bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractIn 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

AbstractGeneral 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

AbstractThe 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

AbstractLow 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

AbstractLand 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

AbstractBased 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

AbstractHybrid 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

AbstractTransorbital 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

AbstractThis 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

AbstractThe 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

AbstractHuman 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

AbstractInjury 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

AbstractScutellaria 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.