bluuebunny/crossref_metadata_2025 huggingface dataset:
The Escherichia coli chromosome moves to the replisome
Authors: Gras Konrad , Fange David , Elf Johan
Published: July 2024

In Escherichia coli, it is debated whether the two replisomes move independently along the two chromosome arms during replication or if they remain spatially confined. Here, we use high-throughput fluorescence microscopy to simultaneously determine the location and short-time-scale (1 s) movement of the replisome and a chromosomal locus throughout the cell cycle. The assay is performed for several loci. We find that (i) the two replisomes are confined to a region of ~250 nm and ~120 nm along the cell’s long and short axis, respectively, (ii) the chromosomal loci move to and through this region sequentially based on their distance from the origin of replication, and (iii) when a locus is being replicated, its short time-scale movement slows down. This behavior is the same at different growth rates. In conclusion, our data supports a model with DNA moving towards spatially confined replisomes at replication.
Realization of a two-dimensional Weyl semimetal and topological Fermi strings
Authors: Lu Qiangsheng , Reddy P. V. Sreenivasa , Jeon Hoyeon , Mazza Alessandro R. , Brahlek Matthew , Wu Weikang , Yang Shengyuan A. , Cook Jacob , Conner Clayton , Zhang Xiaoqian , Chakraborty Amarnath , Yao Yueh-Ting , Tien Hung-Ju , Tseng Chun-Han , Yang Po-Yuan , Lien Shang-Wei , Lin Hsin , Chiang Tai-Chang , Vignale Giovanni , Li An-Ping , Chang Tay-Rong , Moore Rob G. , Bian Guang
Published: July 2024

A two-dimensional (2D) Weyl semimetal, akin to a spinful variant of graphene, represents a topological matter characterized by Weyl fermion-like quasiparticles in low dimensions. The spinful linear band structure in two dimensions gives rise to distinctive topological properties, accompanied by the emergence of Fermi string edge states. We report the experimental realization of a 2D Weyl semimetal, bismuthene monolayer grown on SnS(Se) substrates. Using spin and angle-resolved photoemission and scanning tunneling spectroscopies, we directly observe spin-polarized Weyl cones, Weyl nodes, and Fermi strings, providing consistent evidence of their inherent topological characteristics. Our work opens the door for the experimental study of Weyl fermions in low-dimensional materials.
Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms
Authors: Bertrums Eline J. M. , de Kanter Jurrian K. , Derks Lucca L. M. , Verheul Mark , Trabut Laurianne , van Roosmalen Markus J. , Hasle Henrik , Antoniou Evangelia , Reinhardt Dirk , Dworzak Michael N. , Mühlegger Nora , van den Heuvel-Eibrink Marry M. , Zwaan C. Michel , Goemans Bianca F. , van Boxtel Ruben
Published: July 2024

Therapy-related myeloid neoplasms (t-MN) arise as a complication of chemo- and/or radiotherapy. Although t-MN can occur both in adult and childhood cancer survivors, the mechanisms driving therapy-related leukemogenesis likely vary across different ages. Chemotherapy is thought to induce driver mutations in children, whereas in adults pre-existing mutant clones are selected by the exposure. However, selective pressures induced by chemotherapy early in life are less well studied. Here, we use single-cell whole genome sequencing and phylogenetic inference to show that the founding cell of t-MN in children starts expanding after cessation of platinum exposure. In patients with Li-Fraumeni syndrome, characterized by a germline TP53 mutation, we find that the t-MN already expands during treatment, suggesting that platinum-induced growth inhibition is TP53-dependent. Our results demonstrate that germline aberrations can interact with treatment exposures in inducing t-MN, which is important for the development of more targeted, patient-specific treatment regimens and follow-up.
Learning a reactive potential for silica-water through uncertainty attribution
Authors: Roy Swagata , Dürholt Johannes P. , Asche Thomas S. , Zipoli Federico , Gómez-Bombarelli Rafael
Published: July 2024

The reactivity of silicates in aqueous solution is relevant to various chemistries ranging from silicate minerals in geology, to the C-S-H phase in cement, nanoporous zeolite catalysts, or highly porous precipitated silica. While simulations of chemical reactions can provide insight at the molecular level, balancing accuracy and scale in reactive simulations in the condensed phase is a challenge. Here, we demonstrate how a machine-learning reactive interatomic potential trained on PaiNN architecture can accurately capture silicate-water reactivity. The model was trained on a dataset comprising 400,000 energies and forces of molecular clusters at the ωB97X-D3/def2-TZVP level. To ensure the robustness of the model, we introduce a general active learning strategy based on the attribution of the model uncertainty, that automatically isolates uncertain regions of bulk simulations to be calculated as small-sized clusters. The potential reproduces static and dynamic properties of liquid water and solid crystalline silicates, despite having been trained exclusively on cluster data. Furthermore, we utilize enhanced sampling simulations to recover the self-ionization reactivity of water accurately, and the acidity of silicate oligomers, and lastly study the silicate dimerization reaction in a water solution at neutral conditions and find that the reaction occurs through a flanking mechanism.
DHX9 SUMOylation is required for the suppression of R-loop-associated genome instability
Authors: Yang Bing-Ze , Liu Mei-Yin , Chiu Kuan-Lin , Chien Yuh-Ling , Cheng Ching-An , Chen Yu-Lin , Tsui Li-Yu , Lin Keng-Ru , Chu Hsueh-Ping Catherine , Wu Ching-Shyi Peter
Published: July 2024

RNA helicase DHX9 is essential for genome stability by resolving aberrant R-loops. However, its regulatory mechanisms remain unclear. Here we show that SUMOylation at lysine 120 (K120) is crucial for DHX9 function. Preventing SUMOylation at K120 leads to R-loop dysregulation, increased DNA damage, and cell death. Cells expressing DHX9 K120R mutant which cannot be SUMOylated are more sensitive to genotoxic agents and this sensitivity is mitigated by RNase H overexpression. Unlike the mutant, wild-type DHX9 interacts with R-loop-associated proteins such as PARP1 and DDX21 via SUMO-interacting motifs. Fusion of SUMO2 to the DHX9 K120R mutant enhances its association with these proteins, reduces R-loop accumulation, and alleviates survival defects of DHX9 K120R. Our findings highlight the critical role of DHX9 SUMOylation in maintaining genome stability by regulating protein interactions necessary for R-loop balance.
Alloying and confinement effects on hierarchically nanoporous CuAu for efficient electrocatalytic semi-hydrogenation of terminal alkynes
Authors: Meng Linghu , Kao Cheng-Wei , Wang Zhen , Ma Jun , Huang Peifeng , Zhao Nan , Zheng Xin , Peng Ming , Lu Ying-Rui , Tan Yongwen
Published: July 2024

Electrocatalytic alkynes semi-hydrogenation to produce alkenes with high yield and Faradaic efficiency remains technically challenging because of kinetically favorable hydrogen evolution reaction and over-hydrogenation. Here, we propose a hierarchically nanoporous Cu50Au50 alloy to improve electrocatalytic performance toward semi-hydrogenation of alkynes. Using Operando X-ray absorption spectroscopy and density functional theory calculations, we find that Au modulate the electronic structure of Cu, which could intrinsically inhibit the combination of H* to form H2 and weaken alkene adsorption, thus promoting alkyne semi-hydrogenation and hampering alkene over-hydrogenation. Finite element method simulations and experimental results unveil that hierarchically nanoporous catalysts induce a local microenvironment with abundant K+ cations by enhancing the electric field within the nanopore, accelerating water electrolysis to form more H*, thereby promoting the conversion of alkynes. As a result, the nanoporous Cu50Au50 electrocatalyst achieves highly efficient electrocatalytic semi-hydrogenation of alkynes with 94% conversion, 100% selectivity, and a 92% Faradaic efficiency over wide potential window. This work provides a general guidance of the rational design for high-performance electrocatalytic transfer semi-hydrogenation catalysts.
Clinical impact of drug-drug interactions on abemaciclib in the real-world experience of AB-ITALY study
Authors: Scagnoli Simone , Pisegna Simona , Toss Angela , Caputo Roberta , De Laurentiis Michelino , Palleschi Michela , de Giorgi Ugo , Cortesi Enrico , Fabbri Agnese , Fabi Alessandra , Paris Ida , Orlandi Armando , Curigliano Giuseppe , Criscitiello Carmen , Garrone Ornella , Tomasello Gianluca , D’Auria Giuliana , Vici Patrizia , Ricevuto Enrico , Domati Federica , Piombino Claudia , Parola Sara , Scafetta Roberta , Cirillo Alessio , Taurelli Salimbeni Beatrice , Di Lisa Francesca Sofia , Strigari Lidia , Preissner Robert , Simmaco Maurizio , Santini Daniele , Marchetti Paolo , Botticelli Andrea
Published: July 2024

Abemaciclib demonstrated clinical benefit in women affected by HR+/HER2− advanced breast cancer (aBC). Drug-drug interactions (DDIs) can lead to reduced treatment efficacy or increased toxicity. This retro-prospective study aimed to evaluate outcomes, DDIs’ impact, and toxicities of abemaciclib combined with endocrine therapy in a real-world setting. Patients from 12 referral Italian hospitals with HR+/HER2− aBC who received abemaciclib were included. Clinical data about comorbidities, concurrent medications, outcomes, and adverse events (AE) were collected. Drug-PIN® (Personalized Interactions Network) is a tool recognizing the role of multiple interactions between active and/or pro-drug forms combined with biochemical and demographic patient data. The software was used to define the Drug-PIN score and Drug-PIN tier (green, yellow, dark yellow, and red) for each patient. Univariate and multivariate analyses were performed to identify predictors of patients’ PFS or toxicity. One hundred seventy-three patients were included. 13% of patients had >75years. The overall response rate (ORR) was 63%. The general population’s median PFS (mPFS) was 22 months (mo), while mOS were not reached. Patients treated with abemaciclib in combination with AI and fulvestrant had a mPFS of 36 and 19 mo, respectively. The most common toxicities were diarrhea, asthenia, and neutropenia detected in 63%,49%, and 49% of patients. The number of concomitant medications and comorbidities were not associated with survival outcomes (22 vs 17 mo, p = 0.068, p = 0.99). Drug-PIN tier from dark yellow to red and Drug-PIN score >12 were associated with shorter PFS compared to no/low-risk DDIs and score <12 (15 vs 23, p = 0.005, p = 0.0017). Drug interaction was confirmed as an independent biomarker in a multivariate model (p = 0.02). No difference in any grade AE, severe toxicities, and diarrhea were detected among different age subgroups. No association was found between Drug-PIN score or Drug-PIN tier and overall toxicity (p = 0.44), severe AEs (p = 0.11), or drug reduction (p = 0.27). The efficacy and safety of abemaciclib plus ET were confirmed in a real-world setting, even in the elderly population and patients with comorbidities. Evaluation of DDIs with Drug-PIN appears to be an independent predictor of PFS.
A holistic platform for accelerating sorbent-based carbon capture
Authors: Charalambous Charithea , Moubarak Elias , Schilling Johannes , Sanchez Fernandez Eva , Wang Jin-Yu , Herraiz Laura , Mcilwaine Fergus , Peh Shing Bo , Garvin Matthew , Jablonka Kevin Maik , Moosavi Seyed Mohamad , Van Herck Joren , Ozturk Aysu Yurdusen , Pourghaderi Alireza , Song Ah-Young , Mouchaham Georges , Serre Christian , Reimer Jeffrey A. , Bardow André , Smit Berend , Garcia Susana
Published: July 2024

Reducing carbon dioxide (CO2) emissions urgently requires the large-scale deployment of carbon-capture technologies. These technologies must separate CO2 from various sources and deliver it to different sinks1,2. The quest for optimal solutions for specific source–sink pairs is a complex, multi-objective challenge involving multiple stakeholders and depends on social, economic and regional contexts. Currently, research follows a sequential approach: chemists focus on materials design3 and engineers on optimizing processes4,5, which are then operated at a scale that impacts the economy and the environment. Assessing these impacts, such as the greenhouse gas emissions over the plant’s lifetime, is typically one of the final steps6. Here we introduce the PrISMa (Process-Informed design of tailor-made Sorbent Materials) platform, which integrates materials, process design, techno-economics and life-cycle assessment. We compare more than 60 case studies capturing CO2 from various sources in 5 global regions using different technologies. The platform simultaneously informs various stakeholders about the cost-effectiveness of technologies, process configurations and locations, reveals the molecular characteristics of the top-performing sorbents, and provides insights on environmental impacts, co-benefits and trade-offs. By uniting stakeholders at an early research stage, PrISMa accelerates carbon-capture technology development during this critical period as we aim for a net-zero world.
Sources of gene expression variation in a globally diverse human cohort
Authors: Taylor Dylan J. , Chhetri Surya B. , Tassia Michael G. , Biddanda Arjun , Yan Stephanie M. , Wojcik Genevieve L. , Battle Alexis , McCoy Rajiv C.
Published: July 2024

Genetic variation that influences gene expression and splicing is a key source of phenotypic diversity1–5. Although invaluable, studies investigating these links in humans have been strongly biased towards participants of European ancestries, which constrains generalizability and hinders evolutionary research. Here to address these limitations, we developed MAGE, an open-access RNA sequencing dataset of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project6, spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, which mirrored the variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (cis-expression quantitative trait loci (eQTLs) and cis-splicing QTLs (sQTLs), respectively). We identified more than 15,000 putatively causal eQTLs and more than 16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1,310 eQTLs and 1,657 sQTLs that are largely private to underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations. Moreover, the apparent ‘population-specific’ effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands our understanding of human gene expression diversity and provides an inclusive resource for studying the evolution and function of human genomes.
Dataset of Post-Event Survey of the 2024 Noto Peninsula Earthquake Tsunami in Japan
Authors: Yuhi Masatoshi , Umeda Shinya , Arita Mamoru , Ninomiya Junichi , Gokon Hideomi , Arikawa Taro , Baba Toshitaka , Imamura Fumihiko , Kumagai Kenzou , Kure Shuichi , Miyashita Takuya , Suppasri Anawat , Kawai Akio , Nobuoka Hisamichi , Shibayama Tomoya , Koshimura Shunichi , Mori Nobuhito
Published: July 2024

An earthquake with a moment magnitude of 7.5 (Mw) struck the northern Noto Peninsula, Ishikawa Prefecture, Japan, at 16:10 local time on January 1, 2024. This earthquake triggered a tsunami that propagated along the coastline of Ishikawa, Toyama, and Niigata Prefectures facing the Sea of Japan and significantly damaged coastal communities and infrastructure. Approximately 70 researchers from 23 universities or other institutes throughout Japan formed a joint research group to conduct a post-tsunami survey along a 340 km stretch of the coast. Based on the watermarks and traces of the tsunami, the inundation and run-up heights were surveyed using total stations, automatic optical levels, laser range finders, and a real-time kinematic (RTK) Global Navigation Satellite System (GNSS). The tidal correction was adjusted using astronomical tidal tables. In total, 303 survey records have been compiled, generating the NP2024TS (Noto Peninsula 2024 Tsunami Survey) dataset. This dataset provides comprehensive information on the inundation and run-up heights of the tsunami, which is useful for understanding tsunami characteristics and validating numerical tsunami models.
Comparative transcriptomics analysis of tolerant and sensitive genotypes reveals genes involved in the response to cold stress in bitter gourd (Momordica charantia L.)
Authors: Ning Yu , Liu Zhiyang , Liu Jing , Qi Renjie , Xia Pengfei , Yuan Xihan , Xu Hai , Chen Longzheng
Published: July 2024

Bitter gourd is an economically important horticultural crop for its edible and medicinal value. However, the regulatory mechanisms of bitter gourd in response to cold stress are still poorly elucidated. In this study, phytohormone determination and comparative transcriptome analyses in XY (cold-tolerant) and QF (cold-sensitive) after low temperature treatment were conducted. Under cold stress, the endogenous contents of abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA) in XY were significantly increased at 24 h after treatment (HAT), indicating that ABA, JA and SA might function in regulating cold resistance. RNA-seq results revealed that more differentially expressed genes were identified at 6 HAT in QF and 24 HAT in XY, respectively. KEGG analysis suggested that the plant hormone signal transduction pathway was significantly enriched in both genotypes at all the time points. In addition, transcription factors showing different expression patterns between XY and QF were identified, including CBF3, ERF2, NAC90, WRKY51 and WRKY70. Weighted gene co-expression network analysis suggested MARK1, ERF17, UGT74E2, GH3.1 and PPR as hub genes. These results will deepen the understanding of molecular mechanism of bitter gourd in response to cold stress and the identified genes may help to facilitate the genetic improvement of cold-resistant cultivars.
Exploring phylogeny and genomic vulnerability of Melastoma (Melastomataceae) endemic to a World Natural Heritage site, the Bonin Islands
Authors: Kobayashi Yukihiro , Komaki Yoshiteru , Isagi Yuji
Published: July 2024

Melastoma (Melastomataceae) includes ca. 100 species across tropical to subtropical regions of Asia and Oceania. The Bonin Islands harbor three endemic taxa: M. tetramerum, M. tetramerum var. pentapetalum, and M. candidum var. alessandrense. Of these, M. tetramerum is critically endangered and faces near extinction in the wild. This study investigates the phylogenetic relationships among these endemic Melastoma species in the Bonin Islands based on the whole chloroplast genome and nuclear SNPs. The results revealed that M. candidum var. alessandrense was placed in the clade of the widespread East Asian M. candidum and has a distinct evolutionary origin from the other two taxa. The population genomics analyses (heterozygosity, rates of deleterious mutations, and numbers and lengths of runs of homozygosity) indicated lower genetic diversity and more vulnerable genomes of endemic Melastoma, especially M. tetramerum var. pentapetalum. M. tetramerum var. pentapetalum is not a target of any protection programs, however, conservation plans might be required for this variety because M. tetramerum var. pentapetalum would have a more vulnerable genome than M. tetramerum, which faces near extinction in the wild. This information can facilitate the development of effective conservation strategies in a precautionary way that anticipates imminent threats to the survival of the species.
The rate of W chromosome degeneration across multiple avian neo-sex chromosomes
Authors: Sigeman Hanna , Downing Philip A. , Zhang Hongkai , Hansson Bengt
Published: July 2024

When sex chromosomes evolve recombination suppression, the sex-limited chromosome (Y/W) commonly degenerate by losing functional genes. The rate of Y/W degeneration is believed to slow down over time as the most essential genes are maintained by purifying selection, but supporting data are scarce especially for ZW systems. Here, we study W degeneration in Sylvioidea songbirds where multiple autosomal translocations to the sex chromosomes, and multiple recombination suppression events causing separate evolutionary strata, have occurred during the last ~ 28.1–4.5 million years (Myr). We show that the translocated regions have maintained 68.3–97.7% of their original gene content, compared to only 4.2% on the much older ancestral W chromosome. By mapping W gene losses onto a dated phylogeny, we estimate an average gene loss rate of 1.0% per Myr, with only moderate variation between four independent lineages. Consistent with previous studies, evolutionarily constrained and haploinsufficient genes were preferentially maintained on W. However, the gene loss rate did not show any consistent association with strata age or with the number of W genes at strata formation. Our study provides a unique account on the pace of W gene loss and reinforces the significance of purifying selection in maintaining essential genes on sex chromosomes.
Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching
Authors: Grafmüller Jannis , Möllmer Jens , Muehe E. Marie , Kammann Claudia I. , Kray Daniel , Schmidt Hans-Peter , Hagemann Nikolas
Published: July 2024

Mechanized biochar field application remains challenging due to biochar’s poor flowability and bulk density. Granulation of biochar with fertilizer provides a product ready for application with well-established machinery. However, it’s unknown whether granulated biochar-based fertilizers (gBBF) are as effective as co-application of non-granulated biochar with fertilizer. Here, we compared a gBBF with a mineral compound fertilizer (control), and with a non-granulated biochar that was co-applied at a rate of 1.1 t ha−1 with the fertilizer in a white cabbage greenhouse pot trial. Half the pots received heavy rain simulation treatments to investigate nutrient leaching. Crop yields were not significantly increased by biochar without leaching compared to the control. With leaching, cabbage yield increased with gBBF and biochar-co-application by 14% (p > 0.05) and 34% (p < 0.05), respectively. Nitrogen leaching was reduced by 26–35% with both biochar amendments. Biochar significantly reduced potassium, magnesium, and sulfur leaching. Most nitrogen associated with gBBF was released during the trial and the granulated biochar regained its microporosity. Enriching fertilizers with biochar by granulation or co-application can improve crop yields and decrease nutrient leaching. While the gBBF yielded less biomass compared to biochar co-application, improved mechanized field application after granulation could facilitate the implementation of biochar application in agriculture.
Clinical outcomes of posterior scleral reinforcement in Chinese high myopia children
Authors: Ye Haiyun , Tang Ruizhi , Fang Wangyi , Di Yue , Qiao Tong
Published: July 2024

We aim to observe the posterior scleral reinforcement (PSR) clinical outcomes of children with high myopia and analyze the retinal vessel alteration before and after PSR by using angiography optical coherence tomography (angio-OCT). Fifty-six pediatric participants (112 eyes) clinically diagnosed high myopia were recruited and were treated by PSR in Shanghai Children’s Hospital from June 1, 2021 to May 1, 2023. The average age ranged from 5.42 to 14.83 years (mean 8.83 years) and mean follow up duration was 8.7 months (3–24 months). The axial length (AL) was significantly shortened after PSR (p < 0.05). The spherical equivalent (SE) and the best-corrected visual acuity (BCVA) were also improved without severe rejection in the follow-up. Compared with baseline, angio-OCT parafoveal vessel indices including vascular area density (VAD) and vascular skeleton density (VSD) on the superficial capillary plexus layer (SCPL), as well as VAD and vessel perimeter index (VPI) on the deep capillary plexus layer (DCPL), were significantly increased after PSR surgery (p < 0.05). VPI on the SCPL, vascular diameter index (VDI) and VSD on the DCPL were also improved without statistical difference after PSR. The VSD on SCPL, VAD on DCPL of the right eyes and the VPI on SCPL of the left eyes were significantly increased after PSR (p < 0.05). PSR surgery can shorten the AL and can stable BCVA and SE in high myopia children. The angio-OCT parameters indicated that the retinal microcirculation supply was significantly improved after PSR.
A paradigm shift in diagnosis and treatment innovation for mucinous cystic neoplasms of the liver
Authors: Shi Bin , Yu Peng , Meng Lingzhan , Li Hu , Wang Zizheng , Cao Li , Yan Jin , Shao Yanling , Zhang Ying , Zhu Zhenyu
Published: July 2024

This study comprehensively explores the clinical characteristics, diagnostic approaches, and treatment methods for liver mucinous cystic neoplasms (MCN). A retrospective analysis was conducted on seven individuals diagnosed with MCN, admitted to the Fifth Medical Center of the PLA General Hospital between October 2016 and May 2023. Preoperative AFP was negative, while CA19-9 was elevated in two cases. Surgical resection was performed for all patients. The patients showed favorable postoperative recovery. Follow-up revealed an excellent overall survival rate, except for one case of invasive carcinoma resulting in tumor recurrence and metastasis 6 months after surgery. MCN poses a diagnostic challenge due to the absence of distinct clinical and radiological features, leading to potential misdiagnosis and inappropriate treatment. Patients with suspected liver cystic diseases should consider the possibility of MCN. Surgical resection has proven to be a practical approach with satisfactory therapeutic outcomes.
Design and application of coal gangue sorting system based on deep learning
Authors: Zhang Kun , Wang Zhen , Zhang Zengbao , Shi Zhiyuan , Qi Yuhao , Du Mingchao , Chen Yong , Liu Tijun , Chen Yumeng , Yin Zhuang
Published: July 2024

With the advancement of science and technology, coal-washing plants are transitioning to intelligent, information-based, and professional sorting systems. This shift accelerates the construction a modern economic system characterized by green and low-carbon development, thereby promoting the high-quality advancement of the coal industry. Traditional manual gangue picking and multi-axis robotic arm gangue selection currently suffer from low recognition accuracy, slow sorting efficiency, and high worker labor intensity. This paper proposes a deep learning-based, non-contact gangue recognition and pneumatic intelligent sorting system. The system constructs a dynamic database containing key feature information such as the target gangue's contour, quality, and center of mass. The system elucidates the relationships between ejection speed, mass, volume, angle of incidence, and the impact energy matching mechanism. Demonstration experiments using the system prototype for coal gangue sorting reveal that, compared to existing robotic arm sorting methods in coal washing plants, this system achieves a gangue identification accuracy exceeding 97%, a sorting rate above 91%, and a separation time of less than 3 s from identification to separation, thereby effectively enhancing raw coal purity.
The hard life of an octopus embryo is seen through gene expression, energy metabolism, and its ability to neutralize radical oxygen species
Authors: Ramos-Rodríguez Sadot , Ortega-Ramírez Karen , Méndez-Can Luisa , Galindo-Sánchez Clara , Galindo-Torres Pavel , Ventura-López Claudia , Mascaro´ Maite , Caamal-Monsreal Claudia , Rodríguez Gabriela , Díaz Fernando , Rosas Carlos
Published: July 2024

The reproductive process in Octopus maya was analyzed to establish the amount of reactive oxygen species that the embryos inherit from females, during yolk synthesis. At the same time, respiratory metabolism, ROS production, and the expression of some genes of the antioxidant system were monitored to understand the ability of embryos to neutralize maternal ROS and those produced during development. The results indicate that carbonylated proteins and peroxidized lipids (LPO) were transferred from females to the embryos, presumably derived from the metabolic processes carried out during yolk synthesis in the ovary. Along with ROS, females also transferred to embryos glutathione (GSH), a key element of the antioxidant defense system, thus facilitating the neutralization of inherited ROS and those produced during development. Embryos are capable of neutralizing ROS thanks to the early expression of genes such as catalase (CAT) and superoxide dismutase (SOD), which give rise to the synthesis of enzymes when the circulatory system is activated. Also, it was observed that the levels of the routine metabolic rate of embryos are almost as high as those of the maximum activity metabolism, which leads, on the one hand, to the elevated production of ROS and suggests that, at this stage of the life cycle in octopuses, energy production is maximum and is physically limited by the biological properties inherent to the structure of embryonic life (oxygen transfer through the chorion, gill surface, pumping capacity, etc.). Due to its role in regulating vascularization, a high expression of HIf-1A during organogenesis suggests that circulatory system development has begun in this phase of embryo development. The results indicate that the routine metabolic rate and the ability of O. maya embryos to neutralize the ROS are probably the maximum possible. Under such circumstances, embryos cannot generate more energy to combat the free radicals produced by their metabolism, even when environmental factors such as high temperatures or contaminants could demand excess energy.
Microbial and physicochemical changes in green bell peppers treated with ultrasonic-assisted washing in combination with Thymus vulgaris essential oil nanocapsules
Authors: Akbari Saiede , Radi Mohsen , Hosseinifarahi Mehdi , Amiri Sedigheh
Published: July 2024

In this study, the effect of Thymus vulgaris essential oil (TVO) nanoemulsion (NE, 500 mg/L) in combination with ultrasound (ultrasound-NE) on the microbial and physiological quality of green bell pepper was investigated. The TVO-NE droplet size and zeta potential were 84.26 nm and − 0.77 mV, respectively. The minimum inhibitory concentrations of the TVO and TVO-NE against E. coli and S. aureus were about 0.07 and 7 g/L, respectively. The NE-ultrasound treatment exhibited the lowest peroxidase activity and respiration rate with no detrimental effect on texture, total phenolic content, antioxidant activity, pH, and TSS. Although the NE-ultrasound treatment showed the highest weight loss and electrolytic leakage, it exhibited the best visual color and appearance. The NE-ultrasound treatment descended the total viable/mold and yeast counts significantly compared to control. Results showed that treating the bell peppers with NE-ultrasound can result in bell peppers with good postharvest quality and extended shelf life.
Prediction of protein secondary structure by the improved TCN-BiLSTM-MHA model with knowledge distillation
Authors: Zhao Lufei , Li Jingyi , Zhan Weiqiang , Jiang Xuchu , Zhang Biao
Published: July 2024

Secondary structure prediction is a key step in understanding protein function and biological properties and is highly important in the fields of new drug development, disease treatment, bioengineering, etc. Accurately predicting the secondary structure of proteins helps to reveal how proteins are folded and how they function in cells. The application of deep learning models in protein structure prediction is particularly important because of their ability to process complex sequence information and extract meaningful patterns and features, thus significantly improving the accuracy and efficiency of prediction. In this study, a combined model integrating an improved temporal convolutional network (TCN), bidirectional long short-term memory (BiLSTM), and a multi-head attention (MHA) mechanism is proposed to enhance the accuracy of protein prediction in both eight-state and three-state structures. One-hot encoding features and word vector representations of physicochemical properties are incorporated. A significant emphasis is placed on knowledge distillation techniques utilizing the ProtT5 pretrained model, leading to performance improvements. The improved TCN, achieved through multiscale fusion and bidirectional operations, allows for better extraction of amino acid sequence features than traditional TCN models. The model demonstrated excellent prediction performance on multiple datasets. For the TS115, CB513 and PDB (2018–2020) datasets, the prediction accuracy of the eight-state structure of the six datasets in this paper reached 88.2%, 84.9%, and 95.3%, respectively, and the prediction accuracy of the three-state structure reached 91.3%, 90.3%, and 96.8%, respectively. This study not only improves the accuracy of protein secondary structure prediction but also provides an important tool for understanding protein structure and function, which is particularly applicable to resource-constrained contexts and provides a valuable tool for understanding protein structure and function.
Plasma B-type natriuretic peptide is independently associated with cardiovascular events and mortality in patients with chronic kidney disease
Authors: Hayashida Hiroyuki , Haruyama Naoki , Fukui Akiko , Yoshitomi Ryota , Fujisawa Hironobu , Nakayama Masaru
Published: July 2024

The association between B-type natriuretic peptide (BNP) and cardiovascular (CV) events and mortality has not been well characterized in patients with chronic kidney disease (CKD). We prospectively investigated whether BNP was associated with CV events or mortality beyond cardiac alterations in 1078 patients with CKD. Participants were divided into the following 3 groups according to circulating BNP concentration: < 40 pg/mL, low; 40–100 pg/mL, middle; and > 100 pg/mL, high. Primary outcome was fatal or nonfatal CV events, and alternative outcome was a composite of fatal or nonfatal CV events, or non-CV deaths. During a median follow-up of 2.6 years, CV and composite events occurred in 158 and 248 participants, respectively. Cox analyses after adjustment for covariates, including cardiac parameters, showed that the hazard ratios (HRs) (95% confidence intervals [CIs]) for CV events of middle and high groups were 1.00 (0.63, 1.58) and 1.72 (1.06, 2.79), respectively, compared with low group. Additionally, similar results were obtained for composite events; the HRs (95% CIs) of middle and high groups were 1.10 (0.77, 1.57) and 1.54 (1.04, 2.27), respectively, compared with low group. Thus, in CKD, high BNP concentrations were independently associated with CV events and mortality, independent of cardiac alterations.
A multicenter study of long-term outcomes of relapsing polychondritis in Iran
Authors: Jafarpour Mehdi , Saberivand Maryam , Saemi Maryam , Sahebari Maryam , Seyedmardani Seyedmostafa , Salesi Mansour , Hosseinpoor Sarah , Faezi Tahereh , Esalatmanesh Kamal , Hajialilo Mehrzad , Kolahi Sousan , Myrfeizi Zahra , Khabbazi Alireza
Published: July 2024

Relapsing polychondritis (RP) is a systemic immune mediated disease characterized by recurrent episodes of inflammation in various cartilage-rich areas. RP may cause extensive tissue destruction and is associated with significant morbidity and mortality. In this multicenter study, we considered the remission status and long-term outcomes of RP in patients who were followed-up in six referral rheumatology centers in Iran. Outcomes of disease was assessed by remission status and RP induced damage. A total of 29 patients with RP were examined for enrollment in the study, and 26 patients with a minimum follow-up period of 6 months were included in the RP outcome analysis. Median time to control of symptoms and sustained remission were 5 and 23 weeks, respectively. Prednisolone was discontinued in 8 (30.8%) patients and medication-free remission was achieved in 7 (23.1%) patients. Regarding the disease course, 34.6% of patients had a relapsing–remitting course, 42.3% had a monophasic course, and 23.1% had an always-active course. Despite extensive treatment with immunosuppressive medications, RP induced damage was developed in 21 (80.8%) patients. Ear deformity and osteoporosis were the most common RP induced damage. Long-term remission and medications-free remission in RP is accessible. However, RP related damage occur in majority of patients.
Synchronous Eurasian heat extremes tied to boreal summer combined extratropical intraseasonal waves
Authors: Yang Jing , Zhu Tao , Vitart Frederic , Wang Bin , Xiang Baoqiang , Bao Qing , Lee June-Yi
Published: July 2024

Heat extremes frequently hit different regions synchronously during boreal summer over the Eurasian continent. A remarkable coupling is first revealed between Eurasian heat extreme occurrence and individual extratropical intraseasonal oscillation (EISO). Further, the combined EISOs facilitate and largely increase the occurrence probabilities of synchronous Eurasian heat extremes. These dominant combined EISOs together contribute 20–45% to the total heat extreme days over the five Eurasian regions where the climatological heat extremes occur most frequently. A multi-model hindcast further shows that the subseasonal prediction exhibits higher skills for synchronous heat extremes over the combined-EISO hotspot regions when the associated combined EISOs are active, supporting the notion that the monitoring and prediction of EISOs are crucial for heat extremes’ early warning. Skillful prediction of EISOs opens a pathway for heat extremes’ prediction by extending it from the weather to the subseasonal timescales.
Multi-omics machine learning to study host-microbiome interactions in early-onset colorectal cancer
Authors: Jayakrishnan Thejus T. , Sangwan Naseer , Barot Shimoli V. , Farha Nicole , Mariam Arshiya , Xiang Shao , Aucejo Federico , Conces Madison , Nair Kanika G. , Krishnamurthi Smitha S. , Schmit Stephanie L. , Liska David , Rotroff Daniel M. , Khorana Alok A. , Kamath Suneel D.
Published: July 2024

The incidence of early-onset colorectal cancer (eoCRC) is rising, and its pathogenesis is not completely understood. We hypothesized that machine learning utilizing paired tissue microbiome and plasma metabolome features could uncover distinct host-microbiome associations between eoCRC and average-onset CRC (aoCRC). Individuals with stages I–IV CRC (n = 64) were categorized as eoCRC (age ≤ 50, n = 20) or aoCRC (age ≥ 60, n = 44). Untargeted plasma metabolomics and 16S rRNA amplicon sequencing (microbiome analysis) of tumor tissue were performed. We fit DIABLO (Data Integration Analysis for Biomarker Discovery using Latent variable approaches for Omics studies) to construct a supervised machine-learning classifier using paired multi-omics (microbiome and metabolomics) data and identify associations unique to eoCRC. A differential association network analysis was also performed. Distinct clustering patterns emerged in multi-omic dimension reduction analysis. The metabolomics classifier achieved an AUC of 0.98, compared to AUC 0.61 for microbiome-based classifier. Circular correlation technique highlighted several key associations. Metabolites glycerol and pseudouridine (higher abundance in individuals with aoCRC) had negative correlations with Parasutterella, and Ruminococcaceae (higher abundance in individuals with eoCRC). Cholesterol and xylitol correlated negatively with Erysipelatoclostridium and Eubacterium, and showed a positive correlation with Acidovorax with higher abundance in individuals with eoCRC. Network analysis revealed different clustering patterns and associations for several metabolites e.g.: urea cycle metabolites and microbes such as Akkermansia. We show that multi-omics analysis can be utilized to study host-microbiome correlations in eoCRC and demonstrates promising biomarker potential of a metabolomics classifier. The distinct host-microbiome correlations for urea cycle in eoCRC may offer opportunities for therapeutic interventions.
Life and death of a thin liquid film
Authors: Rahman Muhammad Rizwanur , Shen Li , Ewen James P. , Heyes David M. , Dini Daniele , Smith Edward R.
Published: July 2024

Thin films, bubbles and membranes are central to numerous natural and engineering processes, i.e., in solar cells, coatings, biosensors, foams, and emulsions. Yet, the characterization and understanding of their rupture is limited by the scarcity of atomic detail. We present here the complete life-cycle of freely suspended films using non-equilibrium molecular dynamics simulations of a simple atomic fluid free of surfactants and surface impurities, thus isolating the fundamental rupture mechanisms. We identified a short-term ‘memory’ by rewinding in time from a rupture event, extracting deterministic behaviors from apparent stochasticity. A comprehensive investigation of the key rupture-stages including both unrestrained and frustrated propagation is made—characterization of the latter leads to a first-order correction to the classical film-retraction theory. The highly resolved time window reveals that the different modes of the morphological development, typically characterized as nucleation and spinodal rupture, continuously evolve seamlessly with time from one into the other.
The effect of antibiotic selection on collateral effects and evolvability of uropathogenic Escherichia coli
Authors: James Beth , Reesaul Hishikha , Kashif Sidra , Behruznia Mahboobeh , Meehan Conor J. , Domingo-Sananes Maria Rosa , Hubbard Alasdair T. M.
Published: July 2024

Trimethoprim is recommended as a first-line treatment of urinary tract infections (UTIs) in the UK. In 2018, 31.4% of Escherichia coli isolated from UTIs in England were trimethoprim-resistant, leading to overreliance on other first and second-line antibiotics. Here, we assessed whether, in principle, prior selection with trimethoprim results in collateral effects to other antibiotics recommended for the treatment of UTIs. As collateral effects, we considered changes in susceptibility, mutation-selection window and population establishment probability. We selected 10 trimethoprim-resistant derivatives from three clinical isolates of uropathogenic Escherichia coli. We found that mutations conferring trimethoprim resistance did not have any collateral effects on fosfomycin. In contrast, resistance to trimethoprim resulted in decreased susceptibility (collateral resistance) to nitrofurantoin, below the clinical breakpoint and narrowed the mutation-selection window, thereby reducing the maximum concentration for selection of nitrofurantoin resistance mutations. Our analyses demonstrate that multiple collateral responses should be accounted for when predicting and optimising antibiotic use, limiting future antimicrobial resistance emergence.
Nonlinear orbital and spin Edelstein effect in centrosymmetric metals
Authors: Baek Insu , Han Seungyun , Cheon Suik , Lee Hyun-Woo
Published: July 2024

Nonlinear spintronics combines nonlinear dynamics with spintronics, opening up new possibilities beyond linear responses. A recent theoretical work [Xiao et al. Phys. Rev. Lett.130, 166302 (2023)] predicts the nonlinear generation of spin density [nonlinear spin Edelstein effect (NSEE)] in centrosymmetric metals based on symmetry analysis combined with first-principle calculation. This paper focuses on the fundamental role of orbital degrees of freedom for the nonlinear generation in centrosymmetric systems. Using a combination of tight-binding model and density functional theory calculations, we demonstrate that nonlinear orbital density can arise independently of spin–orbit coupling. In contrast, spin density follows through spin–orbit coupling. We further elucidate the microscopic mechanism responsible for this phenomenon, which involves the NSEE induced by electric-field-induced orbital Rashba texture. In addition, we also explore the potential applications of the nonlinear orbital and spin Edelstein effect for magnetic-field-free switching of magnetization.
In-plane hyperbolic phonon polaritons: materials, properties, and nanophotonic devices
Authors: Ma Yunxiu , Zhong Gang , Dai Zhigao , Ou Qingdong
Published: July 2024

In-plane hyperbolic phonon polaritons (HPhPs) are phonon-mediated hybrid electromagnetic modes, particularly in two-dimensional (2D) van der Waals (vdW) crystals, which have attracted increasing attention because of their peculiar optical properties and promising nanophotonic applications. Here, we review the most recent advances in in-plane HPhPs in terms of materials, optical properties and nanophotonic devices. We begin with a survey of recently discovered in-plane anisotropic vdW materials and bulk crystals that naturally exhibit in-plane HPhPs. The fundamental properties of HPhPs in these anisotropic materials are then discussed, focusing on propagation directionality such as direction rotation, unidirectional excitation, canalization, negative reflection, and negative refraction. Finally, we discuss the present applications of in-plane HPhPs in nanophotonic devices and offer a perspective on future developments of in-plane HPhPs towards nanophotonic chips.
A CRISPR/Cas12a-powered gold/nickel foam surface-enhanced Raman spectroscopy biosensor for nucleic acid specific detection in foods
Authors: Liu Yan , Gou Shirui , Qiu Long , Xu Zhiwen , Yang Haifeng , Yang Shiping , Zhao Yu
Published: July 2024

AuNFs was used as a SERS substrate combined with CRISPR/Cas12a to achieve the specific detection of viral nucleic acids. At the same time, AuNFs could avoid the influence of Mg2+ in the CRISPR system in common SERS detection.
Medical and molecular biophysical techniques as substantial tools in the era of mRNA-based vaccine technology
Authors: Hussain Abid , Wang Maoye , Yu Dan , Zhang Jiahui , Naseer Qais Ahmad , Ullah Aftab , Milon Essola Julien , Zhang Xu
Published: July 2024

Biophysical techniques involved in the formulation of mRNA products.
Biomimetic hierarchical porous high entropy alloy for significantly enhancing overall seawater splitting
Authors: Wang Wei , Wang Weiqi , Cheng Jun , Lu Xing , Lu Yunzhuo
Published: July 2024

Biomimetic hierarchical porous high entropy alloy for significantly enhancing overall seawater splitting.
Synthesis of a highly conductive coordination polymer film via a vapor–solid phase chemical conversion process
Authors: Li Ze , Jin Yigang , Li Chunlei , Chang Zixin , Wu Sha , Sun Yimeng , Jiang Lang , Xu Wei
Published: July 2024

We have demonstrated a novel method to fabricate Ag5BHT c-CP thin films that exhibit excellent electrical conductivity and high charge mobility.
Rational design of organic ligands for metal–organic frameworks as electrocatalysts for CO2 reduction
Authors: Zhang Ya , Sun Wei-Yin
Published: July 2024

This feature article summarizes the rational design strategies of organic ligands and their impact on the electrocatalytic CO2 reduction performance of MOFs to aim at inspiring the development of advanced MOF-based electrocatalysts in the future.
A naphthalimide-based fluorescent platform for endoplasmic reticulum targeted imaging
Authors: Li Yiwei , Zhang Nan , Wang Yan , Lu Shanshan , Sheng Jing , Liu Xiangjun , Wei Yongbiao , Shangguan Dihua
Published: July 2024

A series of ER-targeted naphthalimide dyes were developed, and showed promise in tracking ER autophagy under ER stress.
Incorporation of CF3-pseudoprolines into polyproline type II foldamers confers promising biophysical features
Authors: Cayrou Chloé , Walrant Astrid , Ravault Delphine , Guitot Karine , Noinville Sylvie , Sagan Sandrine , Brigaud Thierry , Gonzalez Simon , Ongeri Sandrine , Chaume Grégory
Published: July 2024

Introduction of CF3-oxazolidines in polyproline type II foldamers maintains PPII helicity, non-cytotoxicity and stability towards proteolysis. The CF3 groups enhanced hydrophobicity and are used as easy-to-handle 19F NMR probes.