bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated transcriptome and metabolomics analyses revealed key functional genes in Canna indica under Cr stress
Authors: Zhu Sixi , Zhao Wei , Sheng Luying , Yang Xiuqin , Mao Huan , Sun Suxia , Chen Zhongbing 
Published: June 2024

AbstractChromium (Cr) can interfere with plant gene expression, change the content of metabolites and affect plant growth. However, the molecular response mechanism of wetland plants at different time sequences under Cr stress has yet to be fully understood. In this study, Canna indica was exposed to 100 mg/kg Cr-contaminated soil for 0, 7, 14, and 21 days and analyzed using untargeted metabolomics (LC–MS) and transcriptomics. The results showed that Cr stress increased the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX) and peroxidase (POD), the contents of glutathione (GSH), malondialdehyde (MDA), and oxygen free radical (ROS), and inhibited the biosynthesis of photosynthetic pigments, thus leading to changes in plant growth and biomass. Metabonomics analysis showed that Cr stress mainly affected 12 metabolic pathways, involving 38 differentially expressed metabolites, including amino acids, phenylpropane, and flavonoids. By transcriptome analysis, a total of 16,247 differentially expressed genes (DEGs, 7710 up-regulated genes, and 8537 down-regulated genes) were identified, among which, at the early stage of stress (Cr contaminate seven days), C. indica responds to Cr toxicity mainly through galactose, starch and sucrose metabolism. With the extension of stress time, plant hormone signal transduction and MAPK signaling pathway in C. indica in the Cr14 (Cr contaminate 14 days) treatment group were significantly affected. Finally, in the late stage of stress (Cr21), C. indica co-defuses Cr toxicity by activating its Glutathione metabolism and Phenylpropanoid biosynthesis. In conclusion, this study revealed the molecular response mechanism of C. indica to Cr stress at different times through multi-omics methods.
NNICE: a deep quantile neural network algorithm for expression deconvolution
Authors: Jin Yong Won , Hu Pingzhao , Liu Qian 
Published: June 2024

AbstractThe composition of cell-type is a key indicator of health. Advancements in bulk gene expression data curation, single cell RNA-sequencing technologies, and computational deconvolution approaches offer a new perspective to learn about the composition of different cell types in a quick and affordable way. In this study, we developed a quantile regression and deep learning-based method called Neural Network Immune Contexture Estimator (NNICE) to estimate the cell type abundance and its uncertainty by automatically deconvolving bulk RNA-seq data. The proposed NNICE model was able to successfully recover ground-truth cell type fraction values given unseen bulk mixture gene expression profiles from the same dataset it was trained on. Compared with baseline methods, NNICE achieved better performance on deconvolve both pseudo-bulk gene expressions (Pearson correlation R = 0.9) and real bulk gene expression data (Pearson correlation R = 0.9) across all cell types. In conclusion, NNICE combines statistic inference with deep learning to provide accurate and interpretable cell type deconvolution from bulk gene expression.
Effect of measurement procedure errors on assessing lung fluid via remote dielectric sensing system
Authors: Chen Wei-Ting , Tsai Yi-Ju , Chou Hsiao-Chen , Pu Yi-Chih , Chien Jung-Yien , Huang Chun-Ta 
Published: June 2024

AbstractThe study assessed the impact of procedural errors on the remote dielectric sensing system (ReDS), a non-invasive lung fluid assessment technology, in an Asian cohort. Healthy volunteers underwent ReDS measurements following manufacturer’s instructions, with two consecutive measurements one minute apart. A subset of 20 participants had modified procedure settings. Reliability was measured using intraclass correlation coefficient (ICC). The study included 86 healthy volunteers, and all ReDS measurements fell within the recommended normal range. The intra-rater reliability of ReDS measurements was excellent, with an ICC of 0.968. Among the subset of 20 subjects, deviations in height and weight did not significantly affect ReDS values. However, deviations in chest size by ± 3 cm had a noticeable impact on ReDS measures, and incorrect station selection led to fluctuations in ReDS readings. In conclusion, the ReDS system demonstrated excellent intra-rater reliability and applicability in an Asian cohort. Procedural errors, such as chest size measurement and station selection, significantly influenced ReDS measurements. Adherence to standardized operating procedures is crucial to ensure accurate and consistent results. These findings highlight the importance of adherence to manufacturer instructions when utilizing ReDS for lung fluid assessment, thereby enhancing its reliability and clinical applicability.
Membrane depolarization mediates both the inhibition of neural activity and cell-type-differences in response to high-frequency stimulation
Authors: Lee Jae-Ik , Werginz Paul , Kameneva Tatiana , Im Maesoon , Fried Shelley I. 
Published: June 2024

AbstractNeuromodulation using high frequency (>1 kHz) electric stimulation (HFS) enables preferential activation or inhibition of individual neural types, offering the possibility of more effective treatments across a broad spectrum of neurological diseases. To improve effectiveness, it is important to better understand the mechanisms governing activation and inhibition with HFS so that selectivity can be optimized. In this study, we measure the membrane potential (Vm) and spiking responses of ON and OFF α-sustained retinal ganglion cells (RGCs) to a wide range of stimulus frequencies (100–2500 Hz) and amplitudes (10–100 µA). Our findings indicate that HFS induces shifts in Vm, with both the strength and polarity of the shifts dependent on the stimulus conditions. Spiking responses in each cell directly correlate with the shifts in Vm, where strong depolarization leads to spiking suppression. Comparisons between the two cell types reveal that ON cells are more depolarized by a given amplitude of HFS than OFF cells—this sensitivity difference enables the selective targeting. Computational modeling indicates that ion-channel dynamics largely account for the shifts in Vm, suggesting that a better understanding of the differences in ion-channel properties across cell types may improve the selectivity and ultimately, enhance HFS-based neurostimulation strategies.
The clock in growing hyphae and their synchronization in Neurospora crassa
Authors: Cheong Jia Hwei , Qiu Xiao , Liu Yang , Krach Emily , Guo Yinping , Bhusal Shishir , Schüttler Heinz-Bernd , Arnold Jonathan , Mao Leidong 
Published: June 2024

AbstractUtilizing a microfluidic chip with serpentine channels, we inoculated the chip with an agar plug with Neurospora crassa mycelium and successfully captured individual hyphae in channels. For the first time, we report the presence of an autonomous clock in hyphae. Fluorescence of a mCherry reporter gene driven by a clock-controlled gene-2 promoter (ccg-2p) was measured simultaneously along hyphae every half an hour for at least 6 days. We entrained single hyphae to light over a wide range of day lengths, including 6,12, 24, and 36 h days. Hyphae tracked in individual serpentine channels were highly synchronized (K = 0.60-0.78). Furthermore, hyphae also displayed temperature compensation properties, where the oscillation period was stable over a physiological range of temperatures from 24 °C to 30 °C (Q10 = 1.00-1.10). A Clock Tube Model developed could mimic hyphal growth observed in the serpentine chip and provides a mechanism for the stable banding patterns seen in race tubes at the macroscopic scale and synchronization through molecules riding the growth wave in the device.
Exploring the sequence-function space of microbial fucosidases
Authors: Martínez Gascueña Ana , Wu Haiyang , Wang Rui , Owen C. David , Hernando Pedro J. , Monaco Serena , Penner Matthew , Xing Ke , Le Gall Gwenaelle , Gardner Richard , Ndeh Didier , Urbanowicz Paulina A. , Spencer Daniel I. R. , Walsh Martin , Angulo Jesus , Juge Nathalie 
Published: June 2024

AbstractMicrobial α-l-fucosidases catalyse the hydrolysis of terminal α-l-fucosidic linkages and can perform transglycosylation reactions. Based on sequence identity, α-l-fucosidases are classified in glycoside hydrolases (GHs) families of the carbohydrate-active enzyme database. Here we explored the sequence-function space of GH29 fucosidases. Based on sequence similarity network (SSN) analyses, 15 GH29 α-l-fucosidases were selected for functional characterisation. HPAEC-PAD and LC-FD-MS/MS analyses revealed substrate and linkage specificities for α1,2, α1,3, α1,4 and α1,6 linked fucosylated oligosaccharides and glycoconjugates, consistent with their SSN clustering. The structural basis for the substrate specificity of GH29 fucosidase from Bifidobacterium asteroides towards α1,6 linkages and FA2G2 N-glycan was determined by X-ray crystallography and STD NMR. The capacity of GH29 fucosidases to carry out transfucosylation reactions with GlcNAc and 3FN as acceptors was evaluated by TLC combined with ESI–MS and NMR. These experimental data supported the use of SSN to further explore the GH29 sequence-function space through machine-learning models. Our lightweight protein language models could accurately allocate test sequences in their respective SSN clusters and assign 34,258 non-redundant GH29 sequences into SSN clusters. It is expected that the combination of these computational approaches will be used in the future for the identification of novel GHs with desired specificities.
Climate change-resilient snowpack estimation in the Western United States
Authors: Cowherd Marianne , Mital Utkarsh , Rahimi Stefan , Girotto Manuela , Schwartz Andrew , Feldman Daniel 
Published: June 2024

AbstractIn the 21st century, warmer temperatures and changing atmospheric circulation will likely produce unprecedented changes in Western United States snowfall1–3, with impacts on the timing, amount, and spatial patterns of snowpack4–7. The ~900 snow pillow stations are indispensable to water resource management by measuring snow-water equivalent (SWE)8,9in strategic but fixed locations10,11. However, this network may not be impacted by climate change in the same way as the surrounding area12and thus fail to accurately represent unmeasured locations; climate change thereby threatens our ability to measure the effects of climate change on snow. In this work, we show that maintaining the current peak SWE estimation skill is nonetheless possible. We find that explicitly including spatial correlations—either from gridded observations or learned by the model—improves skill at predicting distributed snowpack from sparse observations by 184%. Existing artificial intelligence methods can be useful tools to harness the many available sources of snowpack information to estimate snowpack in a nonstationary climate.
Structural regulation-induced Li-electron disentanglement for stabilized oxygen redox of Li-excess disordered rock-salt cathode materials
Authors: Jiao Sichen , Sun Yujian , Shi Dekai , Zhang Yuanpeng , Wang Xuelong , Liu Jue , Kang Le , Wang Fangwei , Yu Xiqian , Li Hong , Chen Liquan , Huang Xuejie 
Published: June 2024

A novel redox mechanism, characterized by the disentangled removal of lithium ions and electrons, has been achieved to stabilize oxygen redox reactions through the regulation of short-range ordering in disordered oxide cathode materials.
KDGAN: Knowledge distillation‐based model copyright protection for secure and communication‐efficient model publishing
Authors: Xie Bingyi , Xu Honghui , Seo Daehee , Shin DongMyung , Cai Zhipeng 
Published: June 2024

AbstractDeep learning‐based models have become ubiquitous across a wide range of applications, including computer vision, natural language processing, and robotics. Despite their efficacy, one of the significant challenges associated with deep neural network (DNN) models is the potential risk of copyright leakage due to the inherent vulnerability of the entire model architecture and the communication burden of the large models during publishing. So far, it is still challenging for us to safeguard the intellectual property rights of these DNN models while reducing the communication time during model publishing. To this end, this paper introduces a novel approach using knowledge distillation techniques aimed at training a surrogate model to stand in for the original DNN model. To be specific, a knowledge distillation generative adversarial network (KDGAN) model is proposed to train a student model capable of achieving remarkable performance levels while simultaneously safeguarding the copyright integrity of the original large teacher model and improving communication efficiency during model publishing. Herein, comprehensive experiments are conducted to showcase the efficacy of model copyright protection, communication‐efficient model publishing, and the superiority of the proposed KDGAN model over other copyright protection mechanisms.
Endoscopic scoring indices for assessing disease severity in familial adenomatous polyposis: Systematic review
Authors: Silverman Anna Lerman , Bouchiba Hicham , Aelvoet Arthur , MacDonald John , Dekker Evelien , Zayadi Alexa , Le Jessica , Feagan Brian , Jairath Vipul , Ma Christopher , Samadder Jewel 
Published: June 2024

Abstract
Background and study aims There is limited consensus on the optimal method for measuring disease severity in familial adenomatous polyposis (FAP). We aimed to systematically review the operating properties of existing endoscopic severity indices for FAP.
Methods We searched MEDLINE, EMBASE, and the Cochrane Library from inception to February 2023 to identify randomized controlled trials (RCTs) that utilized endoscopic outcomes or studies that evaluated the operating properties of endoscopic disease severity indices in FAP.
Results A total of 134 studies were included. We evaluated scoring indices and component items of scoring indices, such as polyp count, polyp size, and histology. Partial validation was observed for polyp count and size. The most commonly reported scoring index was the Spigelman classification system, which was used for assessing the severity of duodenal involvement. A single study reported almost perfect interobserver and intra-observer agreement for this system. The InSIGHT polyposis staging system, which was used for assessing colorectal polyp burden, has been partially validated. It showed substantial interobserver reliability; however, the intra-observer reliability was not assessed. Novel criteria for high-risk gastric polyps have been developed and assessed for interobserver reliability. However, these criteria showed a poor level of agreement. Other scoring indices assessing the anal transition zone, duodenal, and colorectal polyps have not undergone validation.
Conclusions There are no fully validated endoscopic disease severity indices for FAP. Development and validation of a reliable and responsive endoscopic disease severity instrument will be informative for clinical care and RCTs of pharmacological therapies for FAP.
DEX Inhibits H/R-induced Cardiomyocyte Ferroptosis by the miR-141-3p/lncRNA TUG1 Axis
Authors: Zhu Mei , Yuan Zhiguo , Wen Chuanyun , Wei Xiaojia 
Published: June 2024

Abstract
Background Ferroptosis is emerging as a critical pathway in ischemia/reperfusion (I/R) injury, contributing to compromised cardiac function and predisposing individuals to sepsis and myocardial failure. The study investigates the underlying mechanism of dexmedetomidine (DEX) in hypoxia/reoxygenation (H/R)-induced ferroptosis in cardiomyocytes, aiming to identify novel targets for myocardial I/R injury treatment.
Methods H9C2 cells were subjected to H/R and treated with varying concentrations of DEX. Additionally, H9C2 cells were transfected with miR-141-3p inhibitor followed by H/R treatment. Levels of miR-141-3p, long noncoding RNA (lncRNA) taurine upregulated 1 (TUG1), Fe2+, glutathione (GSH), and malondialdehyde were assessed. Reactive oxygen species (ROS) generation was measured via fluorescent labeling. Expression of ferroptosis-related proteins glutathione peroxidase 4 (GPX4) and acyl-CoA synthetase long-chain family member 4 (ACSL4) was determined using Western blot. The interaction between miR-141-3p and lncRNA TUG1 was evaluated through RNA pull-down assay and dual-luciferase reporter gene assays. The stability of lncRNA TUG1 was assessed using actinomycin D.
Results DEX ameliorated H/R-induced cardiomyocyte injury and elevated miR-141-3p expression in cardiomyocytes. DEX treatment increased cell viability, Fe2+, and ROS levels while decreasing ACSL4 protein expression. Furthermore, DEX upregulated GSH and GPX4 protein levels. miR-141-3p targeted lncRNA TUG1, reducing its stability and overall expression. Inhibition of miR-141-3p or overexpression of lncRNA TUG1 partially reversed the inhibitory effect of DEX on H/R-induced ferroptosis in cardiomyocytes.
Conclusion DEX mitigated H/R-induced ferroptosis in cardiomyocytes by upregulating miR-141-3p expression and downregulating lncRNA TUG1 expression, unveiling a potential therapeutic strategy for myocardial I/R injury.
Mucinous Cystic Neoplasm of the Liver: Case Report and Review of the Literature
Authors: Nambhanath Sreeshna , Srinivas Teerthanath , Bhat Shubha P. , Kailath Minu Cherian , Suresh Babu Sreelekshmi 
Published: June 2024

AbstractMucinous cystic neoplasms of the liver (MCN-L) are a rare benign neoplasm of the biliary system that grows slowly with vague clinical symptoms. The malignant transformation in these tumors is high, and preoperative diagnosis using radiography or endoscopy is challenging. We present a case report of a 58-year-old female patient who presented with diffuse abdominal pain and nonprojectile vomiting. Abdominal ultrasound revealed characteristics that point to a hydatid cyst. The enhanced computed tomography revealed a well-defined multiloculated thin-walled fluid density lesion in the left lobe of the liver. After a left hemi-hepatectomy, a multiloculated cystic lesion in the liver with mucinous material as the content was discovered. Histopathology showed multiple cystic spaces were lined by mucin-secreting columnar epithelium without nuclear atypia, the wall of the cysts showed ovarian-like stroma, and the diagnosis of MCN-L was made. There was no recurrence after 6 months of regular follow-up.
Can digital transformation curtail carbon emissions? Evidence from a quasi-natural experiment
Authors: Lin Zihao 
Published: June 2024

AbstractDigital infrastructure construction (DIC) is a crucial component of digital transformation, yet its impact on the sustainable development of cities remains uncertain. To address this question, this study employs the Difference-in-Differences (DID) model to evaluate the effects of a typical DIC policy, the Broadband China Pilot (BBCP) policy. The research sample covers data from Chinese cities from 2009 to 2019. The DID estimation demonstrates that the BBCP policy effectively decreased carbon emissions (COE). Robustness tests, such as parallel trend tests, placebo tests, propensity score matching DID, and local projection DID, all confirm the negative impact of the BBCP policy on COE. Heterogeneity analysis reveals that the BBCP policy has a greater mitigation effect on COE in non-resource cities. The BBCP policy has a stronger effect on reducing the COE in cities with a higher proportion of green funds or lower fiscal expenditures. Further analysis indicates that the BBCP policy significantly improves low-carbon ecological efficiency and reduces COE intensity. The results of the mechanism analysis reveal that the BBCP policy lowers COE by enhancing the industrial structure and promoting green technological progress. The study provides policy recommendations in the realm of DIC for developing countries to achieve digital transformation and low COE development concurrently. This research can assist governments in better considering how to implement DIC policies to construct ecologically sustainable cities with low COE.
Wildland fire evacuations in Canada from 1980 to 2021
Authors: Christianson Amy Cardinal , Johnston Lynn M. , Oliver Jacqueline A. , Watson David , Young David , MacDonald Heather , Little John , Macnab Bruce , Gonzalez Bautista Noemie 
Published: June 2024

Background Every year, people in Canada are evacuated due to wildland fires to avoid death, injury, and illness from fire and smoke events. Aims In this paper, we provide an overview of evacuations recorded in the Canadian Wildland Fire Evacuation Database between 1980 and 2021. Methods Our analysis covers evacuations in Canada from 1980 to 2021. We provide summary statistics including number of evacuations and evacuees, evacuation duration, seasonality, evacuation causes, community types, structure losses, and fatalities. We also investigate temporal and spatial patterns. Key results Between 1980 and 2021, there were 1393 wildland fire evacuation events with 576,747 people evacuated. During this period, there was an overall increase in frequency of evacuations, number of evacuees, and duration of events. Structure loss occurred during 194 evacuation events, with 4105 homes burned. We estimate wildland fire evacuations cost at least CAD3.7 billion (excluding structural losses), jumping to CAD4.6 billion if we include productivity losses. Indigenous peoples are disproportionately impacted in wildfire evacuations compared to the general Canadian population. Conclusions Wildland fire evacuations continue to occur across Canada and are increasing. Implications The findings from this study give us a better understanding of the characteristics of wildland fire evacuations, which can help guide emergency management.
The Ossetic transitive preterite
Authors: Kim Ronald I. 
Published: June 2024

AbstractIn contrast to most Middle and Modern Iranian languages, which have developed a preterite based on an ergative construction with the Old Iranian past passive participle, Ossetic has distinct formations for the intransitive and transitive preterite, and the latter has no close correlate in any other Iranian language. It is argued that only a periphrasis with Old Iranian *dā- ‘put’ can adequately account for the formal peculiarities of the Ossetic transitive preterite, namely its geminate dental and person-number endings. Despite its formal resemblance to the periphrasis reconstructed for the Germanic weak preterite, this construction probably did not arise via contact between the Sarmatian tribes and Germanic peoples in the first centuries CE.
Attenuation characteristics of coda wave in Northern Aceh, Sumatra, Indonesia
Authors: Anggono T , Syuhada S , Pranata B , Febriani F , Zulfakriza Z , Handayani L , Amran A , Prasetio AD , Hasib M , Dewi CN , Ramdhan M , Setyonegoro W 
Published: June 2024

Abstract
Sumatra Island is located in the subduction zone between Indo-Australian and Eurasian Plates. The tectonic activity has resulted in an active region. Hence, it may cause more heterogeneous crust in the region. To understand the relationship between the attenuation factor and the tectonic setting, we apply coda wave attenuation study Sumatra Island. This preliminary result focuses at the northern Aceh from observation at LHMI station. A total of about 123 earthquake waveforms of local distance (less than 3°) with depth less than 40 km is analyzed in this study. We employ a back-scattering model assumption to determine the attenuation of coda waves. Our coda wave quality factor (Qc
) estimation covers frequencies from 1 to 8 Hz. Onset of the coda window is determined by considering twice the arrival time of shear wave, with varying window lengths between 20 and 120 s. The Q0
(Qc
at frequency 1 Hz) varies from 65.84 ± 5.50 to 183.09 ± 7.17. We observe a decrease in the factor of frequency dependence (η) between 1.14 ± 0.06 and 1.04 ± 0.03. Depth dependent of coda wave attenuation can be seen from the increase of Q0
(which is Qc
at 1 Hz) with window length. We suggest that the Low Q0
(< 200) and high η (> 1) may be associated with high tectonic activity in this region.