bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence and determinants of adverse events in individuals with HIV commencing Dolutegravir-based antiretroviral therapy in mainland Tanzania
Authors: Fimbo Adam , Mwalwisi Yonah H. , Mwamwitwa Kissa , Matiko Damas , Mfinanga Elirehema , Lyimo Johnson , Sabasaba Amon , Missago Seth , Bukundi Elias , Gotora Goodluck , Respick Dorice , Nkayamba Alex , Masunga Emmanuel , Mnkugwe Rajabu Hussein , Kunambi Peter P. , Munishi Castory , Musanhu Christine Chiedza , Minzi Omary M. S. , Mlugu Eulambius M. 
Published: January 2024

AbstractTanzania adopted a Dolutegravir (DTG)-based regimen as first-line treatment in 2019 following the World Health Organization recommendation. Data on the DTG safety profile from sub-Saharan Africa including Tanzania are limited. We investigated the incidence of DTG-related adverse events (AEs) and associated factors among people living with HIV (PLHIV) initiated on a DTG regimen. A prospective cohort study was conducted from 25 Care and Treatment Clinics in mainland Tanzania. PLHIV aged 12 years and above who were initiated on a DTG-based regimen were actively followed up for three months. The Cox regression model was used to determine the predictors of occurrence of AEs over time. A p-value of 0.05 was considered statistically significant. From January 2020 to June 2022, a cohort of 935 participants who were both newly diagnosed and ART-experienced who transitioned to a DTG-based regimen was enrolled. Out of 935 participants, 59 (6.3%) reported a total of 62 AEs. The most frequently experienced AE was skin itching and rashes (15/62; 24.2%). DTG-associated neuropsychiatric AEs were less common and included headache (6 [9.6%]) and sleep disturbances (3 [4.8%]). The overall incidence of occurrence of the first AEs was 96.7 per 1000 person-months [95% C.I: 74.4–125.7] with the highest incidence observed among the elderly (≥ 60 years). Individuals on WHO HIV Clinical Stage 2 had a 2.7 significantly higher risk of developing AEs (adjusted hazard ratio = 2.73, 95% CI = 1.46–5.12, p = 0.017). We report a low incidence of grade I (mild) and grade II (moderate) DTG-associated AEs suggesting that the regimen is generally safe in the population. Continued monitoring of DTG safety in the population is recommended.
Exploration of neuroprotective effect from Coriandrum sativum L. ethanolic seeds extracts on brain of obese rats
Authors: Hardiany Novi Silvia , Dewi Putri Krishna Kumara , Dewi Syarifah , Tejo Bimo A. 
Published: January 2024

AbstractIn this study, the potential neuroprotective ability of coriander seeds (Coriandrum sativum L.) ethanolic extract (CSES) as a neuroprotectant agent in the brains of high-fat diet-induced obese rats was analyzed. The study investigated how CSES impacts oxidative stress markers (i.e., malondialdehyde/MDA, glutathione/GSH and catalase), inflammation marker (i.e., Interleukin-6/IL-6), cellular senescence markers (i.e., senescence-associated β-galactoside/SA-β-Gal activity and p16), brain damage marker (i.e., Neuron-specific Enolase/NSE), and neurogenesis markers (i.e., mature Brain-derived Neurotropic Factor/BDNF, pro-BDNF, and mature/pro-BDNF ratio). Male adult Wistar rats were fed a high-fat diet and given CSES once daily, at 100 mg/kg body weight, for 12 weeks. CSES significantly reduced MDA concentration (p = < 0.001), SA-β-Gal activity (p = 0.010), and increased GSH concentration (p = 0.047) in the brain of obese rats; however, the decrease of IL-6, NSE, and p16 as well as the increase of catalase specific activity and BDNF expression were not significant. Moreover, the mature/pro-BDNF ratio was significantly higher in the brains of non-obese rats, both given the control diet and the high-fat diet compared to the control. Our results suggest that obese rats benefited from consuming CSES, showing improved oxidative stress levels, reduced cellular senescence and increased endogenous antioxidants, making CSES a potential neuroprotective agent.
Short-term wind speed prediction based on improved Hilbert–Huang transform method coupled with NAR dynamic neural network model
Authors: Chen Jian , Guo Zhikai , Zhang Luyao , Zhang Shanju 
Published: January 2024

AbstractWind energy, as a renewable energy source, offers the advantage of clean and pollution-free power generation. Its abundant resources have positioned wind power as the fastest-growing and most widely adopted method of electricity generation. Wind speed stands as a key characteristic when studying wind energy resources. This study primarily focuses on predictive models for wind speed in wind energy generation. The intense intermittency, randomness, and uncontrollability of wind speeds in wind power generation present challenges, leading to high development costs and posing stability challenges to power systems. Consequently, scientifically forecasting wind speed variations becomes imperative to ensure the safety of wind power equipment, maintain grid integration of wind power, and ensure the secure and stable operation of power systems. This holds significant guiding value and significance for power production scheduling institutions. Due to the complexity of wind speed, scientifically predicting its fluctuations is crucial for ensuring the safety of wind power equipment, maintaining wind power integration systems, and ensuring the secure and stable operation of power systems. This research aims to enhance the accuracy and stability of wind speed prediction, thereby reducing the costs associated with wind power generation and promoting the sustainable development of renewable energy. This paper utilizes an improved Hilbert–Huang transform (HHT) using complementary ensemble empirical mode decomposition (CEEMD) to overcome issues in the traditional empirical mode decomposition (EMD) method, such as component mode mixing and white noise interference. Such an approach not only enhances the efficiency of wind speed data processing but also better accommodates strong stochastic and nonlinear characteristics. Furthermore, by employing mathematical analytical methods to compute weights for each component, a dynamic neural network model is constructed to optimize wind speed time series modeling, aiming for a more accurate prediction of wind speed fluctuations. Finally, the optimized HHT-NAR model is applied in wind speed forecasting within the Xinjiang region, demonstrating significant improvements in reducing root mean square errors and enhancing coefficient of determination. This model not only showcases theoretical innovation but also exhibits superior performance in practical applications, providing an effective predictive tool within the field of wind energy generation.
Modulation of antioxidant defense and PSII components by exogenously applied acetate mitigates salinity stress in Avena sativa
Authors: Kappachery Sajeesh , AlHosani Mohamed , Khan Tanveer Alam , AlKharoossi Sara Nouh , AlMansoori Nemah , AlShehhi Sara Ali Saeed , AlMansoori Hamda , AlKarbi Maha , Sasi Shina , Karumannil Sameera , Elangovan Sampath Kumar , Shah Iltaf , Gururani Mayank Anand 
Published: January 2024

AbstractSalinity stress has detrimental effects on various aspects of plant development. However, our understanding of strategies to mitigate these effects in crop plants remains limited. Recent research has shed light on the potential of sodium acetate as a mitigating component against salinity stress in several plant species. Here, we show the role of acetate sodium in counteracting the adverse effects on oat (Avena sativa) plants subjected to NaCl-induced salinity stress, including its impact on plant morphology, photosynthetic parameters, and gene expression related to photosynthesis and antioxidant capacity, ultimately leading to osmoprotection. The five-week experiment involved subjecting oat plants to four different conditions: water, salt (NaCl), sodium acetate, and a combination of salt and sodium acetate. The presence of NaCl significantly inhibited plant growth and root elongation, disrupted chlorophylls and carotenoids content, impaired chlorophyll fluorescence, and down-regulated genes associated with the plant antioxidant defense system. Furthermore, our findings reveal that when stressed plants were treated with sodium acetate, it partially reversed these adverse effects across all analyzed parameters. This reversal was particularly evident in the increased content of proline, thereby ensuring osmoprotection for oat plants, even under stressful conditions. These results provide compelling evidence regarding the positive impact of sodium acetate on various plant development parameters, with a particular focus on the enhancement of photosynthetic activity.
Evaluation of calcium carbide residue and fly ash as sustainable binders for environmentally friendly loess soil stabilization
Authors: Julphunthong Phongthorn , Joyklad Panuwat , Manprom Papantasorn , Chompoorat Thanakorn , Palou Martin-Tchingnabé , Suriwong Tawat 
Published: January 2024

AbstractThe incorporation of waste materials into cementitious binders serves as a strategy to diminish waste volume and lower carbon emissions. This study presents an in-depth evaluation of calcium carbide residue and coal fly ash as alternative binders. The assessment of raw materials emphasized their chemical composition and potential for pozzolanic reactions. Based on these factors, the optimal ratio of Ca/(SiO2 + Al2O3) in the raw materials was determined to be 1.5. Therefore, this study was designed to vary the raw material composition with a CaO/(SiO2 + Al2O3) ratio ranging from 1.7 to 0.9. Upon investigating the effect of the raw material proportion on the compressive strength of pastes and mortars, the composition yielding the highest compressive strength was selected for its potential application as a stabilizer for loess soil. A mixture of calcium carbide residue and coal fly ash with a Ca/(SiO2 + Al2O3) ratio of 1.5 resulted in the highest compressive strength at long curing periods in both pastes and mortars. Mineralogical and microstructural analyses revealed several products, beyond those formed from the pozzolanic reactions, that occurred and enhanced the compressive strength of samples. The highest performing mixture of carbide residue and coal fly ash was then used to stabilize loess soil at 10–25 wt%. The unconfined compressive strength, along with mass and strength loss due to wetting and drying cycles, was also studied. It was observed that the unconfined compressive strength of the stabilized soils remained consistent after six wet-dry cycles but decreased after twelve cycles due to microcracks. The findings suggest that carefully designed mixtures based on the chemical interactions of calcium carbide residue and coal fly ash can offer a sustainable, efficient approach for soil stabilization, potentially revolutionizing construction practices.
Unsupervised anomaly detection for earthquake detection on Korea high-speed trains using autoencoder-based deep learning models
Authors: Seo Jeonguk , Kim Yunu , Ha Jisung , Kwak Dongyoup , Ko Minsam , Yoo Mintaek 
Published: January 2024

AbstractWe propose a method for detecting earthquakes for high-speed trains based on unsupervised anomaly-detection techniques. In particular, we utilized autoencoder-based deep learning models for unsupervised learning using only normal training vibration data. Datasets were generated from South Korean high-speed train data, and seismic data were measured using seismometers nationwide. The proposed method is compared with the conventional Short Time Average over Long Time Average (STA/LTA) model, considering earthquake detection capabilities, focusing on a Peak Ground Acceleration (PGA) threshold of 0.07, a criterion for track derailment. The results show that the proposed model exhibit improved earthquake detection capabilities than STA/LTA for PGA of 0.07 or higher. Furthermore, the proposed model reduced false earthquake detections under normal operating conditions and accurately identified normal states. In contrast, the STA/LTA method demonstrated a high rate of false earthquake detection under normal operating conditions, underscoring its propensity for inaccurate detection in many instances. The proposed approach shows promising performance even in situations with limited seismic data and offers a viable solution for earthquake detection in regions with relatively few seismic events.
Autosurv: interpretable deep learning framework for cancer survival analysis incorporating clinical and multi-omics data
Authors: Jiang Lindong , Xu Chao , Bai Yuntong , Liu Anqi , Gong Yun , Wang Yu-Ping , Deng Hong-Wen 
Published: January 2024

AbstractAccurate prognosis for cancer patients can provide critical information for optimizing treatment plans and improving life quality. Combining omics data and demographic/clinical information can offer a more comprehensive view of cancer prognosis than using omics or clinical data alone and can also reveal the underlying disease mechanisms at the molecular level. In this study, we developed and validated a deep learning framework to extract information from high-dimensional gene expression and miRNA expression data and conduct prognosis prediction for breast cancer and ovarian-cancer patients using multiple independent multi-omics datasets. Our model achieved significantly better prognosis prediction than the current machine learning and deep learning approaches in various settings. Moreover, an interpretation method was applied to tackle the “black-box” nature of deep neural networks and we identified features (i.e., genes, miRNA, demographic/clinical variables) that were important to distinguish predicted high- and low-risk patients. The significance of the identified features was partially supported by previous studies.
Paneth-like cells produced from OLFM4+ stem cells support OLFM4+ stem cell growth in advanced colorectal cancer
Authors: Sakahara Mizuho , Okamoto Takuya , Srivastava Upasna , Natsume Yasuko , Yamanaka Hitomi , Suzuki Yutaka , Obama Kazutaka , Nagayama Satoshi , Yao Ryoji 
Published: January 2024

AbstractTumor tissues consist of heterogeneous cells that originate from stem cells; however, their cell fate determination program remains incompletely understood. Using patient-derived organoids established from patients with advanced colorectal cancer (CRC), we evaluated the potential of olfactomedin 4 (OLFM4)+ stem cells to produce a bifurcated lineage of progenies with absorptive and secretory properties. In the early phases of organoid reconstruction, OLFM4+ cells preferentially gave rise to secretory cells. Additionally, we found that Paneth-like cells, which do not exist in the normal colon, were induced in response to Notch signaling inhibition. Video recordings of single OLFM4+ cells revealed that organoids containing Paneth-like cells were effectively propagated and that their selective ablation led to organoid collapse. In tumor tissues, Paneth-like cells were identified only in the region where tumor cells lost cell adhesion. These findings indicate that Paneth-like cells are directly produced by OLFM4+ stem cells and that their interaction contributes to tumor formation by providing niche factors. This study reveals the importance of the cell fate specification program for building a complete tumor cellular ecosystem, which might be targeted with novel therapeutics.
Probing the allosteric NBD-TMD crosstalk in the ABC transporter MsbA by solid-state NMR
Authors: Novischi S. Y. Phoebe , Karoly-Lakatos Andrea , Chok Kerby , Bonifer Christian , Becker-Baldus Johanna , Glaubitz Clemens 
Published: January 2024

AbstractThe ABC transporter MsbA plays a critical role in Gram-negative bacteria in the regulation of the outer membrane by translocating core-LPS across the inner membrane. Additionally, a broad substrate specificity for lipophilic drugs has been shown. The allosteric interplay between substrate binding in the transmembrane domains and ATP binding and turnover in the nucleotide-binding domains must be mediated via the NBD/TMD interface. Previous studies suggested the involvement of two intracellular loops called coupling helix 1 and 2 (CH1, CH2). Here, we demonstrate by solid-state NMR spectroscopy that substantial chemical shift changes within both CH1 and CH2 occur upon substrate binding, in the ATP hydrolysis transition state, and upon inhibitor binding. CH2 is domain-swapped within the MsbA structure, and it is noteworthy that substrate binding induces a larger response in CH2 compared to CH1. Our data demonstrate that CH1 and CH2 undergo structural changes as part of the TMD-NBD cross-talk.
Curvature sensing lipid dynamics in a mitochondrial inner membrane model
Authors: Golla Vinaya Kumar , Boyd Kevin J. , May Eric R. 
Published: January 2024

AbstractMembrane curvature is essential for many cellular structures and processes, and factors such as leaflet asymmetry, lipid composition, and proteins all play important roles. Cardiolipin is the signature lipid of mitochondrial membranes and is essential for maintaining the highly curved shapes of the inner mitochondrial membrane (IMM) and the spatial arrangement of membrane proteins. In this study, we investigate the partitioning behavior of various lipids present in the IMM using coarse-grained molecular dynamics simulations. This study explores curved bilayer systems containing phosphatidylcholine (PC), phosphatidylethanolamine (PE), and cardiolipin (CDL) in binary and ternary component mixtures. Curvature properties such as mean and Gaussian curvatures, as well as the distribution of lipids into the various curved regions of the cristae models, are quantified. Overall, this work represents an advance beyond previous studies on lipid curvature sensing by simulating these systems in a geometry that has the morphological features and scales of curvature consistent with regions of the IMM. We find that CDL has a stronger preference for accumulating in regions of negative curvature than PE lipids, in agreement with previous results. Furthermore, we find lipid partitioning propensity is dominated by sensitivity to mean curvature, while there is a weaker correlation with Gaussian curvature.
Suppressing MTERF3 inhibits proliferation of human hepatocellular carcinoma via ROS-mediated p38 MAPK activation
Authors: Zheng Zhihai , Zhao Youjuan , Yu Hongjia , Wang Tingting , Li Jinhai , Xu Liang , Ding Chunming , He Lan , Wu Lijun , Dong Zhixiong 
Published: January 2024

AbstractMitochondrial transcription termination factor 3 (MTERF3) negatively regulates mitochondrial DNA transcription. However, its role in hepatocellular carcinoma (HCC) progression remains elusive. Here, we investigate the expression and function of MTERF3 in HCC. MTERF3 is overexpressed in HCC tumor tissues and higher expression of MTERF3 positively correlates with poor overall survival of HCC patients. Knockdown of MTERF3 induces mitochondrial dysfunction, S-G2/M cell cycle arrest and apoptosis, resulting in cell proliferation inhibition. In contrast, overexpression of MTERF3 promotes cell cycle progression and cell proliferation. Mechanistically, mitochondrial dysfunction induced by MTERF3 knockdown promotes ROS accumulation, activating p38 MAPK signaling pathway to suppress HCC cell proliferation. In conclusion, ROS accumulation induced by MTERF3 knockdown inhibits HCC cell proliferation via p38 MAPK signaling pathway suggesting a promising target in HCC patients.
Characterizing immune variation and diagnostic indicators of preeclampsia by single-cell RNA sequencing and machine learning
Authors: Zhou Wenwen , Chen Yixuan , Zheng Yuhui , Bai Yong , Yin Jianhua , Wu Xiao-Xia , Hong Mei , Liang Langchao , Zhang Jing , Gao Ya , Sun Ning , Li Jiankang , Zhang Yiwei , Wu Linlin , Jin Xin , Niu Jianmin 
Published: January 2024

AbstractPreeclampsia is a multifactorial and heterogeneous complication of pregnancy. Here, we utilize single-cell RNA sequencing to dissect the involvement of circulating immune cells in preeclampsia. Our findings reveal downregulation of immune response in lymphocyte subsets in preeclampsia, such as reduction in natural killer cells and cytotoxic genes expression, and expansion of regulatory T cells. But the activation of naïve T cell and monocyte subsets, as well as increased MHC-II-mediated pathway in antigen-presenting cells were still observed in preeclampsia. Notably, we identified key monocyte subsets in preeclampsia, with significantly increased expression of angiogenesis pathways and pro-inflammatory S100 family genes in VCAN+monocytes and IFN+non-classical monocytes. Furthermore, four cell-type-specific machine-learning models have been developed to identify potential diagnostic indicators of preeclampsia. Collectively, our study demonstrates transcriptomic alternations of circulating immune cells and identifies immune components that could be involved in pathophysiology of preeclampsia.
Antagonistic interactions safeguard mitotic propagation of genetic and epigenetic information in zebrafish
Authors: Lawir Divine-Fondzenyuy , Soza-Ried Cristian , Iwanami Norimasa , Siamishi Iliana , Bylund Göran O. , O´Meara Connor , Sikora Katarzyna , Kanzler Benoît , Johansson Erik , Schorpp Michael , Cauchy Pierre , Boehm Thomas 
Published: January 2024

AbstractThe stability of cellular phenotypes in developing organisms depends on error-free transmission of epigenetic and genetic information during mitosis. Methylation of cytosine residues in genomic DNA is a key epigenetic mark that modulates gene expression and prevents genome instability. Here, we report on a genetic test of the relationship between DNA replication and methylation in the context of the developing vertebrate organism instead of cell lines. Our analysis is based on the identification of hypomorphic alleles of dnmt1, encoding the DNA maintenance methylase Dnmt1, and pole1, encoding the catalytic subunit of leading-strand DNA polymerase epsilon holoenzyme (Pole). Homozygous dnmt1 mutants exhibit genome-wide DNA hypomethylation, whereas the pole1 mutation is associated with increased DNA methylation levels. In dnmt1/pole1 double-mutant zebrafish larvae, DNA methylation levels are restored to near normal values, associated with partial rescue of mutant-associated transcriptional changes and phenotypes. Hence, a balancing antagonism between DNA replication and maintenance methylation buffers against replicative errors contributing to the robustness of vertebrate development.
Infant diarrheal disease in rhesus macaques impedes microbiome maturation and is linked to uncultured Campylobacter species
Authors: Rhoades Nicholas S. , Cinco Isaac R. , Hendrickson Sara M. , Prongay Kamm , Haertel Andrew J. , Flores Gilberto E. , Slifka Mark K. , Messaoudi Ilhem 
Published: January 2024

AbstractDiarrheal diseases remain one of the leading causes of death for children under 5 globally, disproportionately impacting those living in low- and middle-income countries (LMIC). Campylobacter spp., a zoonotic pathogen, is one of the leading causes of food-borne infection in humans. Yet to be cultured Campylobacter spp. contribute to the total burden in diarrheal disease in children living in LMIC thus hampering interventions. We performed microbiome profiling and metagenomic genome assembly on samples collected from over 100 infant rhesus macaques longitudinally and during cases of clinical diarrhea within the first year of life. Acute diarrhea was associated with long-lasting taxonomic and functional shifts of the infant gut microbiome indicative of microbiome immaturity. We constructed 36 Campylobacter metagenomic assembled genomes (MAGs), many of which fell within 4 yet to be cultured species. Finally, we compared the uncultured Campylobacter MAGs assembled from infant macaques with publicly available human metagenomes to show that these uncultured species are also found in human fecal samples from LMIC. These data highlight the importance of unculturable Campylobacter spp. as an important target for reducing disease burden in LMIC children.