bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the Estimation of the Diffuse Component of Photosynthetically Active Radiation (PAR)
Authors: Lozano I. , Alados I. , Sánchez‐Hernández G. , Guerrero‐Rascado J. L. , Foyo‐Moreno I.
Published: November 2023

Most weather forecasting models are not able to accurately reproduce the great variability existing in the measurements of the diffuse component of photosynthetically active radiation (PAR; 400–700 nm) under all sky conditions. Based on the well‐known relationship between the diffuse fraction (k) and the clearness index (kt), this study addresses improvements in estimations by proposing adaptations of previous models, which were previously applied only to the total solar irradiance (TSI; 280–3,000 nm). In order to reproduce this variability, additional parameters were introduced. The models were tested employing a multisite database gathered at the Mediterranean basin. Since Artificial Neural Network (ANN) models are not limited to fixed coefficients to predict the diffuse fraction of PAR (kPAR), these types of models are more accurate than empirical ones, reaching determination coefficients (r2) up to 0.998. However, the simpler linear model proposed by Foyo‐Moreno et al. (2018), https://doi.org/10.1016/j.atmosres.2017.12.012 shows a similar performance to the ANN models, directly predicting the diffuse component of PAR (PARDiffuse) from TSIDiffuse, with a r2 up to 0.997. Results obtained here also determine that the most important variables for estimating PARDiffuse are kt or kt,PAR, and the apparent solar time (AST). Therefore, PARDiffuse can be modeled using TSI measured in most radiometric stations, reaching r2 up to 0.858 for empirical models and 0.970 for ANN models. This modified approach will allow for the very accurate construction of long‐term data series of PARDiffuse in regions where continuous measurements of PAR are not available.
Mindfulness-based therapy improves brain functional network reconfiguration efficiency
Authors: Yue Wan Lin , Ng Kwun Kei , Koh Amelia Jialing , Perini Francesca , Doshi Kinjal , Zhou Juan Helen , Lim Julian
Published: November 2023

Mindfulness-based interventions are showing increasing promise as a treatment for psychological disorders, with improvements in cognition and emotion regulation after intervention. Understanding the changes in functional brain activity and neural plasticity that underlie these benefits from mindfulness interventions is thus of interest in current neuroimaging research. Previous studies have found functional brain changes during resting and task states to be associated with mindfulness both cross-sectionally and longitudinally, particularly in the executive control, default mode and salience networks. However, limited research has combined information from rest and task to study mindfulness-related functional changes in the brain, particularly in the context of intervention studies with active controls. Recent work has found that the reconfiguration efficiency of brain activity patterns between rest and task states is behaviorally relevant in healthy young adults. Thus, we applied this measure to investigate how mindfulness intervention changed functional reconfiguration between rest and a breath-counting task in elderly participants with self-reported sleep difficulties. Improving on previous longitudinal designs, we compared the intervention effects of a mindfulness-based therapy to an active control (sleep hygiene) intervention. We found that mindfulness intervention improved self-reported mindfulness measures and brain functional reconfiguration efficiency in the executive control, default mode and salience networks, though the brain and behavioral changes were not associated with each other. Our findings suggest that neuroplasticity may be induced through regular mindfulness practice, thus bringing the intrinsic functional configuration in participants’ brains closer to a state required for mindful awareness.
Soft tissue expansion using self-inflating osmotic hydrogel expanders prior to bone augmentation: healing and complications. Evidence-based review
Authors: Ellesøe Adam Gade , Shado Rawand , Pereira Ines Novo , Madruga David , Hassan Haidar
Published: November 2023

Aim

This review aims to assess complication rates, soft tissue gain, and bone gain associated with the use of self-inflating osmotic hydrogel tissue expanders (SOHTEs) for soft tissue expansion (STE).

Methods

A comprehensive search on Pubmed and Google Scholar databases was conducted to identify human studies using SOHTEs for STE; last searched in March 2023. Expansion phase details and expander variables were documented. Complication rates, soft tissue gain, and bone gain reported in each study were also recorded. The inclusion criteria encompassed human studies ranging from evidence levels II–IV (Oxford Centre for Evidence-Based Medicine Levels of Evidence), without specific date limits. For assessing bias in randomized controlled trials (RCTs), a Risk of Bias tool was employed. The synthesised results were presented through tables, sunburst plots, and bar charts.

Results

A total of 13 studies were identified, comprising 4 RCTs, 1 cohort study, and 8 case-series. Employment of SOHTEs yielded an overall complication rate of 17% (24/140 sites), with expander perforation accounting for 9.3% (13/140) of the sites. Specific complication rates included dehiscence (1.4%, 2/140 sites), paraesthesia (1.4%, 2/140 sites), and infection (1.4%, 2/140 sites). All randomized controlled trials (RCTs) were categorised at Level II. The remaining investigations primarily consisted of Level IV case-series lacking controls. All studies demonstrated some concerns towards bias.

Conclusion

STE studies using SOHTEs exhibit a reduction in complications associated with bone augmentation in scenarios of inadequate soft tissue coverage. Preliminary evidence suggests potential benefits even in cases with sufficient soft tissue. Adherence to procedural precautions may reduce the risk of expander perforations, further diminishing complications. Subsequent studies should incorporate individual patient and expander variables in their reports to explore the impact of expansion phases on complication rates, as well as bone and soft tissue augmentation.
Integration of FUNDC1-associated mitochondrial protein import and mitochondrial quality control contributes to TDP-43 degradation
Authors: Ma Jinfa , Liu Lei , Song Lu , Liu Jianghong , Yang Lingyao , Chen Quan , Wu Jane Y. , Zhu Li
Published: November 2023

Though TDP-43 protein can be translocated into mitochondria and causes mitochondrial damage in TDP-43 proteinopathy, little is known about how TDP-43 is imported into mitochondria. In addition, whether mitochondrial damage is caused by mitochondrial mislocalization of TDP-43 or a side effect of mitochondria-mediated TDP-43 degradation remains to be investigated. Here, our bioinformatical analyses reveal that mitophagy receptor gene FUNDC1 is co-expressed with TDP-43, and both TDP-43 and FUNDC1 expression is correlated with genes associated with mitochondrial protein import pathway in brain samples of patients diagnosed with TDP-43 proteinopathy. FUNDC1 promotes mitochondrial translocation of TDP-43 possibly by promoting TDP-43-TOM70 and DNAJA2-TOM70 interactions, which is independent of the LC3 interacting region of FUNDC1 in cellular experiments. In the transgenic fly model of TDP-43 proteinopathy, overexpressing FUNDC1 enhances TDP-43 induced mitochondrial damage, whereas down-regulating FUNDC1 reverses TDP-43 induced mitochondrial damage. FUNDC1 regulates mitochondria-mediated TDP-43 degradation not only by regulating mitochondrial TDP-43 import, but also by increasing LONP1 level and by activating mitophagy, which plays important roles in cytosolic TDP-43 clearance. Together, this study not only uncovers the mechanism of mitochondrial TDP-43 import, but also unravels the active role played by mitochondria in regulating TDP-43 homeostasis.
MELK promotes HCC carcinogenesis through modulating cuproptosis-related gene DLAT-mediated mitochondrial function
Authors: Li Zhipeng , Zhou Huaxin , Zhai Xiangyu , Gao Lin , Yang Mengfan , An Baokun , Xia Tong , Du Gang , Li Xiaoming , Wang Wei , Jin Bin
Published: November 2023

Cuproptosis caused by copper overload is mediated by a novel regulatory mechanism that differs from previously documented mechanisms regulating cell death. Cells dependent on mitochondrial respiration showed increased sensitivity to a copper ionophore elesclomol that induced cuproptosis. Maternal embryonic leucine zipper kinase(MELK) promotes tumorigenesis and tumor progression through the PI3K/mTOR pathway, which exerts its effects partly by targeting the pyruvate dehydrogenase complex(PDHc) and reprogramming the morphology and function of mitochondria. However, the role of MELK in cuproptosis remains unclear. Here, we validated that elevated MELK expression enhanced the activity of PI3K/mTOR signaling and subsequently promoted Dihydrolipoamide S-Acetyltransferase (DLAT) expression and stabilized mitochondrial function. This regulatory effect helped to improve mitochondrial respiration, eliminate excessive intracellular reactive oxygen species (ROS), reduce intracellular oxidative stress/damage and the possibility of mitochondria-induced cell fate alternations, and ultimately promote the progression of HCC. Meanwhile, elesclomol reduced translocase of outer mitochondrial membrane 20(TOM 20) expression and increased DLAT oligomers. Moreover, the above changes of MELK to HCC were abolished by elesclomol. In conclusion, MELK enhanced the levels of the cuproptosis-related signature(CRS) gene DLAT (especially the proportion of DLAT monomer) by activating the PI3K/mTOR pathway, thereby promoting elesclomol drug resistance, altering mitochondrial function, and ultimately promoting HCC progression.
The roles of m6A methylation in cervical cancer: functions, molecular mechanisms, and clinical applications
Authors: Mao Zhonghao , Wang Bingyu , Zhang Teng , Cui Baoxia
Published: November 2023

Cervical cancer (CC) is a gynecological neoplasm with the highest incidence rate, primarily attributed to the persistent infection of high-risk Human papillomavirus (HPV). Despite extensive research, the pathogenesis of CC remains unclear. N6-methyladenosine (m6A) methylation, the most prevalent form of epigenetic modification in RNA, is intricately linked to cell proliferation, metastasis, metabolism, and therapeutic resistance within the tumor microenvironment (TME) of CC. The involvement of the writer, reader, and eraser in m6A modification impacts the advancement of tumors through the regulation of RNA stability, nuclear export, translation efficiency, and RNA degradation. Here, we discuss the biogenesis of m6A, the atypical expressions of m6A regulators, the mechanisms of molecular interactions, and their functions in CC. Furthermore, we elucidate m6A modification of non-coding RNA. In the context of precision medicine, and with the advancements of genomics, proteomics, and high-throughput sequencing technologies, we summarize the application of m6A in the clinical diagnosis and treatment of CC. Additionally, new perspectives on detection methods, immune regulation, and nano-drug development are presented, which lay the foundation for further research of m6A and provide new ideas for the clinical treatment of CC.
An on-demand bioresorbable neurostimulator
Authors: Lee Dong-Min , Kang Minki , Hyun Inah , Park Byung-Joon , Kim Hye Jin , Nam Soo Hyun , Yoon Hong-Joon , Ryu Hanjun , Park Hyun-moon , Choi Byung-Ok , Kim Sang-Woo
Published: November 2023

Bioresorbable bioelectronics, with their natural degradation properties, hold significant potential to eliminate the need for surgical removal. Despite notable achievements, two major challenges hinder their practical application in medical settings. First, they necessitate sustainable energy solutions with biodegradable components via biosafe powering mechanisms. More importantly, reliability in their function is undermined by unpredictable device lifetimes due to the complex polymer degradation kinetics. Here, we propose an on-demand bioresorbable neurostimulator to address these issues, thus allowing for clinical operations to be manipulated using biosafe ultrasound sources. Our ultrasound-mediated transient mechanism enables (1) electrical stimulation through transcutaneous ultrasound-driven triboelectricity and (2) rapid device elimination using high-intensity ultrasound without adverse health effects. Furthermore, we perform neurophysiological analyses to show that our neurostimulator provides therapeutic benefits for both compression peripheral nerve injury and hereditary peripheral neuropathy. We anticipate that the on-demand bioresorbable neurostimulator will prove useful in the development of medical implants to treat peripheral neuropathy.
Lung SORT LNPs enable precise homology-directed repair mediated CRISPR/Cas genome correction in cystic fibrosis models
Authors: Wei Tuo , Sun Yehui , Cheng Qiang , Chatterjee Sumanta , Traylor Zachary , Johnson Lindsay T. , Coquelin Melissa L. , Wang Jialu , Torres Michael J. , Lian Xizhen , Wang Xu , Xiao Yufen , Hodges Craig A. , Siegwart Daniel J.
Published: November 2023

Approximately 10% of Cystic Fibrosis (CF) patients, particularly those with CF transmembrane conductance regulator (CFTR) gene nonsense mutations, lack effective treatments. The potential of gene correction therapy through delivery of the CRISPR/Cas system to CF-relevant organs/cells is hindered by the lack of efficient genome editor delivery carriers. Herein, we report improved Lung Selective Organ Targeting Lipid Nanoparticles (SORT LNPs) for efficient delivery of Cas9 mRNA, sgRNA, and donor ssDNA templates, enabling precise homology-directed repair-mediated gene correction in CF models. Optimized Lung SORT LNPs deliver mRNA to lung basal cells in Ai9 reporter mice. SORT LNP treatment successfully corrected the CFTR mutations in homozygous G542X mice and in patient-derived human bronchial epithelial cells with homozygous F508del mutations, leading to the restoration of CFTR protein expression and chloride transport function. This proof-of-concept study will contribute to accelerating the clinical development of mRNA LNPs for CF treatment through CRISPR/Cas gene correction.
Nanomedicine-based co-delivery of a calcium channel inhibitor and a small molecule targeting CD47 for lung cancer immunotherapy
Authors: Guo Yuedong , Bao Qunqun , Hu Ping , Shi Jianlin
Published: November 2023

Pro-tumoral macrophages in lung tumors present a significant challenge in immunotherapy. Here, we introduce a pH-responsive nanomedicine approach for activating anti-tumoral macrophages and dendritic cells. Using a layered double hydroxide nanosheet carrier, we co-deliver a T-type calcium channel inhibitor (TTA-Q6) and a CD47 inhibitor (RRX-001) into lung tumors. In the tumor acidic environment, TTA-Q6 is released, disrupting cancer cell calcium uptake, causing endoplasmic reticulum stress and inducing calreticulin transfer to the cell surface. Surface calreticulin activates macrophages and triggers dendritic cell maturation, promoting effective antigen presentation and therefore activating antitumor T cells. Simultaneously, RRX-001 reduces CD47 protein levels, aiding in preventing immune escape by calreticulin-rich cancer cells. In lung tumor models in male mice, this combined approach shows anti-tumor effects and immunity against tumor re-exposure, highlighting its potential for lung cancer immunotherapy.
A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
Authors: Ma Bin , Lu Caiyu , Wang Yiling , Yu Jingwen , Zhao Kankan , Xue Ran , Ren Hao , Lv Xiaofei , Pan Ronghui , Zhang Jiabao , Zhu Yongguan , Xu Jianming
Published: November 2023

Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome’s functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.
SARS-CoV-2 hijacks a cell damage response, which induces transcription of a more efficient Spike S-acyltransferase
Authors: S. Mesquita Francisco , Abrami Laurence , Bracq Lucie , Panyain Nattawadee , Mercier Vincent , Kunz Béatrice , Chuat Audrey , Carlevaro-Fita Joana , Trono Didier , van der Goot F. Gisou
Published: November 2023

SARS-CoV-2 infection requires Spike protein-mediated fusion between the viral and cellular membranes. The fusogenic activity of Spike depends on its post-translational lipid modification by host S-acyltransferases, predominantly ZDHHC20. Previous observations indicate that SARS-CoV-2 infection augments the S-acylation of Spike when compared to mere Spike transfection. Here, we find that SARS-CoV-2 infection triggers a change in the transcriptional start site of the zdhhc20 gene, both in cells and in an in vivo infection model, resulting in a 67-amino–acid-long N-terminally extended protein with approx. 40 times higher Spike acylating activity, resulting in enhanced fusion of viruses with host cells. Furthermore, we observed the same induced transcriptional change in response to other challenges, such as chemically induced colitis and pore-forming toxins, indicating that SARS-CoV-2 hijacks an existing cell damage response pathway to optimize it fusion glycoprotein.
Topological magnons driven by the Dzyaloshinskii-Moriya interaction in the centrosymmetric ferromagnet Mn5Ge3
Authors: dos Santos Dias M. , Biniskos N. , dos Santos F. J. , Schmalzl K. , Persson J. , Bourdarot F. , Marzari N. , Blügel S. , Brückel T. , Lounis S.
Published: November 2023

The phase of the quantum-mechanical wave function can encode a topological structure with wide-ranging physical consequences, such as anomalous transport effects and the existence of edge states robust against perturbations. While this has been exhaustively demonstrated for electrons, properties associated with the elementary quasiparticles in magnetic materials are still underexplored. Here, we show theoretically and via inelastic neutron scattering experiments that the bulk ferromagnet Mn5Ge3 hosts gapped topological Dirac magnons. Although inversion symmetry prohibits a net Dzyaloshinskii-Moriya interaction in the unit cell, it is locally allowed and is responsible for the gap opening in the magnon spectrum. This gap is predicted and experimentally verified to close by rotating the magnetization away from the c-axis with an applied magnetic field. Hence, Mn5Ge3 realizes a gapped Dirac magnon material in three dimensions. Its tunability by chemical doping or by thin film nanostructuring defines an exciting new platform to explore and design topological magnons. More generally, our experimental route to verify and control the topological character of the magnons is applicable to bulk centrosymmetric hexagonal materials, which calls for systematic investigation.
Direct observation of intrinsic room-temperature ferroelectricity in 2D layered CuCrP2S6
Authors: Io Weng Fu , Pang Sin -Yi , Wong Lok Wing , Zhao Yuqian , Ding Ran , Mao Jianfeng , Zhao Yifei , Guo Feng , Yuan Shuoguo , Zhao Jiong , Yi Jiabao , Hao Jianhua
Published: November 2023

Multiferroic materials have ignited enormous interest owing to their co-existence of ferroelectricity and ferromagnetism, which hold substantial promise for advanced device applications. However, the size effect, dangling bonds, and interface effect in traditional multiferroics severely hinder their potential in nanoscale device applications. Recent theoretical and experimental studies have evidenced the possibility of realizing two-dimensional (2D) multiferroicity in van der Waals (vdW) layered CuCrP2S6. However, the incorporation of magnetic Cr ions in the ferroelectric framework leads to antiferroelectric and antiferromagnetic orderings, while macroscopic spontaneous polarization is always absent. Herein, we report the direct observation of robust out-of-plane ferroelectricity in 2D vdW CuCrP2S6 at room temperature with a comprehensive investigation. Modification of the ferroelectric polarization states in 2D CuCrP2S6 nanoflakes is experimentally demonstrated. Moreover, external electric field-induced polarization switching and hysteresis loops are obtained in CuCrP2S6 down to ~2.6 nm (4 layers). By using atomically resolved scanning transmission electron microscopy, we unveil the origin of the emerged room-temperature ferroelectricity in 2D CuCrP2S6. Our work can facilitate the development of multifunctional nanodevices and provide important insights into the nature of ferroelectric ordering of this 2D vdW material.
Data-driven discovery of electrocatalysts for CO2 reduction using active motifs-based machine learning
Authors: Mok Dong Hyeon , Li Hong , Zhang Guiru , Lee Chaehyeon , Jiang Kun , Back Seoin
Published: November 2023

The electrochemical carbon dioxide reduction reaction (CO2RR) is an attractive approach for mitigating CO2 emissions and generating value-added products. Consequently, discovery of promising CO2RR catalysts has become a crucial task, and machine learning (ML) has been utilized to accelerate catalyst discovery. However, current ML approaches are limited to exploring narrow chemical spaces and provide only fragmentary catalytic activity, even though CO2RR produces various chemicals. Here, by merging pre-developed ML model and a CO2RR selectivity map, we establish high-throughput virtual screening strategy to suggest active and selective catalysts for CO2RR without being limited to a database. Further, this strategy can provide guidance on stoichiometry and morphology of the catalyst to researchers. We predict the activity and selectivity of 465 metallic catalysts toward four expected reaction products. During this process, we discover previously unreported and promising behavior of Cu-Ga and Cu-Pd alloys. These findings are then validated through experimental methods.
Dynamic construction of refractive index-dependent vibrations using surface plasmon-phonon polaritons
Authors: Zhou Hong , Ren Zhihao , Li Dongxiao , Xu Cheng , Mu Xiaojing , Lee Chengkuo
Published: November 2023

One of the fundamental hurdles in infrared spectroscopy is the failure of molecular identification when their infrared vibrational fingerprints overlap. Refractive index (RI) is another intrinsic property of molecules associated with electronic polarizability, but with limited contribution to molecular identification in mixed environments currently. Here, we investigate the coupling mode of localized surface plasmon and surface phonon polaritons for vibrational de-overlapping. The coupling mode is sensitive to the molecular refractive index, attributed to the RI-induced vibrational variations of surface phonon polaritons (SPhP) within the Reststrahlen band, referred to as RI-dependent SPhP vibrations. The RI-dependent SPhP vibrations are linked to molecular RI features. According to the deep-learning-augmented demonstration of bond-breaking-bond-making dynamic profiling in biological reaction, we substantiate that the RI-dependent SPhP vibrations effectively disentangle overlapping vibrational modes, achieving a 92% identification accuracy even for the strongly overlapping vibrational modes in the reaction. Our findings offer insights into the realm of light-matter interaction and provide a valuable toolkit for biomedicine applications.
Relational visual representations underlie human social interaction recognition
Authors: Malik Manasi , Isik Leyla
Published: November 2023

Humans effortlessly recognize social interactions from visual input. Attempts to model this ability have typically relied on generative inverse planning models, which make predictions by inverting a generative model of agents’ interactions based on their inferred goals, suggesting humans use a similar process of mental inference to recognize interactions. However, growing behavioral and neuroscience evidence suggests that recognizing social interactions is a visual process, separate from complex mental state inference. Yet despite their success in other domains, visual neural network models have been unable to reproduce human-like interaction recognition. We hypothesize that humans rely on relational visual information in particular, and develop a relational, graph neural network model, SocialGNN. Unlike prior models, SocialGNN accurately predicts human interaction judgments across both animated and natural videos. These results suggest that humans can make complex social interaction judgments without an explicit model of the social and physical world, and that structured, relational visual representations are key to this behavior.
Virtual lesions in MEG reveal increasing vulnerability of the language network from early childhood through adolescence
Authors: Williamson Brady J. , Greiner Hansel M. , Kadis Darren S.
Published: November 2023

In childhood, language outcomes following brain injury are inversely related to age. Neuroimaging findings suggest that extensive representation and/or topological redundancy may confer the pediatric advantage. Here, we assess whole brain and language network resilience using in silico attacks, for 85 children participating in a magnetoencephalography (MEG) study. Nodes are targeted based on eigenvector centrality, betweenness centrality, or at random. The size of each connected component is assessed after iterated node removal; the percolation point, or moment of dis-integration, is defined as the first instance where the second largest component peaks in size. To overcome known effects of fixed thresholding on subsequent graph and resilience analyses, we study percolation across all possible network densities, within a Functional Data Analysis (FDA) framework. We observe age-related increases in vulnerability for random and betweenness centrality-based attacks for whole-brain and stories networks (adjusted-p < 0.05). Here we show that changes in topology underlie increasing language network vulnerability in development.
Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Authors: Sheridan Paul O. , Meng Yiyu , Williams Tom A. , Gubry-Rangin Cécile
Published: November 2023

Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.
Synthesis of dienes from pyrrolidines using skeletal modification
Authors: Qin Haitao , Guo Ting , Lin Ken , Li Guigen , Lu Hongjian
Published: November 2023

Saturated N-heterocyclic pyrrolidines are common in natural products, medicinal compounds and agrochemicals. However, reconstruction of their skeletal structures creating new chemical space is a challenging task, and limited methods exist for this purpose. In this study, we report a skeletal modification strategy for conversion of polar cyclic pyrrolidines into nonpolar linear dienes through a N-atom removal and deconstruction process. This involves N-sulfonylazidonation followed by rearrangement of the resulting sulfamoyl azide intermediates. This can be an energetically unfavorable process, which involves the formation of active C–C π bonds, the consumption of inert C–N and C–C σ bonds and the destruction of stable five-membered rings, but we have used it here to produce versatile conjugated and nonconjugated dienes with links of varying lengths. We also studied the application of this method in late-stage skeletal modification of bioactive compounds, formal traceless C(sp2)–H functionalization and formal N-atom deletion.
Predicting early breast cancer recurrence from histopathological images in the Carolina Breast Cancer Study
Authors: Shi Yifeng , Olsson Linnea T. , Hoadley Katherine A. , Calhoun Benjamin C. , Marron J. S. , Geradts Joseph , Niethammer Marc , Troester Melissa A.
Published: November 2023

Approaches for rapidly identifying patients at high risk of early breast cancer recurrence are needed. Image-based methods for prescreening hematoxylin and eosin (H&E) stained tumor slides could offer temporal and financial efficiency. We evaluated a data set of 704 1-mm tumor core H&E images (2–4 cores per case), corresponding to 202 participants (101 who recurred; 101 non-recurrent matched on age and follow-up time) from breast cancers diagnosed between 2008–2012 in the Carolina Breast Cancer Study. We leveraged deep learning to extract image information and trained a model to identify recurrence. Cross-validation accuracy for predicting recurrence was 62.4% [95% CI: 55.7, 69.1], similar to grade (65.8% [95% CI: 59.3, 72.3]) and ER status (66.3% [95% CI: 59.8, 72.8]). Interestingly, 70% (19/27) of early-recurrent low-intermediate grade tumors were identified by our image model. Relative to existing markers, image-based analyses provide complementary information for predicting early recurrence.
Interpass temperature effects on WAAM ER316L stainless steel corrosion using potentiostatic pulse tests
Authors: Penot Corentin , Wharton Julian , Addison Adrian , Wang Yikun , Lu Qing
Published: November 2023

The effect of interpass temperature on the microstructure and pit nucleation behaviour in wire and arc additive manufacturing (WAAM) deposited ER316L stainless steel is investigated. Lowering the interpass temperature increases the ferrite content and decreases the sigma phase precipitation. Potentiostatic pulse measurements show that the WAAM ER316L pits develop predominantly near sigma phases and have higher pit density compared to a wrought 316L (UNS S31600). The pitting susceptibility of WAAM ER316L increases with increasing interpass temperature due to the precipitation of larger sigma phase enhancing the elemental segregation.
Global dataset of soil organic carbon in tidal marshes
Authors: Maxwell Tania L. , Rovai André S. , Adame Maria Fernanda , Adams Janine B. , Álvarez-Rogel José , Austin William E. N. , Beasy Kim , Boscutti Francesco , Böttcher Michael E. , Bouma Tjeerd J. , Bulmer Richard H. , Burden Annette , Burke Shannon A. , Camacho Saritta , Chaudhary Doongar R. , Chmura Gail L. , Copertino Margareth , Cott Grace M. , Craft Christopher , Day John , de los Santos Carmen B. , Denis Lionel , Ding Weixin , Ellison Joanna C. , Ewers Lewis Carolyn J. , Giani Luise , Gispert Maria , Gontharet Swanne , González-Pérez José A. , González-Alcaraz M. Nazaret , Gorham Connor , Graversen Anna Elizabeth L. , Grey Anthony , Guerra Roberta , He Qiang , Holmquist James R. , Jones Alice R. , Juanes José A. , Kelleher Brian P. , Kohfeld Karen E. , Krause-Jensen Dorte , Lafratta Anna , Lavery Paul S. , Laws Edward A. , Leiva-Dueñas Carmen , Loh Pei Sun , Lovelock Catherine E. , Lundquist Carolyn J. , Macreadie Peter I. , Mazarrasa Inés , Megonigal J. Patrick , Neto Joao M. , Nogueira Juliana , Osland Michael J. , Pagès Jordi F. , Perera Nipuni , Pfeiffer Eva-Maria , Pollmann Thomas , Raw Jacqueline L. , Recio María , Ruiz-Fernández Ana Carolina , Russell Sophie K. , Rybczyk John M. , Sammul Marek , Sanders Christian , Santos Rui , Serrano Oscar , Siewert Matthias , Smeaton Craig , Song Zhaoliang , Trasar-Cepeda Carmen , Twilley Robert R. , Van de Broek Marijn , Vitti Stefano , Antisari Livia Vittori , Voltz Baptiste , Wails Christy N. , Ward Raymond D. , Ward Melissa , Wolfe Jaxine , Yang Renmin , Zubrzycki Sebastian , Landis Emily , Smart Lindsey , Spalding Mark , Worthington Thomas A.
Published: November 2023

Tidal marshes store large amounts of organic carbon in their soils. Field data quantifying soil organic carbon (SOC) stocks provide an important resource for researchers, natural resource managers, and policy-makers working towards the protection, restoration, and valuation of these ecosystems. We collated a global dataset of tidal marsh soil organic carbon (MarSOC) from 99 studies that includes location, soil depth, site name, dry bulk density, SOC, and/or soil organic matter (SOM). The MarSOC dataset includes 17,454 data points from 2,329 unique locations, and 29 countries. We generated a general transfer function for the conversion of SOM to SOC. Using this data we estimated a median (± median absolute deviation) value of 79.2 ± 38.1 Mg SOC ha−1 in the top 30 cm and 231 ± 134 Mg SOC ha−1 in the top 1 m of tidal marsh soils globally. This data can serve as a basis for future work, and may contribute to incorporation of tidal marsh ecosystems into climate change mitigation and adaptation strategies and policies.
Rapid surveillance of New York City healthcare center egress behaviors during the 2020 COVID-19 lockdown
Authors: Kirchner Thomas , Jiang Haoran , Gao Hong , Kabutaulaka Germaine , Cheong Darlene , Jiang Yungi , Khan Aseah , Qiu Weiyi , Tai Nikki , Truong Tiffany , Virk Maimunah , Gmelch Peter , Carey Chris , Laefer Debra
Published: November 2023

This rapid response surveillance project was funded by the National Science Foundation (NSF) to collect “perishable” data on egress behaviors and neighborhood conditions surrounding healthcare centers (HCCs) in New York City (NYC) during the initial NYC COVID-19 PAUSE ordinance from March 22nd to May 19th, 2020. Anonymized data on NYC HCC egress behaviors were collected by observational field workers using phone-based mapping applications. Each egress trip record includes the day of week, time of day, destination category type, along with an array of behavioral outcome categories, ambient weather conditions and socio-economic factors. Egress trajectories with precise estimates of distance traveled and the spatial dispersion or “spread” around each HCC were added via post-processing. The data collection and cleaning process resulted in 5,030 individual egress records from 18 facilities over a 9-week period.
Twenty-nine years of continuous monthly capture-mark-recapture data of multimammate mice (Mastomys natalensis) in Morogoro, Tanzania
Authors: Leirs Herwig , Kirkpatrick Lucinda , Sluydts Vincent , Sabuni Christopher , Borremans Benny , Katakweba Abdul , Massawe Apia , Makundi Rhodes , Mulungu Loth , Machang’u Robert , Mariën Joachim
Published: November 2023

The multimammate mice (Mastomys natalensis) is the most-studied rodent species in sub-Saharan Africa, where it is an important pest species in agriculture and carrier of zoonotic diseases (e.g. Lassa virus). Here, we provide a unique dataset that consists of twenty-nine years of continuous monthly capture-mark-recapture entries on one 3 ha mosaic field (MOSA) in Morogoro, Tanzania. It is one of the most accurate and long-running capture-recapture time series on a small mammal species worldwide and unique to Africa. The database can be used by ecologists to test hypotheses on the population dynamics of small mammals (e.g. to test the effect of climate change), or to validate new algorithms on real long-term field data (e.g. new survival analyses techniques). It is also useful for both scientists and decision-makers who want to optimize rodent control strategies and predict outbreaks of multimammate mice.
IDH1R132H mutation increases radiotherapy efficacy and a 4-gene radiotherapy-related signature of WHO grade 4 gliomas
Authors: Han Xuetao , Zhou Huandi , Sun Wei , Hou Liubing , Wang Yanqiang , Wang Hong , Lv Zhongqiang , Xue Xiaoying
Published: November 2023

The prognosis for the WHO grade 4 IDH-mutant astrocytoma is better than IDH-wildtype glioblastoma (GBM) patients. The purpose of this study is to explore the potential mechanism of how IDH1 mutation can increase the efficacy of radiotherapy and to establish a risk-score model to predict the efficacy of radiotherapy in WHO grade 4 gliomas. First, we conducted experimental study on the effect of IDH1R132H mutation on glioma cells in vitro. Radiosensitivity of glioma cells was detected by γ-H2AX after 5 Gy radiation. Cell proliferation, migration and invasion were determined respectively by CCK-8, EDU, monolayer cell migration scratch assay and Transwell assay. Then we analyzed IDH1 gene status and the survival of WHO grade 4 glioma patients received radiotherapy in our center and verified our results by analyzing CGGA and TCGA database. For the risk-score model, we use CGGA data to find genetic differences between WHO grade 4 IDH-mutant astrocytoma and IDH-wildtype GBM patients, and determined a 4-gene radiotherapy-related signature through survival analysis by R software. Evaluation and verification through different glioma validation sets and different statistical methods. For in vitro experiments, we established glioma cells stably overexpressing IDH1 wild-type and IDH1-mutant proteins. γ-H2AX assay showed that IDH1-mutant glioma cells had higher radiosensitivity than wild-type. CCK-8 and EDU assay showed that proliferation capacity of IDH1-mutant glioma cells declined. Transwell assay and monolayer cell migration scratch assay also showed that IDH1-mutant glioma cells reduced migration and invasion capabilities. Among the 83 WHO grade 4 glioma patients who received radiotherapy in our center, WHO grade 4 IDH-mutant astrocytoma patients had longer OS and PFS versus IDH-wildtype GBM (P = 0.0336, P = 0.0324, respectively). TCGA and CGGA database analysis had the similar results. Through complex analysis of CGGA and TCGA databases, we established a risk-model that can predict the efficacy of radiotherapy for WHO grade 4 glioma patients. The 4-gene radiotherapy-related signature including ADD3, GRHPR, RHBDL1 and SLC9A9. Patients in the high-risk group had worse OS compared to low-risk group (P = 0.0001). High- and low-risk groups of patients receiving radiotherapy have significant survival differences, while patients who did not receive radiotherapy have no survival difference both in CGGA and TCGA databases. WHO grade 4 IDH-mutant astrocytoma is more radiosensitive than IDH-wildtype GBM patients. Our 4-gene radiotherapy-related signature can predict the radiation efficacy of WHO grade 4 glioma patients, and it may provide some reference for clinical treatment options.
COVID-19 screening in low resource settings using artificial intelligence for chest radiographs and point-of-care blood tests
Authors: Murphy Keelin , Muhairwe Josephine , Schalekamp Steven , van Ginneken Bram , Ayakaka Irene , Mashaete Kamele , Katende Bulemba , van Heerden Alastair , Bosman Shannon , Madonsela Thandanani , Gonzalez Fernandez Lucia , Signorell Aita , Bresser Moniek , Reither Klaus , Glass Tracy R.
Published: November 2023

Artificial intelligence (AI) systems for detection of COVID-19 using chest X-Ray (CXR) imaging and point-of-care blood tests were applied to data from four low resource African settings. The performance of these systems to detect COVID-19 using various input data was analysed and compared with antigen-based rapid diagnostic tests. Participants were tested using the gold standard of RT-PCR test (nasopharyngeal swab) to determine whether they were infected with SARS-CoV-2. A total of 3737 (260 RT-PCR positive) participants were included. In our cohort, AI for CXR images was a poor predictor of COVID-19 (AUC = 0.60), since the majority of positive cases had mild symptoms and no visible pneumonia in the lungs. AI systems using differential white blood cell counts (WBC), or a combination of WBC and C-Reactive Protein (CRP) both achieved an AUC of 0.74 with a suggested optimal cut-off point at 83% sensitivity and 63% specificity. The antigen-RDT tests in this trial obtained 65% sensitivity at 98% specificity. This study is the first to validate AI tools for COVID-19 detection in an African setting. It demonstrates that screening for COVID-19 using AI with point-of-care blood tests is feasible and can operate at a higher sensitivity level than antigen testing.
Ab initio structural dynamics of pure and nitrogen-containing amorphous carbon
Authors: Steele Brad A. , Bastea Sorin , Kuo I-Feng W.
Published: November 2023

Amorphous carbon (a-C) has attracted considerable interest due to its desirable properties, which are strongly dependent on its structure, density and impurities. Using ab initio molecular dynamics simulations we show that the sp2/sp3 content and underlying structural order of a-C produced via liquid quenching evolve at high temperatures and pressures on sub-nanosecond timescales. Graphite-like densities ($$\lesssim$$
≲
2.7 g/cc) favor the formation of layered arrangements characterized by sp2 disordered bonding resembling recently synthesized monolayer amorphous carbon (MAC), while at diamond-like densities ($$\gtrsim$$
≳
3.3 g/cc) the resulting structures are dominated by disordered tetrahedral sp3 hybridization typical of diamond-like amorphous carbon (DLC). At intermediate densities the system is a highly compressible mixture of coexisting sp2 and sp3 regions that continue to segregate over 10’s of picoseconds. The addition of nitrogen (20.3%) (a-CN) generates major system features similar with those of a-C, but has the unexpected effect of reinforcing the thermodynamically disfavored carbon structural motifs at low and high densities, while inhibiting phase separation in the intermediate region. At the same time, no nitrogen elimination from the carbon framework is observed above $$\simeq$$
≃
2.8 g/cc, suggesting that nitrogen impurities are likely to remain embedded in the carbon structures during fast temperature quenches at high pressures.
Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance
Authors: Bloemen Bram , Gand Mathieu , Vanneste Kevin , Marchal Kathleen , Roosens Nancy H. C. , De Keersmaecker Sigrid C. J.
Published: November 2023

Rapid, accurate and comprehensive diagnostics are essential for outbreak prevention and pathogen surveillance. Real-time, on-site metagenomics on miniaturized devices, such as Oxford Nanopore Technologies MinION sequencing, could provide a promising approach. However, current sample preparation protocols often require substantial equipment and dedicated laboratories, limiting their use. In this study, we developed a rapid on-site applicable DNA extraction and library preparation approach for nanopore sequencing, using portable devices. The optimized method consists of a portable mechanical lysis approach followed by magnetic bead-based DNA purification and automated sequencing library preparation, and resulted in a throughput comparable to a current optimal, laboratory-based protocol using enzymatic digestion to lyse cells. By using spike-in reference communities, we compared the on-site method with other workflows, and demonstrated reliable taxonomic profiling, despite method-specific biases. We also demonstrated the added value of long-read sequencing by recovering reads containing full-length antimicrobial resistance genes, and attributing them to a host species based on the additional genomic information they contain. Our method may provide a rapid, widely-applicable approach for microbial detection and surveillance in a variety of on-site settings.
Molecular genetic divergence analysis amongst high curcumin lines of Golden Crop (Curcuma longa L.) using SSR marker and use in trait-specific breeding
Authors: Gogoi Anindita , Munda Sunita , Paw Manabi , Begum Twahira , Siddiqui Manzer H. , Gaafar Abdel-Rhman Z. , Kesawat Mahipal Singh , Lal Mohan
Published: November 2023

Curcuma longa L., is recognized worldwide as a medicinally and economically important plant species due to its curcumin content which is an industrially important compound. In this study, a total of 329 accessions were collected from four states of India and planted in the experimental farm of CSIR-NEIST, Jorhat, India, in augmented design. Among these, 152 high curcumin (> 1.50%) accessions were screened for molecular divergence study using 39 SSR primers. The primers showed the most efficient outcome with 2–8 allele/ loci and a total 163 number of alleles with 100% polymorphism. Cluster analysis revealed the construction of three clusters, out of which one cluster was geographically dependent, and germplasm was particularly from Assam state. Jaccard's pairwise coefficient showed maximum genetic dissimilarity of (0.75) between accession RRLJCL 3 and RRLJCL 126, indicating high variation as it was from two different states viz Arunachal Pradesh and Nagaland respectively and minimum genetic dissimilarity of (0.09) between RRLJCL 58 and RRLJCL 59 indicating significantly less variation as the two accessions were from same state, i.e., Arunachal Pradesh. Analysis of Molecular Variance (AMOVA) revealed high molecular variation within the population (87%) and significantly less variation among the population (13%). Additionally, Neighbour Joining dendrogram, Principal Component Analysis (PCA), and bar plot structure revealed similar clustering of germplasm. This diversity assessment will help in selecting the trait-specific genotypes, crop improvement program, conservation of gene pool, marker-assisted breeding, and quantitative trait loci identification. Moreover, to the best of our knowledge, it is the first molecular diversity report among 152 high curcumin lines of C. longa from North East India using 39 SSR primers.