bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo spectroscopy and machine learning for the early detection and classification of different stresses in apple trees
Authors: Prechsl Ulrich E. , Mejia-Aguilar Abraham , Cullinan Cameron B. 
Published: September 2023

AbstractThe use of in vivo spectroscopy to detect plant stress in its early stages has the potential to enhance food safety and reduce the need for plant protection products. However, differentiating between various stress types before symptoms appear remains poorly studied. In this study, we investigated the potential of Vis–NIR spectroscopy to differentiate between stress types in apple trees (Malus x domestica Borkh.) exposed to apple scab, waterlogging, and herbicides in a greenhouse. Using a spectroradiometer, we collected spectral signatures of leaves still attached to the tree and utilized machine learning techniques to develop predictive models for detecting stress presence and classifying stress type as early as 1–5 days after exposure. Our findings suggest that changes in spectral reflectance at multiple regions accurately differentiate various types of plant stress on apple trees. Our models were highly accurate (accuracies between 0.94 and 1) when detecting the general presence of stress at an early stage. The wavelengths important for classification relate to photosynthesis via pigment functioning (684 nm) and leaf water (~ 1800–1900 nm), which may be associated with altered gas exchange as a short-term stress response. Overall, our study demonstrates the potential of spectral technology and machine learning for early diagnosis of plant stress, which could lead to reduced environmental burden through optimizing resource utilization in agriculture.
Varied effects of tobacco smoke and e-cigarette vapor suggest that nicotine does not affect endothelium-dependent relaxation and nitric oxide signaling
Authors: Wölkart Gerald , Kollau Alexander , Russwurm Michael , Koesling Doris , Schrammel Astrid , Mayer Bernd 
Published: September 2023

AbstractChronic smoking causes dysfunction of vascular endothelial cells, evident as a reduction of flow-mediated dilation in smokers, but the role of nicotine is still controversial. Given the increasing use of e-cigarettes and other nicotine products, it appears essential to clarify this issue. We studied extracts from cigarette smoke (CSE) and vapor from e-cigarettes (EVE) and heated tobacco (HTE) for their effects on vascular relaxation, endothelial nitric oxide signaling, and the activity of soluble guanylyl cyclase. The average nicotine concentrations of CSE, EVE, and HTE were 164, 800, and 85 µM, respectively. At a dilution of 1:3, CSE almost entirely inhibited the relaxation of rat aortas and porcine coronary arteries to acetylcholine and bradykinin, respectively, while undiluted EVE, with a 15-fold higher nicotine concentration, had no significant effect. With about 50% inhibition at 1:2 dilution, the effect of HTE was between CSE and EVE. Neither extract affected endothelium-independent relaxation to an NO donor. At the dilutions tested, CSE was not toxic to cultured endothelial cells but, in contrast to EVE, impaired NO signaling and inhibited NO stimulation of soluble guanylyl cyclase. Our results demonstrate that nicotine does not mediate the impaired endothelium-dependent vascular relaxation caused by smoking.
Electric field stimulation unmasks a subtle role for T-type calcium channels in regulating lymphatic contraction
Authors: Davis Michael J. , Castorena-Gonzalez Jorge A. , Zawieja Scott D. 
Published: September 2023

AbstractWe previously identified two isoforms of T-type, voltage-gated calcium (Cav3) channels (Cav3.1, Cav3.2) that are functionally expressed in murine lymphatic muscle cells; however, contractile tests of lymphatic vessels from single and double Cav3 knock-out (DKO) mice, exhibited nearly identical parameters of spontaneous twitch contractions as wild-type (WT) vessels, suggesting that Cav3 channels play no significant role. Here, we considered the possibility that the contribution of Cav3 channels might be too subtle to detect in standard contraction analyses. We compared the sensitivity of lymphatic vessels from WT and Cav3 DKO mice to the L-type calcium channel (Cav1.2) inhibitor nifedipine and found that the latter vessels were significantly more sensitive to inhibition, suggesting that the contribution of Cav3 channels might normally be masked by Cav1.2 channel activity. We hypothesized that shifting the resting membrane potential (Vm) of lymphatic muscle to a more negative voltage might enhance the contribution of Cav3 channels. Because even slight hyperpolarization is known to completely silence spontaneous contractions, we devised a method to evoke nerve-independent, twitch contractions from mouse lymphatic vessels using single, short pulses of electric field stimulation (EFS). TTX was present throughout to block the potential contributions of voltage-gated Na+ channels in perivascular nerves and lymphatic muscle. In WT vessels, EFS evoked single contractions that were comparable in amplitude and degree of entrainment to those occurring spontaneously. When Cav1.2 channels were blocked or deleted, only small residual EFS-evoked contractions (~ 5% of normal amplitude) were present. These residual, EFS-evoked contractions were enhanced (to 10–15%) by the KATP channel activator pinacidil (PIN) but were absent in Cav3 DKO vessels. Our results point to a subtle contribution of Cav3 channels to lymphatic contractions that can be unmasked in the absence of Cav1.2 channel activity and when the resting Vm is more hyperpolarized than normal.
Soil horizons regulate bacterial community structure and functions in Dabie Mountain of the East China
Authors: Luo Xia , Gong Yinping , Xu Feiyan , Wang Shuai , Tao Yingying , Yang Mengmeng 
Published: September 2023

AbstractSoil bacterial communities regulate nutrient cycling and plant growth in forests. Although these bacterial communities vary with soil nutrients and plant traits, the variation and degree with soil horizons in different forest types remain unclear. Here, bacterial communities of 44 soil samples from organic horizon (O horizon) and mineral horizon (M horizon) of three forest types (Cunninghamia, broad-leaved and Pinus forests) in subtropical forests of Dabie Mountain, China were analyzed based on amplicon sequencing. We assessed the effects of soil horizons and forest types on bacterial communities. The results showed that the bacterial richness and diversity were significantly higher in the O horizon than in the M horizon. Furthermore, the bacterial community composition and functions were also remarkably different between the two soil horizons. Furthermore, forest types could affect bacterial community composition but not for diversity and functions. Moreover, soil organic matter, including the total organic carbon, available phosphorus, total organic nitrogen, available potassium, ammonium nitrogen, and pH were main drivers for bacterial community composition. The results propose robust evidence that soil horizons strongly driven bacterial community composition and diversity, and suggest that microhabitat of soil bacterial communities is important to maintain the stability of forest ecosystem.
GS-DeepNet: mastering tokamak plasma equilibria with deep neural networks and the Grad–Shafranov equation
Authors: Joung Semin , Ghim Y.-C. , Kim Jaewook , Kwak Sehyun , Kwon Daeho , Sung C. , Kim D. , Kim Hyun-Seok , Bak J. G. , Yoon S. W. 
Published: September 2023

AbstractThe force-balanced state of magnetically confined plasmas heated up to 100 million degrees Celsius must be sustained long enough to achieve a burning-plasma state, such as in the case of ITER, a fusion reactor that promises a net energy gain. This force balance between the Lorentz force and the pressure gradient force, known as a plasma equilibrium, can be theoretically portrayed together with Maxwell’s equations as plasmas are collections of charged particles. Nevertheless, identifying the plasma equilibrium in real time is challenging owing to its free-boundary and ill-posed conditions, which conventionally involves iterative numerical approach with a certain degree of subjective human decisions such as including or excluding certain magnetic measurements to achieve numerical convergence on the solution as well as to avoid unphysical solutions. Here, we introduce GS-DeepNet, which learns plasma equilibria through solely unsupervised learning, without using traditional numerical algorithms. GS-DeepNet includes two neural networks and teaches itself. One neural network generates a possible candidate of an equilibrium following Maxwell’s equations and is taught by the other network satisfying the force balance under the equilibrium. Measurements constrain both networks. Our GS-DeepNet achieves reliable equilibria with uncertainties in contrast with existing methods, leading to possible better control of fusion-grade plasmas.
Age-related increases in right hemisphere support for prosodic processing in children
Authors: Li Kristen E. , Dimitrijevic Andrew , Gordon Karen A. , Pang Elizabeth W. , Greiner Hansel M. , Kadis Darren S. 
Published: September 2023

AbstractLanguage comprehension is a complex process involving an extensive brain network. Brain regions responsible for prosodic processing have been studied in adults; however, much less is known about the neural bases of prosodic processing in children. Using magnetoencephalography (MEG), we mapped regions supporting speech envelope tracking (a marker of prosodic processing) in 80 typically developing children, ages 4–18 years, completing a stories listening paradigm. Neuromagnetic signals coherent with the speech envelope were localized using dynamic imaging of coherent sources (DICS). Across the group, we observed coherence in bilateral perisylvian cortex. We observed age-related increases in coherence to the speech envelope in the right superior temporal gyrus (r = 0.31, df = 78, p = 0.0047) and primary auditory cortex (r = 0.27, df = 78, p = 0.016); age-related decreases in coherence to the speech envelope were observed in the left superior temporal gyrus (r = − 0.25, df = 78, p = 0.026). This pattern may indicate a refinement of the networks responsible for prosodic processing during development, where language areas in the right hemisphere become increasingly specialized for prosodic processing. Altogether, these results reveal a distinct neurodevelopmental trajectory for the processing of prosodic cues, highlighting the presence of supportive language functions in the right hemisphere. Findings from this dataset of typically developing children may serve as a potential reference timeline for assessing children with neurodevelopmental hearing and speech disorders.
Rate of return to work in patients with stroke under the health and employment support program of Rosai hospitals in Japan
Authors: Umemura Takeru , Hachisuka Kenji , Saeki Satoru , Nishizawa Shigeru , Yamamoto Junkoh 
Published: September 2023

AbstractTo facilitate return to work (RTW) in patients with stroke, a health and employment support (HES) program was started at Rosai hospitals in Japan. This study aimed to determine the rate of RTW in patients with stroke under this support program. We collected demographic and clinical data of patients with stroke from the implementation reports of the HES program. The program provided coordinated dual support, such as acute medical treatments, and stroke and vocational rehabilitation on the medical side, and management and support on the workplace side. The primary endpoint was RTW. Successful and unsuccessful RTW were examined using the χ2 test. The RTW rate curves were analyzed using the Kaplan–Meier method. We enrolled 483 patients; 355 (73%) and 128 (27%) patients had successful and unsuccessful RTW, respectively. Stroke types, neurological findings, and activities of daily living were significant factors for RTW. The Kaplan–Meier method revealed that left hemiplegia, right hemiplegia, and neuropsychological deficits, except for combined disability (hemiplegia with neuropsychological deficits), had similar RTW curves with an RTW rate of > 70%.
Research on modeling joining and joining modification method of hybrid FE-SEA model
Authors: Su Jintao , Zheng Ling , Nie Jinquan 
Published: September 2023

AbstractSince the connection method at the boundary of the hybrid FE-SEA (finite element-statistical energy analysis, FE-SEA) model affects the overall calculation accuracy of the model, the missing or inaccurate connection relation will lead to a large error in the model calculation. In order to effectively solve the calculation error caused by the connection problem of hybrid FE-SEA model, this paper starts from the modeling methods and connection relations of “hybrid-point” connection, “hybrid-line” connection and “hybrid-surface” connection. In order to solve the modeling method and correction problems of the “hybrid-point” connection in the hybrid FE-SEA model, the “out-of-plane” wave motion equation at the “hybrid-point” connection was established by using the superposition principle of plane waveforms in polar coordinate system. The “hybrid-point” connection and wave-number relation in Cartesian coordinate system are studied. The radiation radius correction method of “hybrid-point” connection is proposed. An example is given to verify the effectiveness of the method. In order to solve the modeling and correction problem of “hybrid-line” in hybrid model, a “hybrid-line” connected triangular waveform function model was established by using the method of linear difference. The direct field dynamic stiffness matrix of “hybrid-line” connection in node coordinate system is studied. According to the shape function of the “hybrid-line” connection wavenumber space, a method to correct the shape function of the “hybrid-line” connection is proposed, and the validity of the method is verified.
Vitamin D3 regulates PM-driven primary human neutrophil inflammatory responses
Authors: Kewcharoenwong Chidchamai , Khongmee Aranya , Nithichanon Arnone , Palaga Tanapat , Prueksasit Tassanee , Mudway Ian S. , Hawrylowicz Catherine M. , Lertmemongkolchai Ganjana 
Published: September 2023

AbstractRecent evidence has demonstrated that both acute and chronic exposure to particulate air pollution are risk factors for respiratory tract infections and increased mortality from sepsis. There is therefore an urgent need to establish the impact of ambient particulate matter (PM) on innate immune cells and to establish potential strategies to mitigate against adverse effects. PM has previously been reported to have potential adverse effects on neutrophil function. In the present study, we investigated the impact of standard urban PM (SRM1648a, NIST) and PM2.5 collected from Chiang Mai, Thailand, on human peripheral blood neutrophil functions, including LPS-induced migration, IL-8 production, and bacterial killing. Both NIST and the PM2.5, being collected in Chiang Mai, Thailand, increased IL-8 production, but reduced CXCR2 expression and migration of human primary neutrophils stimulated with Escherichia coli LPS. Moreover, PM-pretreated neutrophils from vitamin D-insufficient participants showed reduced E. coli-killing activity. Furthermore, in vitro vitamin D3 supplementation attenuated IL-8 production and improved bacterial killing by cells from vitamin D-insufficient participants. Our findings suggest that provision of vitamin D to individuals with insufficiency may attenuate adverse acute neutrophilic responses to ambient PM.
Structural and functional characterization of USP47 reveals a hot spot for inhibitor design
Authors: Shin Sang Chul , Park Jinyoung , Kim Kyung Hee , Yoon Jung Min , Cho Jinhong , Ha Byung Hak , Oh Yeonji , Choo Hyunah , Song Eun Joo , Kim Eunice EunKyeong 
Published: September 2023

AbstractUSP47 is widely involved in tumor development, metastasis, and other processes while performing a more regulatory role in inflammatory responses, myocardial infarction, and neuronal development. In this study, we investigate the functional and biochemical properties of USP47, whereby depleting USP47 inhibited cancer cell growth in a p53-dependent manner—a phenomenon that enhances during the simultaneous knockdown of USP7. Full-length USP47 shows higher deubiquitinase activity than the catalytic domain. The crystal structures of the catalytic domain, in its free and ubiquitin-bound states, reveal that the misaligned catalytic triads, ultimately, become aligned upon ubiquitin-binding, similar to USP7, thereby becoming ready for catalysis. Yet, the composition and lengths of BL1, BL2, and BL3 of USP47 differ from those for USP7, and they contribute to the observed selectivity. Our study provides molecular details of USP47 regulation, substrate recognition, and the hotspots for drug discovery by targeting USP47.
DNA-bridging by an archaeal histone variant via a unique tetramerisation interface
Authors: Ofer Sapir , Blombach Fabian , Erkelens Amanda M. , Barker Declan , Soloviev Zoja , Schwab Samuel , Smollett Katherine , Matelska Dorota , Fouqueau Thomas , van der Vis Nico , Kent Nicholas A. , Thalassinos Konstantinos , Dame Remus T. , Werner Finn 
Published: September 2023

AbstractIn eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into ‘hypernucleosome’ particles of varying sizes with each dimer wrapping 30 bp of DNA. These are composed of canonical and variant histone paralogues, but the function of these variants is poorly understood. Here, we characterise the structure and function of the histone paralogue MJ1647 from Methanocaldococcus jannaschii that has a unique C-terminal extension enabling homotetramerisation. The 1.9 Å X-ray structure of a dimeric MJ1647 species, structural modelling of the tetramer, and site-directed mutagenesis reveal that the C-terminal tetramerization module consists of two alpha helices in a handshake arrangement. Unlike canonical histones, MJ1647 tetramers can bridge two DNA molecules in vitro. Using single-molecule tethered particle motion and DNA binding assays, we show that MJ1647 tetramers bind ~60 bp DNA and compact DNA in a highly cooperative manner. We furthermore show that MJ1647 effectively competes with the transcription machinery to block access to the promoter in vitro. To the best of our knowledge, MJ1647 is the first histone shown to have DNA bridging properties, which has important implications for genome structure and gene expression in archaea.
Improving genetic risk prediction across diverse population by disentangling ancestry representations
Authors: Gyawali Prashnna K. , Le Guen Yann , Liu Xiaoxia , Belloy Michael E. , Tang Hua , Zou James , He Zihuai 
Published: September 2023

AbstractRisk prediction models using genetic data have seen increasing traction in genomics. However, most of the polygenic risk models were developed using data from participants with similar (mostly European) ancestry. This can lead to biases in the risk predictors resulting in poor generalization when applied to minority populations and admixed individuals such as African Americans. To address this issue, largely due to the prediction models being biased by the underlying population structure, we propose a deep-learning framework that leverages data from diverse population and disentangles ancestry from the phenotype-relevant information in its representation. The ancestry disentangled representation can be used to build risk predictors that perform better across minority populations. We applied the proposed method to the analysis of Alzheimer’s disease genetics. Comparing with standard linear and nonlinear risk prediction methods, the proposed method substantially improves risk prediction in minority populations, including admixed individuals, without needing self-reported ancestry information.
Structural and functional analysis of hyper-thermostable ancestral L-amino acid oxidase that can convert Trp derivatives to D-forms by chemoenzymatic reaction
Authors: Kawamura Yui , Ishida Chiharu , Miyata Ryo , Miyata Azusa , Hayashi Seiichiro , Fujinami Daisuke , Ito Sohei , Nakano Shogo 
Published: September 2023

AbstractProduction of D-amino acids (D-AAs) on a large-scale enables to provide precursors of peptide therapeutics. In this study, we designed a novel L-amino acid oxidase, HTAncLAAO2, by ancestral sequence reconstruction, exhibiting high thermostability and long-term stability. The crystal structure of HTAncLAAO2 was determined at 2.2 Å by X-ray crystallography, revealing that the enzyme has an octameric form like a “ninja-star” feature. Enzymatic property analysis demonstrated that HTAncLAAO2 exhibits three-order larger kcat/Km values towards four L-AAs (L-Phe, L-Leu, L-Met, and L-Ile) than that of L-Trp. Through screening the variants, we obtained the HTAncLAAO2(W220A) variant, which shows a > 6-fold increase in kcat value toward L-Trp compared to the original enzyme. This variant applies to synthesizing enantio-pure D-Trp derivatives from L- or rac-forms at a preparative scale. Given its excellent properties, HTAncLAAO2 would be a starting point for designing novel oxidases with high activity toward various amines and AAs.
Vegetation resilience does not increase consistently with greening in China’s Loess Plateau
Authors: Wang Zhuangzhuang , Fu Bojie , Wu Xutong , Li Yingjie , Feng Yuhao , Wang Shuai , Wei Fangli , Zhang Liwei 
Published: September 2023

AbstractRecent concurrent processes of vegetation greening and reduced resilience (the capacity to recover from disturbances) worldwide have brought many uncertainties into sustainable ecosystems in the future. However, little is known about the conditions and extent to which greening affects resilience changes. Here we assess both vegetation dynamics and resilience in China’s Loess Plateau from 2000 to 2020 using satellite-based vegetation data and an early warning indicator. Our results reveal an overall greening trend in vegetated areas, while resilience shifted from gains to losses at a breakpoint in 2010. Vegetation greening generally contributed to resilience gains, whereas increased temperature and precipitation variability contributed to the resilience loss observed in 2011–2020. These findings provide empirical evidence that vegetation greening does not necessarily correspond to an increase in resilience. We therefore recommend integrating resilience indicators into ecological restoration and conservation efforts to gain a more comprehensive understanding of vegetation states and support effective ecosystem stewardship.