klivényi Péter , Kincses Zsigmond Tamás
Published: April 2023

Transorbital sonography (TOS) could be a swift and convenient method to detect the atrophy of the optic nerve, possibly providing a marker that might reflect other quantitative structural markers of multiple sclerosis (MS). Here we evaluate the utility of TOS as a complementary tool for assessing optic nerve atrophy, and investigate how TOS-derived measures correspond to volumetric brain markers in MS. We recruited 25 healthy controls (HC) and 45 patients with relapsing–remitting MS and performed B-mode ultrasonographic examination of the optic nerve. Patients additionally underwent MRI scans to obtain T1-weighted, FLAIR and STIR images. Optic nerve diameters (OND) were compared between HC, MS patients with and without history of optic neuritis (non-ON) using a mixed-effects ANOVA model. The relationship between within-subject-average OND and global and regional brain volumetric measures was investigated using FSL SIENAX, voxel-based morphometry and FSL FIRST. OND was significantly different between HC-MS (HC = 3.2 ± 0.4 mm, MS = 3 ± 0.4 mm; p < 0.019) and we found significant correlation between average OND and normalised whole brain (β = 0.42, p < 0.005), grey matter (β = 0.33, p < 0.035), white matter (β = 0.38, p < 0.012) and ventricular cerebrospinal fluid volume (β = − 0.36, p < 0.021) in the MS group. History of ON had no impact on the association between OND and volumetric data. In conclusion, OND is a promising surrogate marker in MS, that can be simply and reliably measured using TOS, and its derived measures correspond to brain volumetric measures. It should be further explored in larger and longitudinal studies.
Surface tension coupled non-uniformly imposed flows modulate the activity of reproducing chemotactic bacteria in porous media
Authors: Kuipou William , Mohamadou Alidou
Published: April 2023

This paper investigates a non-homogeneous two-dimensional model for reproducing chemotactic bacteria, immersed in a porous medium that experiences non-uniformly imposed flows. It is shown that independently of the form of the fluid velocity field, the compressible/incompressible nature of the fluid significantly shifts the Turing stability-instability transition line. In dry media, Gaussian perturbations travel faster than the hyperbolic secant ones, yet the latter exhibit better stability properties. The system becomes highly unstable under strong flows and high surface tension. Approximated solutions recovered by injecting Gaussian perturbations overgrow, in addition to triggering concentric breathing features that split the medium into high and low-density domains. Secant perturbations on the other hand scatter slowly and form patterns of non-uniformly distributed peaks for strong flows and high surface tension. These results emphasize that Gaussian perturbations strongly modulate the activity of bacteria, hence can be exploited to perform fast spreading in environments with changing properties. In this sense, Gaussian profiles are better candidates to explain quick bacterial responses to external factors. Secant-type approximated solutions slowly modulate the bacterial activity, hence are better alternatives to dive into weak bacterial progressions in heterogeneous media.
Interpretable machine learning approach for neuron-centric analysis of human cortical cytoarchitecture
Authors: Štajduhar Andrija , Lipić Tomislav , Lončarić Sven , Judaš Miloš , Sedmak Goran
Published: April 2023

The complexity of the cerebral cortex underlies its function and distinguishes us as humans. Here, we present a principled veridical data science methodology for quantitative histology that shifts focus from image-level investigations towards neuron-level representations of cortical regions, with the neurons in the image as a subject of study, rather than pixel-wise image content. Our methodology relies on the automatic segmentation of neurons across whole histological sections and an extensive set of engineered features, which reflect the neuronal phenotype of individual neurons and the properties of neurons’ neighborhoods. The neuron-level representations are used in an interpretable machine learning pipeline for mapping the phenotype to cortical layers. To validate our approach, we created a unique dataset of cortical layers manually annotated by three experts in neuroanatomy and histology. The presented methodology offers high interpretability of the results, providing a deeper understanding of human cortex organization, which may help formulate new scientific hypotheses, as well as to cope with systematic uncertainty in data and model predictions.
Distribution update of water deer (Hydropotes inermis) and prediction of their potential distribution in Northeast China
Authors: Li Zongzhi , Khattak Romaan Hayat , Han Xingzhi , Zhang Nan , Wu Jianping , Liu Zhensheng , Teng Liwei
Published: April 2023

Human interventions have a great potential of spatially cornering and limiting species, therefore investigating the species distribution is one of the most crucial issues for managing wildlife populations and suggesting robust conservation strategies. Water deer (Hydropotes inermis) are widespread in China throughout history and are endemic to East Asia. However, they disappeared from Northeast China for years. We rediscovered the water deer in a previous study in Jilin Province, China. Then, we conducted further research in Northeast China to determine their distribution status, supplying fundamental data for the recovery and expansion of their population. An interview survey, line transect survey and infrared camera monitoring were carried out in some counties/cities in Northeast China from June to December 2021. The results showed that the water deer were distributed in Wuchang city of Heilongjiang Province, Changbai Korean Autonomous County, Baishan Municipal District, Ji’an city, Hunchun city, Huadian city, Antu County and Helong County of Jilin Province, Benxi Manchu Autonomous County, Huanren Manchu Autonomous County, Kuandian Manchu Autonomous County, Fengcheng city and Donggang city of Liaoning Province. The ensemble species distribution model constructed by sdm within the TSS of various models that were set as weight revealed that the potential distribution area of the water deer in the study area was 8764.66 km2 (28.77% of the study area). Combining recent studies concerning the distribution of water deer and the current study, we updated the distribution of wild water deer in Northeast China, which is vital for their conservation worldwide.
Unintentional injury deaths among children under five in Hunan Province, China, 2015–2020
Authors: Zhou Xu , Xie Zhiqun , He Jian , Lin Hong , Xiao Juan , Wang Hua , Fang Junqun , Gao Jie
Published: April 2023

Injury is the most common cause of preventable morbidity and death among children under five. This study aimed to describe the epidemiological characteristics of injury-related mortality rates in children under five and to provide evidence for future preventive strategies. Data were obtained from the Under Five Child Mortality Surveillance System in Hunan Province, China, 2015–2020. Injury-related mortality rates with 95% confidence intervals (CI) were calculated by year, residence, gender, age, and major injury subtype (drowning, suffocation, traffic injuries, falls, and poisoning). And crude odds ratios (ORs) were calculated to examine the association of epidemiological characteristics with injury-related deaths. The Under Five Child Mortality Surveillance System registered 4,286,087 live births, and a total of 22,686 under-five deaths occurred, including 7586 (which accounted for 33.44% of all under-five deaths) injury-related deaths. The injury-related under-five mortality rate was 1.77‰ (95% CI 1.73–1.81). Injury-related deaths were mainly attributed to drowning (2962 cases, 39.05%), suffocation (2300 cases, 30.32%), traffic injuries (1200 cases, 15.82%), falls (627 cases, 8.27%), and poisoning (156 cases, 2.06%). The mortality rates due to drowning, suffocation, traffic injuries, falls, and poisoning were 0.69‰ (95% CI 0.67,0.72), 0.54‰ (95% CI 0.51,0.56), 0.28‰ (95% CI 0.26,0.30), 0.15‰ (95% CI 0.13,0.16), and 0.04‰ (95% CI 0.03,0.04), respectively. From 2015 and 2020, the injury-related mortality rates were 1.78‰, 1.77‰, 1.60‰, 1.78‰, 1.80‰, and 1.98‰, respectively, and showed an upward trend (χ2trend = 7.08, P = 0.01). The injury-related mortality rates were lower in children aged 0–11 months than in those aged 12–59 months (0.52‰ vs. 1.25‰, OR = 0.41, 95% CI 0.39–0.44), lower in urban than rural areas (1.57‰ vs. 1.88‰, OR = 0.84, 95% CI 0.80–0.88), and higher in males than females (2.05‰ vs . 1.45‰, OR = 1.42, 95% CI 1.35–1.49). The number of injury-related deaths decreased with children’s age. Injury-related deaths happened more frequently in cold weather (around February). Almost half (49.79%) of injury-related deaths occurred at home. Most (69.01%) children did not receive treatment after suffering an injury until they died, and most (60.98%) injury-related deaths did not receive treatment because it was too late to get to the hospital. The injury-related mortality rate was relatively high, and we have described its epidemiological characteristics. Several mechanisms have been proposed to explain these phenomena. Our study is of great significance for under-five child injury intervention programs to reduce injury-related deaths.
Identification of three cultivated varieties of Scutellaria baicalensis using the complete chloroplast genome as a super-barcode
Authors: Jiang Yuan , Zhu Chenghao , Wang Shangtao , Wang Fusheng , Sun Zhirong
Published: April 2023

Scutellaria baicalensis has been one of the most commonly used traditional Chinese medicinal plants in China for more than 2000 years. The three new varieties cultivated could not be distinguished by morphology before flowering. It will hinder the promotion of later varieties. Chloroplast DNA has been widely used in species identification. Moreover, previous studies have shown that complete chloroplast genome sequences have been suggested as super barcodes for identifying plants. Therefore, we sequenced and annotated the complete chloroplast genomes of three cultivated varieties. The chloroplast genomes of SBW, SBR, and SBP were 151,702 bp, 151,799 bp, and 151,876 bp, which contained 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The analysis of the repeat sequences, codon usage, and comparison of chloroplast genomes shared a high degree of conservation. However, the sliding window results show significant differences among the three cultivated varieties in matK-rps16 and petA-psbJ. And we found that the matK-rps16 sequence can be used as a barcode for the identification of three varieties. In addition, the complete chloroplast genome contains more variations and can be used as a super-barcode to identify these three cultivated varieties. Based on the protein-coding genes, the phylogenetic tree demonstrated that SBP was more closely related to SBW, in the three cultivated varieties. Interestingly, we found that S. baicalensis and S. rehderiana are closely related, which provides new ideas for the development of S. baicalensis. The divergence time analysis showed that the three cultivated varieties diverged at about 0.10 Mya. Overall, this study showed that the complete chloroplast genome could be used as a super-barcode to identify three cultivated varieties of S. baicalensis and provide biological information, and it also contributes to bioprospecting.
Priority age targets for COVID-19 vaccination in Ethiopia under limited vaccine supply
Authors: Galli Margherita , Zardini Agnese , Gamshie Worku Nigussa , Santini Stefano , Tsegaye Ademe , Trentini Filippo , Marziano Valentina , Guzzetta Giorgio , Manica Mattia , d’Andrea Valeria , Putoto Giovanni , Manenti Fabio , Ajelli Marco , Poletti Piero , Merler Stefano
Published: April 2023

The worldwide inequitable access to vaccination claims for a re-assessment of policies that could minimize the COVID-19 burden in low-income countries. Nine months after the launch of the national vaccination program in March 2021, only 3.4% of the Ethiopian population received two doses of COVID-19 vaccine. We used a SARS-CoV-2 transmission model to estimate the level of immunity accrued before the launch of vaccination in the Southwest Shewa Zone (SWSZ) and to evaluate the impact of alternative age priority vaccination targets in a context of limited vaccine supply. The model was informed with available epidemiological evidence and detailed contact data collected across different geographical settings (urban, rural, or remote). We found that, during the first year of the pandemic, the mean proportion of critical cases occurred in SWSZ attributable to infectors under 30 years of age would range between 24.9 and 48.0%, depending on the geographical setting. During the Delta wave, the contribution of this age group in causing critical cases was estimated to increase on average to 66.7–70.6%. Our findings suggest that, when considering the vaccine product available at the time (ChAdOx1 nCoV-19; 65% efficacy against infection after 2 doses), prioritizing the elderly for vaccination remained the best strategy to minimize the disease burden caused by Delta, irrespectively of the number of available doses. Vaccination of all individuals aged ≥ 50 years would have averted 40 (95%PI: 18–60), 90 (95%PI: 61–111), and 62 (95%PI: 21–108) critical cases per 100,000 residents in urban, rural, and remote areas, respectively. Vaccination of all individuals aged ≥ 30 years would have averted an average of 86–152 critical cases per 100,000 individuals, depending on the setting considered. Despite infections among children and young adults likely caused 70% of critical cases during the Delta wave in SWSZ, most vulnerable ages should remain a key priority target for vaccination against COVID-19.
Improving detention ponds for effective stormwater management and water quality enhancement under future climate change: a simulation study using the PCSWMM model
Authors: Abduljaleel Yasir , Salem Ali , ul Haq Faraz , Awad Ahmed , Amiri Mustapha
Published: April 2023

Urban surfaces are often covered by impermeable materials such as concrete and asphalt which intensify urban runoff and pollutant concentration during storm events, and lead to the deterioration of the quality of surrounding water bodies. Detention ponds are used in urban stormwater management, providing two-fold benefits: flood risk reduction and pollution load minimization. This paper investigates the performance of nine proposed detention ponds (across the city of Renton, Washington, USA) under different climate change scenarios. First, a statistical model was developed to estimate the pollutant load for the current and future periods and to understand the effects of increased rainfall on stormwater runoff and pollutant loads. The Personal Computer Storm Water Management Model (PCSWMM) platform is employed to calibrate an urban drainage model for quantifying stormwater runoff and corresponding pollutant loads. The calibrated model was used to investigate the performance of the proposed nine (9) detention ponds under future climate scenarios of 100-year design storms, leading to identifying if they are likely to reduce stormwater discharge and pollutant loads. Results indicated significant increases in stormwater pollutants due to increases in rainfall from 2023 to 2050 compared to the historical period 2000–2014. We found that the performance of the proposed detention ponds in reducing stormwater pollutants varied depending on the size and location of the detention ponds. Simulations for the future indicated that the selected detention ponds are likely to reduce the concentrations (loads) of different water quality constituents such as ammonia (NH3), nitrogen dioxide (NO2), nitrate (NO3), total phosphate (TP), and suspended solids (SS) ranging from 18 to 86%, 35–70%, 36–65%, 26–91%, and 34–81%, respectively. The study concluded that detention ponds can be used as a reliable solution for reducing stormwater flows and pollutant loads under a warmer future climate and an effective adaptation option to combat climate change related challenges in urban stormwater management.