bluuebunny/crossref_metadata_2025 huggingface dataset:
Incident allergic diseases in post-COVID-19 condition: multinational cohort studies from South Korea, Japan and the UK
Authors: Oh Jiyeon , Lee Myeongcheol , Kim Minji , Kim Hyeon Jin , Lee Seung Won , Rhee Sang Youl , Koyanagi Ai , Smith Lee , Kim Min Seo , Lee Hayeon , Lee Jinseok , Yon Dong Keon
Published: April 2024

As mounting evidence suggests a higher incidence of adverse consequences, such as disruption of the immune system, among patients with a history of COVID-19, we aimed to investigate post-COVID-19 conditions on a comprehensive set of allergic diseases including asthma, allergic rhinitis, atopic dermatitis, and food allergy. We used nationwide claims-based cohorts in South Korea (K-CoV-N; n = 836,164; main cohort) and Japan (JMDC; n = 2,541,021; replication cohort A) and the UK Biobank cohort (UKB; n = 325,843; replication cohort B) after 1:5 propensity score matching. Among the 836,164 individuals in the main cohort (mean age, 50.25 years [SD, 13.86]; 372,914 [44.6%] women), 147,824 were infected with SARS-CoV-2 during the follow-up period (2020−2021). The risk of developing allergic diseases, beyond the first 30 days of diagnosis of COVID-19, significantly increased (HR, 1.20; 95% CI, 1.13−1.27), notably in asthma (HR, 2.25; 95% CI, 1.80−2.83) and allergic rhinitis (HR, 1.23; 95% CI, 1.15−1.32). This risk gradually decreased over time, but it persisted throughout the follow-up period (≥6 months). In addition, the risk increased with increasing severity of COVID-19. Notably, COVID-19 vaccination of at least two doses had a protective effect against subsequent allergic diseases (HR, 0.81; 95% CI, 0.68−0.96). Similar findings were reported in the replication cohorts A and B. Although the potential for misclassification of pre-existing allergic conditions as incident diseases remains a limitation, ethnic diversity for evidence of incident allergic diseases in post-COVID-19 condition has been validated by utilizing multinational and independent population-based cohorts.
Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages
Authors: Liang Jie-Liang , Feng Shi-wei , Lu Jing-li , Wang Xiao-nan , Li Feng-lin , Guo Yu-qian , Liu Shen-yan , Zhuang Yuan-yue , Zhong Sheng-ji , Zheng Jin , Wen Ping , Yi Xinzhu , Jia Pu , Liao Bin , Shu Wen-sheng , Li Jin-tian
Published: April 2024

Phosphorus (P) limitation of ecosystem processes is widespread in terrestrial habitats. While a few auxiliary metabolic genes (AMGs) in bacteriophages from aquatic habitats are reported to have the potential to enhance P-acquisition ability of their hosts, little is known about the diversity and potential ecological function of P-acquisition genes encoded by terrestrial bacteriophages. Here, we analyze 333 soil metagenomes from five terrestrial habitat types across China and identify 75 viral operational taxonomic units (vOTUs) that encode 105 P-acquisition AMGs. These AMGs span 17 distinct functional genes involved in four primary processes of microbial P-acquisition. Among them, over 60% (11/17) have not been reported previously. We experimentally verify in-vitro enzymatic activities of two pyrophosphatases and one alkaline phosphatase encoded by P-acquisition vOTUs. Thirty-six percent of the 75 P-acquisition vOTUs are detectable in a published global topsoil metagenome dataset. Further analyses reveal that, under certain circumstances, the identified P-acquisition AMGs have a greater influence on soil P availability and are more dominant in soil metatranscriptomes than their corresponding bacterial genes. Overall, our results reinforce the necessity of incorporating viral contributions into biogeochemical P cycling.
Monolithically integrated micro-supercapacitors with high areal number density produced by surface adhesive-directed electrolyte assembly
Authors: Wang Sen , Zheng Shuanghao , Shi Xiaoyu , Das Pratteek , Li Linmei , Zhu Yuanyuan , Lu Yao , Feng Xinliang , Wu Zhong-Shuai
Published: April 2024

Accurately placing very small amounts of electrolyte on tiny micro-supercapacitors (MSCs) arrays in close proximity is a major challenge. This difficulty hinders the development of densely-compact monolithically integrated MSCs (MIMSCs). To overcome this grand challenge, we demonstrate a controllable electrolyte directed assembly strategy for precise isolation of densely-packed MSCs at micron scale, achieving scalable production of MIMSCs with ultrahigh areal number density and output voltage. We fabricate a patterned adhesive surface across MIMSCs, that induce electrolyte directed assembly on 10,000 highly adhesive MSC regions, achieving a 100 µm-scale spatial separation between each electrolyte droplet within seconds. The resultant MIMSCs achieve an areal number density of 210 cells cm−2 and a high areal voltage of 555 V cm−2. Further, cycling the MIMSCs at 190 V over 9000 times manifests no performance degradation. A seamlessly integrated system of ultracompact wirelessly-chargeable MIMSCs is also demonstrated to show its practicality and versatile applicability.
Reconstructing the evolution history of networked complex systems
Authors: Wang Junya , Zhang Yi-Jiao , Xu Cong , Li Jiaze , Sun Jiachen , Xie Jiarong , Feng Ling , Zhou Tianshou , Hu Yanqing
Published: April 2024

The evolution processes of complex systems carry key information in the systems’ functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be extracted, including protein-protein interaction, ecology, and social network systems. The recovered evolution process has demonstrations of immense scientific values, such as interpreting the evolution of protein-protein interaction network, facilitating structure prediction, and particularly revealing the key co-evolution features of network structures such as preferential attachment, community structure, local clustering, degree-degree correlation that could not be explained collectively by previous theories. Intriguingly, we discover that for large networks, if the performance of the machine learning model is slightly better than a random guess on the pairwise order of links, reliable restoration of the overall network formation process can be achieved. This suggests that evolution history restoration is generally highly feasible on empirical networks.
Dynamic encoding of temperature in the central circadian circuit coordinates physiological activities
Authors: Li Hailiang , Li Zhiyi , Yuan Xin , Tian Yue , Ye Wenjing , Zeng Pengyu , Li Xiao-Ming , Guo Fang
Published: April 2024

The circadian clock regulates animal physiological activities. How temperature reorganizes circadian-dependent physiological activities remains elusive. Here, using in-vivo two-photon imaging with the temperature control device, we investigated the response of the Drosophila central circadian circuit to temperature variation and identified that DN1as serves as the most sensitive temperature-sensing neurons. The circadian clock gate DN1a’s diurnal temperature response. Trans-synaptic tracing, connectome analysis, and functional imaging data reveal that DN1as bidirectionally targets two circadian neuronal subsets: activity-related E cells and sleep-promoting DN3s. Specifically, behavioral data demonstrate that the DN1a-E cell circuit modulates the evening locomotion peak in response to cold temperature, while the DN1a-DN3 circuit controls the warm temperature-induced nocturnal sleep reduction. Our findings systematically and comprehensively illustrate how the central circadian circuit dynamically integrates temperature and light signals to effectively coordinate wakefulness and sleep at different times of the day, shedding light on the conserved neural mechanisms underlying temperature-regulated circadian physiology in animals.
Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks
Authors: Mohebbi Fatemeh , Zelikovsky Alex , Mangul Serghei , Chowell Gerardo , Skums Pavel
Published: April 2024

The emergence of viral variants with altered phenotypes is a public health challenge underscoring the need for advanced evolutionary forecasting methods. Given extensive epistatic interactions within viral genomes and known viral evolutionary history, efficient genomic surveillance necessitates early detection of emerging viral haplotypes rather than commonly targeted single mutations. Haplotype inference, however, is a significantly more challenging problem precluding the use of traditional approaches. Here, using SARS-CoV-2 evolutionary dynamics as a case study, we show that emerging haplotypes with altered transmissibility can be linked to dense communities in coordinated substitution networks, which become discernible significantly earlier than the haplotypes become prevalent. From these insights, we develop a computational framework for inference of viral variants and validate it by successful early detection of known SARS-CoV-2 strains. Our methodology offers greater scalability than phylogenetic lineage tracing and can be applied to any rapidly evolving pathogen with adequate genomic surveillance data.
Obesity-related T cell dysfunction impairs immunosurveillance and increases cancer risk
Authors: Piening Alexander , Ebert Emily , Gottlieb Carter , Khojandi Niloufar , Kuehm Lindsey M. , Hoft Stella G. , Pyles Kelly D. , McCommis Kyle S. , DiPaolo Richard J. , Ferris Stephen T. , Alspach Elise , Teague Ryan M.
Published: April 2024

Obesity is a well-established risk factor for human cancer, yet the underlying mechanisms remain elusive. Immune dysfunction is commonly associated with obesity but whether compromised immune surveillance contributes to cancer susceptibility in individuals with obesity is unclear. Here we use a mouse model of diet-induced obesity to investigate tumor-infiltrating CD8 + T cell responses in lean, obese, and previously obese hosts that lost weight through either dietary restriction or treatment with semaglutide. While both strategies reduce body mass, only dietary intervention restores T cell function and improves responses to immunotherapy. In mice exposed to a chemical carcinogen, obesity-related immune dysfunction leads to higher incidence of sarcoma development. However, impaired immunoediting in the obese environment enhances tumor immunogenicity, making the malignancies highly sensitive to immunotherapy. These findings offer insight into the complex interplay between obesity, immunity and cancer, and provide explanation for the obesity paradox observed in clinical immunotherapy settings.
Physics-inspired transfer learning for ML-prediction of CNT band gaps from limited data
Authors: Bets Ksenia V. , O’Driscoll Patrick C. , Yakobson Boris I.
Published: April 2024

Recent years have seen a drastic increase in the scientific use of machine learning (ML) techniques, yet their applications remain limited for many fields. Here, we demonstrate techniques that allow overcoming two obstacles to the widespread adoption of ML, particularly relevant to nanomaterials and nanoscience fields. Using the prediction of the band gap values of carbon nanotubes as a typical example, we address the representation of the periodic data as well as training on extremely small datasets. We successfully showed that careful choice of the activation function allows capturing periodic tendencies in the datasets that are common in physical data and previously posed significant difficulty for neural networks. In particular, utilization of the recently proposed parametric periodic Snake activation function shows a dramatic improvement. Furthermore, tackling a typical lack of accurate data, we used the transfer learning technique utilizing more abundant low-quality computational data and achieving outstanding accuracy on a significantly expanded dataspace. This strategy was enabled by the use of a combination of the Snake and ReLU layers, capturing data periodicity and amplitude, respectively. Hence, retraining only ReLU layers allowed the transfer of the periodic tendencies captured from low-quality data to the final high-accuracy neural network. Those techniques are expected to expand the usability of ML approaches in application to physical data in general and the fields of nanomaterials in particular.
Model-based financial regulations impair the transition to net-zero carbon emissions
Authors: Gasparini Matteo , Ives Matthew C. , Carr Ben , Fry Sophie , Beinhocker Eric
Published: April 2024

Investments via the financial system are essential for fostering the green transition. However, the role of existing financial regulations in influencing investment decisions is understudied. Here we analyse data from the European Banking Authority to show that existing financial accounting frameworks might inadvertently be creating disincentives for investments in low-carbon assets. We find that differences in the provision coverage ratio indicate that banks must account for nearly double the loan loss provisions for lending to low-carbon sectors as compared with high-carbon sectors. This bias is probably the result of basing risk estimates on historical data. We show that the average historical financial risk of the oil and gas sector has been consistently estimated to be lower than that of renewable energy. These results indicate that this bias could be present in other model-based regulations, such as capital requirements, and possibly impact the ability of banks to fund green investments.
SARS-CoV-2 variant with the spike protein mutation F306L in the southern border provinces of Thailand
Authors: Sila Thanit , Surasombatpattana Smonrapat , Rajborirug Songyos , Laochareonsuk Wison , Choochuen Pongsakorn , Kongkamol Chanon , Ingviya Thammasin , Prompat Napat , Mahasirimongkol Surakameth , Sangkhathat Surasak , Aiewsakun Pakorn
Published: April 2024

The southernmost part of Thailand is a unique and culturally diverse region that has been greatly affected by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak during the coronavirus disease-2019 pandemic. To gain insights into this situation, we analyzed 1942 whole-genome sequences of SARS-CoV-2 obtained from the five southernmost provinces of Thailand between April 2021 and March 2022, together with those publicly available in the Global Initiative on Sharing All Influenza Data database. Our analysis revealed evidence for transboundary transmissions of the virus in and out of the five southernmost provinces during the study period, from both domestic and international sources. The most prevalent viral variant in our sequence dataset was the Delta B.1.617.2.85 variant, also known as the Delta AY.85 variant, with many samples carrying a non-synonymous mutation F306L in their spike protein. Protein–protein docking and binding interface analyses suggested that the mutation may enhance the binding between the spike protein and host cell receptor protein angiotensin-converting enzyme 2, and we found that the mutation was significantly associated with an increased fatality rate. This mutation has also been observed in other SARS-CoV-2 variants, suggesting that it is of particular interest and should be monitored.
Prediction model for spinal cord injury in spinal tuberculosis patients using multiple machine learning algorithms: a multicentric study
Authors: Feng Sitan , Wang Shujiang , Liu Chong , Wu Shaofeng , Zhang Bin , Lu Chunxian , Huang Chengqian , Chen Tianyou , Zhou Chenxing , Zhu Jichong , Chen Jiarui , Xue Jiang , Wei Wendi , Zhan Xinli
Published: April 2024

Spinal cord injury (SCI) is a prevalent and serious complication among patients with spinal tuberculosis (STB) that can lead to motor and sensory impairment and potentially paraplegia. This research aims to identify factors associated with SCI in STB patients and to develop a clinically significant predictive model. Clinical data from STB patients at a single hospital were collected and divided into training and validation sets. Univariate analysis was employed to screen clinical indicators in the training set. Multiple machine learning (ML) algorithms were utilized to establish predictive models. Model performance was evaluated and compared using receiver operating characteristic (ROC) curves, area under the curve (AUC), calibration curve analysis, decision curve analysis (DCA), and precision-recall (PR) curves. The optimal model was determined, and a prospective cohort from two other hospitals served as a testing set to assess its accuracy. Model interpretation and variable importance ranking were conducted using the DALEX R package. The model was deployed on the web by using the Shiny app. Ten clinical characteristics were utilized for the model. The random forest (RF) model emerged as the optimal choice based on the AUC, PRs, calibration curve analysis, and DCA, achieving a test set AUC of 0.816. Additionally, MONO was identified as the primary predictor of SCI in STB patients through variable importance ranking. The RF predictive model provides an efficient and swift approach for predicting SCI in STB patients.
Integrated management of groundwater quantity, physicochemical properties, and microbial quality in West Nile delta using a new MATLAB code and geographic information system mapping
Authors: Shehata Mohamed , Zaid Samir M. , Al-Goul Soha T. , Shami Ashwag , Al Syaad Khalid M. , Ahmed Ahmed Ezzat , Mostafa Yasser S. , Al-Quwaie Diana A. , Ashkan Mada F. , Alqahtani Fatimah S. , Hassan Yusuf A. , Taha Taha F. , El-Tarabily Khaled A. , AbuQamar Synan F.
Published: April 2024

Groundwater is an excellent alternative to freshwater for drinking, irrigation, and developing arid regions. Agricultural, commercial, industrial, residential, and municipal activities may affect groundwater quantity and quality. Therefore, we aimed to use advanced methods/techniques to monitor the piezometric levels and collect groundwater samples to test their physicochemical and biological characteristics. Our results using software programs showed two main types of groundwater: the most prevalent was the Na–Cl type, which accounts for 94% of the groundwater samples, whereas the Mg–Cl type was found in 6% of samples only. In general, the hydraulic gradient values, ranging from medium to low, could be attributed to the slow movement of groundwater. Salinity distribution in groundwater maps varied between 238 and 1350 mg L−1. Although lower salinity values were observed in northwestern wells, higher values were recorded in southern ones. The collected seventeen water samples exhibited brackish characteristics and were subjected to microbial growth monitoring. Sample WD12 had the lowest total bacterial count (TBC) of 4.8 ± 0.9 colony forming unit (CFU mg L−1), while WD14 had the highest TBC (7.5 ± 0.5 CFU mg L−1). None of the tested water samples, however, contained pathogenic microorganisms. In conclusion, the current simulation models for groundwater drawdown of the Quaternary aquifer system predict a considerable drawdown of water levels over the next 10, 20, and 30 years with the continuous development of the region.
Establishing a reference focal plane using convolutional neural networks and beads for brightfield imaging
Authors: Chalfoun Joe , Lund Steven P. , Ling Chenyi , Peskin Adele , Pierce Laura , Halter Michael , Elliott John , Sarkar Sumona
Published: April 2024

Repeatability of measurements from image analytics is difficult, due to the heterogeneity and complexity of cell samples, exact microscope stage positioning, and slide thickness. We present a method to define and use a reference focal plane that provides repeatable measurements with very high accuracy, by relying on control beads as reference material and a convolutional neural network focused on the control bead images. Previously we defined a reference effective focal plane (REFP) based on the image gradient of bead edges and three specific bead image features. This paper both generalizes and improves on this previous work. First, we refine the definition of the REFP by fitting a cubic spline to describe the relationship between the distance from a bead’s center and pixel intensity and by sharing information across experiments, exposures, and fields of view. Second, we remove our reliance on image features that behave differently from one instrument to another. Instead, we apply a convolutional regression neural network (ResNet 18) trained on cropped bead images that is generalizable to multiple microscopes. Our ResNet 18 network predicts the location of the REFP with only a single inferenced image acquisition that can be taken across a wide range of focal planes and exposure times. We illustrate the different strategies and hyperparameter optimization of the ResNet 18 to achieve a high prediction accuracy with an uncertainty for every image tested coming within the microscope repeatability measure of 7.5 µm from the desired focal plane. We demonstrate the generalizability of this methodology by applying it to two different optical systems and show that this level of accuracy can be achieved using only 6 beads per image.
The Neanderthal niche space of Western Eurasia 145 ka to 30 ka ago
Authors: Yaworsky Peter M. , Nielsen Emil S. , Nielsen Trine K.
Published: April 2024

Neanderthals occupied Western Eurasia between 350 ka and 40 ka ago, during the climatically volatile Pleistocene. A key issue is to what extent Neanderthal populations expanded into areas of Western Eurasia and what conditions facilitated such range expansions. The range extent of Neanderthals is generally based on the distribution of Neanderthal material, but the land-altering nature of glacial periods has erased much of the already sparse material evidence of Neanderthals, particularly in the northern latitudes. To overcome this obstacle species distribution models can estimate past distributions of Neanderthals, however, most implementations are generally constrained spatially and temporally and may be artificially truncating the Neanderthal niche space. Using dated contexts from Neanderthal sites from across Western Eurasia, millennial-scale paleoclimate reconstructions, and a spatiotemporal species distribution model, we infer the fundamental climatic niche space of Neanderthals and estimate the extent of Neanderthal occupation. We find that (a.) despite the long timeframe, Neanderthals occupy a relatively narrow fundamental climatic niche space, (b.) the estimated projected potential Neanderthal niche space suggests a larger geographic range than the material record suggests, and (c.) that there was a general decline in the size of the projected potential Neanderthal niche from 145 ka ago onward, possibly contributing to their extinction.
Key HPI axis receptors facilitate light adaptive behavior in larval zebrafish
Authors: Lee Han B. , Shams Soaleha , Dang Thi Viet Ha , Boyum Grace E. , Modhurima Rodsy , Hall Emma M. , Green Izzabella K. , Cervantes Elizabeth M. , Miguez Fernando E. , Clark Karl J.
Published: April 2024

The vertebrate stress response (SR) is mediated by the hypothalamic–pituitary–adrenal (HPA) axis and contributes to generating context appropriate physiological and behavioral changes. Although the HPA axis plays vital roles both in stressful and basal conditions, research has focused on the response under stress. To understand broader roles of the HPA axis in a changing environment, we characterized an adaptive behavior of larval zebrafish during ambient illumination changes. Genetic abrogation of glucocorticoid receptor (nr3c1) decreased basal locomotor activity in light and darkness. Some key HPI axis receptors (mc2r [ACTH receptor], nr3c1), but not nr3c2 (mineralocorticoid receptor), were required to adapt to light more efficiently but became dispensable when longer illumination was provided. Such light adaptation was more efficient in dimmer light. Our findings show that the HPI axis contributes to the SR, facilitating the phasic response and maintaining an adapted basal state, and that certain adaptations occur without HPI axis activity.
Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR
Authors: Nakamura Tomoka , Takita Teisuke , Kuwata Kohei , Mizutani Kimihiko , Mikami Bunzo , Nakamura Satoshi , Yasukawa Kiyoshi
Published: April 2024

XynR is a thermostable alkaline GH10 xylanase, for which we have previously examined the effects of saturation mutagenesis at position 315 on enzyme alkaliphily, and found that at pH 10, the activities of variants could be ordered as follows: T315Q > T315S = T315N > T315H = wild-type XynR (WT) > 15 other variants. In this study, we sought to elucidate the mechanisms underlying the variable activity of these different variants. Crystallographic analysis revealed that the Ca2+ ion near position 315 in WT was absent in the T315Q variant. We accordingly hypothesized that the enhancement of alkaliphily in T315Q, and probably also in the T315H, T315N, and T315S variants, could be ascribed to an activity-stability trade-off associated with a reduction in stability due to the lack of this Ca2+ ion. Consistent with expectations, the alkaline resistance of T315H, T315N, T315Q, and T315S, evaluated through the pH-dependence of stability at 0 mM CaCl2 under alkaline conditions, was found to be lower than that of WT: the residual activity at pH 11 of WT was 78% while those of T315H, T315N, T315Q, and T315S were 0, 9, 0, and 43%, respectively. In addition, the thermostabilities of these four variants, as assessed using the denaturing temperatures (Tm) at 0 mM CaCl2 based on ellipticity at 222 nm in circular dichroism measurements, were lower than that of WT by 2–8 °C. Furthermore, the Tm values of WT and variants at 5 mM CaCl2 were higher than those at 0 mM CaCl2 by 6–11 °C. Collectively, our findings in this study indicate that mutation of the T residue at position 315 of XynR to H, N, Q, and S causes an increase in the alkaliphily of this enzyme, thereby reducing its stability.
Neuroprotective mechanisms of luteolin in glutamate-induced oxidative stress and autophagy-mediated neuronal cell death
Authors: Vongthip Wudtipong , Nilkhet Sunita , Boonruang Kanokkan , Sukprasansap Monruedee , Tencomnao Tewin , Baek Seung Joon
Published: April 2024

Neurodegenerative diseases, characterized by progressive neuronal dysfunction and loss, pose significant health challenges. Glutamate accumulation contributes to neuronal cell death in diseases such as Alzheimer's disease. This study investigates the neuroprotective potential of Albizia lebbeck leaf extract and its major constituent, luteolin, against glutamate-induced hippocampal neuronal cell death. Glutamate-treated HT-22 cells exhibited reduced viability, altered morphology, increased ROS, and apoptosis, which were attenuated by pre-treatment with A. lebbeck extract and luteolin. Luteolin also restored mitochondrial function, decreased mitochondrial superoxide, and preserved mitochondrial morphology. Notably, we first found that luteolin inhibited the excessive process of mitophagy via the inactivation of BNIP3L/NIX and inhibited lysosomal activity. Our study suggests that glutamate-induced autophagy-mediated cell death is attenuated by luteolin via activation of mTORC1. These findings highlight the potential of A. lebbeck as a neuroprotective agent, with luteolin inhibiting glutamate-induced neurotoxicity by regulating autophagy and mitochondrial dynamics.
Research on factor analysis and method for evaluating grouting effects using machine learning
Authors: Li Wenxin , Chen Juntao , Zhu Jun , Ji Xinbo , Fu Ziqun
Published: April 2024

The evaluation of grouting effects constitutes a critical aspect of grouting engineering. With the maturity of the grouting project, the workload and empirical characteristics of grouting effect evaluation are gradually revealed. In the context of the Qiuji coal mine’s directional drilling and grouting to limestone aquifer reformation, this study thoroughly analyzes the influencing factors of grouting effects from geological and engineering perspectives, comparing these with various engineering indices associated with drilling and grouting. This led to the establishment of a “dual-process, multi-parameter, and multi-factor” system, employing correlation analysis to validate the selected indices’ reasonableness and scientific merit. Utilizing the chosen indices, eight high-performing machine learning models and three parameter optimization algorithms were employed to develop a model for assessing the effectiveness of directional grouting in limestone aquifers. The model’s efficacy was evaluated based on accuracy, recall, precision, and F-score metrics, followed by practical engineering validation. Results indicate that the “dual-process, multi-parameter, multi-factor” system elucidates the relationship between influencing factors and engineering parameters, demonstrating the intricacy of evaluating grouting effects. Analysis revealed that the correlation among the eight selected indicators—including the proportion of boreholes in the target rock strata, drilling length, leakage, water level, pressure of grouting, mass of slurry injected, permeability properties of limestone aquifers before being grouted, permeability properties of limestone aquifers after being grouted—is not substantial, underscoring their viability as independent indicators for grouting effect evaluation. Comparative analysis showed that the Adaboost machine learning model, optimized via a genetic algorithm, demonstrated superior performance and more accurate evaluation results. Engineering validation confirmed that this model provides a more precise and realistic assessment of grouting effects compared to traditional methods.
Modeling future cliff-front waves during sea level rise and implications for coastal cliff retreat rates
Authors: Matsumoto H. , Dickson M. E. , Stephenson W. J. , Thompson C. F. , Young A. P.
Published: April 2024

It is often assumed that future coastal cliff retreat rates will accelerate as global sea level rises, but few studies have investigated how SLR (sea level rise) might change cliff-front wave dynamics. Using a new simple numerical model, this study simulates the number and type (breaking, broken, or unbroken) of cliff-front waves under future SLR scenarios. Previous research shows breaking waves deliver more energy to cliffs than broken waves, and unbroken waves generate minimal impact. Here, we investigated six cliff-platform profiles from three regions (USA, New Zealand, and UK) with varied tidal ranges and wave climates. Model inputs included 2013–2100 hindcast/forecast incident wave height and tidal water level, and three future SLR scenarios. Results show the number of both cliff-front breaking and broken waves generally increase for a high-elevation (relative to tide) cliff-platform junction. In contrast, breaking/broken wave occurrence decrease by 38–92% for a near-horizontal shore platform with a low-elevation cliff-platform junction under a high SRL scenario, leading to high (96–97%) unbroken wave occurrence. Overall, results suggest the response of cliff-front waves to future SLR is complex and depends on shore platform geometries and SLR scenarios, indicating that future cliff retreat rates may not homogeneously accelerate under SLR.
Vibrotactile enhancement of musical engagement
Authors: Siedenburg Kai , Bürgel Michel , Özgür Elif , Scheicht Christoph , Töpken Stephan
Published: April 2024

Sound is sensed by the ear but can also be felt on the skin, by means of vibrotactile stimulation. Only little research has addressed perceptual implications of vibrotactile stimulation in the realm of music. Here, we studied which perceptual dimensions of music listening are affected by vibrotactile stimulation and whether the spatial segregation of vibrations improves vibrotactile stimulation. Forty-one listeners were presented with vibrotactile stimuli via a chair’s surfaces (left and right arm rests, back rest, seat) in addition to music presented over headphones. Vibrations for each surface were derived from individual tracks of the music (multi condition) or conjointly by a mono-rendering, in addition to incongruent and headphones-only conditions. Listeners evaluated unknown music from popular genres according to valence, arousal, groove, the feeling of being part of a live performance, the feeling of being part of the music, and liking. Results indicated that the multi- and mono vibration conditions robustly enhanced the nature of the musical experience compared to listening via headphones alone. Vibrotactile enhancement was strong in the latent dimension of ‘musical engagement’, encompassing the sense of being a part of the music, arousal, and groove. These findings highlight the potential of vibrotactile cues for creating intensive musical experiences.
Genetic determinants of plasma protein levels in the Estonian population
Authors: Kalnapenkis Anette , Jõeloo Maarja , Lepik Kaido , Kukuškina Viktorija , Kals Mart , Alasoo Kaur ,   Estonian Biobank Research Team, Metspalu Andres , Milani Lili , Nelis Mari , Hudjashov Georgi , Mägi Reedik , Esko Tõnu , Võsa Urmo
Published: April 2024

The proteome holds great potential as an intermediate layer between the genome and phenome. Previous protein quantitative trait locus studies have focused mainly on describing the effects of common genetic variations on the proteome. Here, we assessed the impact of the common and rare genetic variations as well as the copy number variants (CNVs) on 326 plasma proteins measured in up to 500 individuals. We identified 184 cis and 94 trans signals for 157 protein traits, which were further fine-mapped to credible sets for 101 cis and 87 trans signals for 151 proteins. Rare genetic variation contributed to the levels of 7 proteins, with 5 cis and 14 trans associations. CNVs were associated with the levels of 11 proteins (7 cis and 5 trans), examples including a 3q12.1 deletion acting as a hub for multiple trans associations; and a CNV overlapping NAIP, a sensor component of the NAIP-NLRC4 inflammasome which is affecting pro-inflammatory cytokine interleukin 18 levels. In summary, this work presents a comprehensive resource of genetic variation affecting the plasma protein levels and provides the interpretation of identified effects.
Effects of ChatGPT’s AI capabilities and human-like traits on spreading information in work environments
Authors: Jo Hyeon , Park Do-Hyung
Published: April 2024

The rapid proliferation and integration of AI chatbots in office environments, specifically the advanced AI model ChatGPT, prompts an examination of how its features and updates impact knowledge processes, satisfaction, and word-of-mouth (WOM) among office workers. This study investigates the determinants of WOM among office workers who are users of ChatGPT. We adopted a quantitative approach, utilizing a stratified random sampling technique to collect data from a diverse group of office workers experienced in using ChatGPT. The hypotheses were rigorously tested through Structural Equation Modeling (SEM) using the SmartPLS 4. The results revealed that system updates, memorability, and non-language barrier attributes of ChatGPT significantly enhanced knowledge acquisition and application. Additionally, the human-like personality traits of ChatGPT significantly increased both utilitarian value and satisfaction. Furthermore, the study showed that knowledge acquisition and application led to a significant increase in utilitarian value and satisfaction, which subsequently increased WOM. Age had a positive influence on WOM, while gender had no significant impact. The findings provide theoretical contributions by expanding our understanding of AI chatbots' role in knowledge processes, satisfaction, and WOM, particularly among office workers.
Analyzing temperature, humidity, and precipitation trends in six regions of Thailand using innovative trend analysis
Authors: Kliengchuay Wissanupong , Mingkhwan Rachaneekorn , Kiangkoo Nuttapohn , Suwanmanee San , Sahanavin Narut , Kongpran Jira , Aung Htoo Wai , Tantrakarnapa Kraichat
Published: April 2024

The change of temperature and weather parameters is a major concern affecting sustainable development and impacting various sectors, such as agriculture, tourism, and industry. Changing weather patterns and their impact on water resources are important climatic factors that society is facing. In Thailand, climatological features such as ambient temperature, relative humidity, and precipitation play a substantial role in affecting extreme weather events, which cause damage to the economy, agriculture, tourism, and livelihood of people. To investigate recent serious changes in annual trends of temperature, relative humidity, and precipitation in Thailand, this study used the Mann–Kendall (MK) test and innovative trend analysis (ITA) methods. The MK test showed that all six regions had an upward trend in temperature and humidity index (humidex, how hot the weather feels to the average person), while relative humidity and precipitation showed both upward and downward trends across different regions. The ITA method further confirmed the upward trend in temperature and humidex and showed that most data points fell above the 1:1 line. However, the upward trend in most variables was not significant at the 5% level. The southern and eastern regions showed a significant upward trend in relative humidity and humidex at a 5% level of significance according to the MK test. The output of this study can help in the understanding of weather variations and predict future situations and can be used for adaptation strategies.
Early screening of colorectal cancer using feature engineering with artificial intelligence-enhanced analysis of nanoscale chromatin modifications
Authors: Chang Andrew , Prabhala Sravya , Daneshkhah Ali , Lin Jianan , Subramanian Hariharan , Roy Hemant Kumar , Backman Vadim
Published: April 2024

Colonoscopy is accurate but inefficient for colorectal cancer (CRC) prevention due to the low (~ 7 to 8%) prevalence of target lesions, advanced adenomas. We leveraged rectal mucosa to identify patients who harbor CRC field carcinogenesis by evaluating chromatin 3D architecture. Supranucleosomal disordered chromatin chains (~ 5 to 20 nm, ~1 kbp) fold into chromatin packing domains (~ 100 to 200 nm, ~ 100 to 1000 kbp). In turn, the fractal-like conformation of DNA within chromatin domains and the folding of the genome into packing domains has been shown to influence multiple facets of gene transcription, including the transcriptional plasticity of cancer cells. We deployed an optical spectroscopic nanosensing technique, chromatin-sensitive partial wave spectroscopic microscopy (csPWS), to evaluate the packing density scaling D of the chromatin chain conformation within packing domains from rectal mucosa in 256 patients with varying degrees of progression to colorectal cancer. We found average packing scaling D of chromatin domains was elevated in tumor cells, histologically normal-appearing cells 4 cm proximal to the tumor, and histologically normal-appearing rectal mucosa compared to cells from control patients (p < 0.001). Nuclear D had a robust correlation with the model of 5-year risk of CRC with r2 = 0.94. Furthermore, rectal D was evaluated as a screening biomarker for patients with advanced adenomas presenting an AUC of 0.85 and 85% sensitivity and specificity. artificial intelligence-enhanced csPWS improved diagnostic performance with AUC = 0.90. Considering the low sensitivity of existing CRC tests, including liquid biopsies, to early-stage cancers our work highlights the potential of chromatin biomarkers of field carcinogenesis in detecting early, significant precancerous colon lesions.
Environmental and sociocultural factors are associated with pain-related brain structure among diverse individuals with chronic musculoskeletal pain: intersectional considerations
Authors: Domenico Lisa H. , Tanner Jared J. , Mickle Angela M. , Terry Ellen L. , Garvan Cynthia , Lai Song , Deshpande Hrishikesh , Staud Roland , Redden David , Price Catherine C. , Goodin Burel R. , Fillingim Roger B. , Sibille Kimberly T.
Published: April 2024

Chronic musculoskeletal pain including knee osteoarthritis (OA) is a leading cause of disability worldwide. Previous research indicates ethnic-race groups differ in the pain and functional limitations experienced with knee OA. However, when socioenvironmental factors are included in analyses, group differences in pain and function wane. Pain-related brain structures are another area where ethnic-race group differences have been observed. Environmental and sociocultural factors e.g., income, education, experiences of discrimination, and social support influence brain structures. We investigate if environmental and sociocultural factors reduce previously observed ethnic-race group differences in pain-related brain structures. Data were analyzed from 147 self-identified non-Hispanic black (NHB) and non-Hispanic white (NHW), middle and older aged adults with knee pain in the past month. Information collected included health and pain history, environmental and sociocultural resources, and brain imaging. The NHB adults were younger and reported lower income and education compared to their NHW peers. In hierarchical multiple regression models, sociocultural and environmental factors explained 6–37% of the variance in pain-related brain regions. Self-identified ethnicity-race provided an additional 4–13% of explanatory value in the amygdala, hippocampus, insula, bilateral primary somatosensory cortex, and thalamus. In the rostral/caudal anterior cingulate and dorsolateral prefrontal cortex, self-identified ethnicity-race was not a predictor after accounting for environmental, sociocultural, and demographic factors. Findings help to disentangle and identify some of the factors contributing to ethnic-race group disparities in pain-related brain structures. Numerous arrays of environmental and sociocultural factors remain to be investigated. Further, the differing sociodemographic representation of our NHB and NHW participants highlights the role for intersectional considerations in future research.
UTRN as a potential biomarker in breast cancer: a comprehensive bioinformatics and in vitro study
Authors: Li Han , Zhang Wenjie , Liu Yang , Cai Zehao , Lan Ailin , Shu Dan , Shen Meiying , Li Kang , Pu Dongyao , Tan Wenhao , Liu Shengchun , Peng Yang
Published: April 2024

Utrophin (UTRN), known as a tumor suppressor, potentially regulates tumor development and the immune microenvironment. However, its impact on breast cancer’s development and treatment remains unstudied. We conducted a thorough examination of UTRN using both bioinformatic and in vitro experiments in this study. We discovered UTRN expression decreased in breast cancer compared to standard samples. High UTRN expression correlated with better prognosis. Drug sensitivity tests and RT-qPCR assays revealed UTRN’s pivotal role in tamoxifen resistance. Furthermore, the Kruskal–Wallis rank test indicated UTRN’s potential as a valuable diagnostic biomarker for breast cancer and its utility in detecting T stage of breast cancer. Additionally, our results demonstrated UTRN’s close association with immune cells, inhibitors, stimulators, receptors, and chemokines in breast cancer (BRCA). This research provides a novel perspective on UTRN’s role in breast cancer’s prognostic and therapeutic value. Low UTRN expression may contribute to tamoxifen resistance and a poor prognosis. Specifically, UTRN can improve clinical decision-making and raise the diagnosis accuracy of breast cancer.
Multiple factors influence claw characteristics in oribatid mites (Acari)
Authors: Kerschbaumer Michaela , Pfingstl Tobias
Published: April 2024

Claws, as nature's multifaceted instruments, play fundamental roles across the animal kingdom, aiding in prey capture and enabling movement across diverse terrains. Claw features often reflect the ecologies of the respective taxa and thus can provide important insights into the different lifestyles. This study explores the claw morphology of monodactylous oribatid mites through geometric morphometrics, analyzing 559 specimens from 49 species across various ecosystems. The research identifies distinct claw characteristics associated with specific habitats, revealing a significant correlation between claw morphology and the mites' environmental adaptations. Littoral mites exhibit notably larger claws compared to terrestrial counterparts, with aquatic and semiaquatic species presenting intermediate traits. The analysis shows an inverse relationship between claw curvature and sharpness, differing from patterns observed in larger animals. A trend of increasing claw bluntness with body size in terrestrial mites echoes biomechanical constraints seen in larger species. The study also observes consistent claw shapes within oribatid superfamilies, suggesting a potential, albeit muted, phylogenetic influence alongside environmental factors. These findings reveal how ecological, evolutionary, and functional aspects influence claw morphology in oribatid mites, enhancing our knowledge of arthropod biology and potentially inspiring biomimetic advances in material science and engineering.
Dual proteomics of infected macrophages reveal bacterial and host players involved in the Francisella intracellular life cycle and cell to cell dissemination by merocytophagy
Authors: Rytter Héloïse , Roger Kevin , Chhuon Cerina , Ding Xiongqi , Coureuil Mathieu , Jamet Anne , Henry Thomas , Guerrera Ida Chiara , Charbit Alain
Published: April 2024

Bacterial pathogens adapt and replicate within host cells, while host cells develop mechanisms to eliminate them. Using a dual proteomic approach, we characterized the intra-macrophage proteome of the facultative intracellular pathogen, Francisella novicida. More than 900 Francisella proteins were identified in infected macrophages after a 10-h infection. Biotin biosynthesis-related proteins were upregulated, emphasizing the role of biotin-associated genes in Francisella replication. Conversely, proteins encoded by the Francisella pathogenicity island (FPI) were downregulated, supporting the importance of the F. tularensis Type VI Secretion System for vacuole escape, not cytosolic replication. In the host cell, over 300 proteins showed differential expression among the 6200 identified during infection. The most upregulated host protein was cis-aconitate decarboxylase IRG1, known for itaconate production with antimicrobial properties in Francisella. Surprisingly, disrupting IRG1 expression did not impact Francisella’s intracellular life cycle, suggesting redundancy with other immune proteins or inclusion in larger complexes. Over-representation analysis highlighted cell–cell contact and actin polymerization in macrophage deregulated proteins. Using flow cytometry and live cell imaging, we demonstrated that merocytophagy involves diverse cell-to-cell contacts and actin polymerization-dependent processes. These findings lay the groundwork for further exploration of merocytophagy and its molecular mechanisms in future research.

Data are available via ProteomeXchange with identifier PXD035145.