bluuebunny/crossref_metadata_2025_split huggingface dataset:
o
8
G Site-Specifically Modified tRF-1-AspGTC: A Novel Therapeutic Target and Biomarker for Pulmonary Hypertension
Authors: Zhang Junting , Li Yiying , Chen Yuan , Zhang Jianchao , Jia Zihui , He Muhua , Liao Xueyi , He Siyu , Bian Jin-Song , Nie Xiao-Wei 
Published: May 2024

BACKGROUND:
Hypoxia and oxidative stress contribute to the development of pulmonary hypertension (PH). tRNA-derived fragments play important roles in RNA interference and cell proliferation, but their epitranscriptional roles in PH development have not been investigated. We aimed to gain insight into the mechanistic contribution of oxidative stress–induced 8-oxoguanine in pulmonary vascular remodeling.

METHODS:
Through small RNA modification array analysis and quantitative polymerase chain reaction, a significant upregulation of the 8-oxoguanine -modified tRF-1-AspGTC was found in the lung tissues and the serum of patients with PH.

RESULTS:

This modification occurs at the position 5 of the tRF-1-AspGTC (5o
8
G tRF). Inhibition of the 5o
8
G tRF reversed hypoxia-induced proliferation and apoptosis resistance in pulmonary artery smooth muscle cells. Further investigation unveiled that the 5o
8
G tRF retargeted mRNA of WNT5A (Wingless-type MMTV integration site family, member 5A) and CASP3 (Caspase3) and inhibited their expression. Ultimately, BMPR2 (Bone morphogenetic protein receptor 2) -reactive oxygen species/5o
8
G tRF/WNT5A signaling pathway exacerbated the progression of PH.

CONCLUSIONS:

Our study highlights the role of site-specific 8-oxoguanine–modified tRF in promoting the development of PH. Our findings present a promising therapeutic avenue for managing PH and propose 5o
8
G tRF as a potential innovative marker for diagnosing this disease.
Does Online Testing Make the Grade? Evidence from a Randomized Controlled Trial
Authors: Atwater Ann , Rush Mark , Saygin Perihan 
Published: May 2024

Abstract
As a result of the increase in online course offerings at colleges and universities, the prevalence of online and computerized examinations has increased over the last two decades. Beyond academia, online examinations have been used to assess competence for certifications by both governments and private firms. Despite this importance, a randomized controlled trial that randomizes individual test takers into online and in-person examinations has not previously been conducted. In this paper, we rectify this by conducting this experiment in a large economics class at a large research university in the American southeast. We supplement our experiment results with a novel methodology of using screening surveys administered to potential volunteers which solicit preference information. We find that online testing reduces examination grades by over a tenth of a standard deviation, relative to in-person assessment. Additional exploratory exercises provide evidence that this effect is driven by students who prefer in-person examinations.
Maintenance of the Zonal Momentum Balance of the Antarctic Circumpolar Current by Barotropic Dynamics
Authors: Zhang Xihan , Nikurashin Maxim , Peña-Molino Beatriz , Rintoul Stephen R. , Doddridge Edward 
Published: May 2024

Abstract
The vertically integrated zonal momentum balance of the Antarctic Circumpolar Current (ACC) is dominated by wind stress at the surface and topographic form stress (TFS) at the bottom. It has been argued that wind stress is transferred from the surface to the bottom by transient baroclinic eddies, via interfacial form stress, to establish the balance between wind stress and TFS. However, ocean models indicate TFS responds rapidly to changes in wind stress, suggesting that barotropic processes play a role in this balance. We investigate the dynamics governing the wind–TFS balance of the ACC and its response to wind using an idealized, wind- and buoyancy-driven channel model. We show that the balance is established and maintained at equilibrium by the barotropic dynamics. The balance results from the continuity of the flow, in which the Ekman transport at the surface, balanced by wind stress, is compensated by a return flow at depth, balanced by TFS. This leads to a match between wind stress and TFS which is independent of momentum stresses in the interior. Transient baroclinic eddies oppose the wind-driven isopycnal steepening via eddy buoyancy fluxes, which act to flatten the isopycnals. The eddy-driven isopycnal flattening corresponds to a reduction in the zonal geostrophic shear and thus a redistribution of the zonal momentum in the interior via eddy momentum stresses. The maintenance of the vertically integrated ACC momentum balance by the barotropic dynamics explains the fast response of the wind–TFS balance to changes in wind forcing.
ST-TransNet: A Spatiotemporal Transformer Network for Uncertainty Estimation from a Single Deterministic Precipitation Forecast
Authors: Wang Jingnan , Wang Xiaodong , Guan Jiping , Zhang Lifeng , Chang Tao , Yu Wei 
Published: May 2024

Abstract
The forecast uncertainty, particularly for precipitation, serves as a crucial indicator of the reliability of deterministic forecasts. Traditionally, forecast uncertainty is estimated by ensemble forecasting, which is computationally expensive since the forecast model is run multiple times with perturbations. Recently, deep learning methods have been explored to learn the statistical properties of ensemble prediction systems due to their low computational costs. However, accurately and effectively capturing the uncertainty information in precipitation forecasts remains challenging. In this study, we present a novel spatiotemporal transformer network (ST-TransNet) as an alternative approach to estimate uncertainty with ensemble spread and probabilistic forecasts, by learning from historical ensemble forecasts. ST-TransNet features a hierarchical structure for extracting multiscale features and incorporates a spatiotemporal transformer module with window-based attention to capture correlations in both spatial and temporal dimensions. Additionally, window-based attention can not only extract local precipitation patterns but also reduce computational costs. The proposed ST-TransNet is evaluated on the TIGGE ensemble forecast dataset and Global Precipitation Measurement (GPM) precipitation products. Results show that ST-TransNet outperforms both traditional and deep learning methods across various metrics. Case studies further demonstrate its ability to generate reasonable and accurate spread and probability forecasts from a single deterministic precipitation forecast. It demonstrates the capacity and efficiency of neural networks in estimating precipitation forecast uncertainty.
The relationship of KRAS expression with KRAS status, prognosis, and tumor-infiltrated T lymphocytes in colorectal cancer
Authors: Zhou Yebohao , Zeng Ziwei , Li Ze , Ruan Lei , Xie Hao , Ye Fujin , Huang Liang , Liu Huashan , Kang Liang 
Published: May 2024

Background: The significance of Kirsten rat sarcoma viral oncogene (KRAS) mutation in colorectal cancer (CRC) is well established; yet, its association with KRAS expression and prognosis warrants further investigation. While high KRAS expression is commonly linked with poorer prognosis in other cancers, its role in CRC remains relatively understudied. Objective: To explore the correlation between KRAS expression, KRAS status, prognosis, and tumor-infiltrating T lymphocyte density in CRC. Design: Single-center retrospective study. Methods: Conducted between 2010 and 2020, this study utilized tumor samples to assess KRAS expression and quantify CD3+/CD8+ T lymphocytes. The Cox proportional hazards model and linear regression analysis were employed to examine the relationship between KRAS expression, prognosis, and tumor-infiltrating T lymphocytes. Results: This study included 265 CRC patients who underwent radical surgery. No significant association was observed between KRAS expression and KRAS status ( p > 0.05). High KRAS expression was associated with poorer overall survival and disease-free survival ( p < 0.05). Subgroup analysis revealed that high KRAS expression remained indicative of a worse prognosis in the group with mismatch repair-deficient (dMMR) and KRAS mutant type ( p < 0.05). Multivariate analysis confirmed KRAS expression as an unfavorable prognostic factor ( p < 0.05). However, the significance of KRAS expression was lost in the dMMR and KRAS mutant-type group regarding overall survival ( p > 0.05). Notably, KRAS expression showed a negative correlation with the density of CD8+ T lymphocytes in tumor tissue ( p < 0.05), a finding also observed in the dMMR group ( p < 0.05). Conclusion: No association was found between KRAS expression and KRAS mutation status in CRC. Higher KRAS expression was indicative of poorer prognosis for CRC patients, except for those with proficient mismatch repair and KRAS wild type. In addition, in patients with dMMR, KRAS expression was associated with a lower density of CD8+ T lymphocytes in tumor tissue.
Decompression Alone vs Decompression and Fusion: Spin in Abstracts of Systematic Reviews and Meta-Analysis
Authors: Taka Taha M. , Avetisian Henry , El-Farra Mohamed H. , Gulbransen Matthew , Danisa Olumide 
Published: May 2024

Study Design Cross-sectional. Objectives Spin, a prevalent bias, can distort outcomes in well-validated research. Treatment of lumbar stenosis with spondylolisthesis through decompression alone (DA) vs decompression and fusion (DF) remains a controversial topic. We aimed to identify the prevalence of spin in meta-analyses and systematic reviews regarding DA vs DF in the treatment of spinal stenosis with concomitant degenerative spondylolisthesis. Methods MEDLINE, Web of Science, and Google Scholar were searched for meta-analyses and systematic reviews comparing DA vs DF treatment of lumbar spinal stenosis accompanied by degenerative spondylolisthesis. Each study was evaluated for the nine most severe spin types. We also explored the association between spin and methodological quality of a systematic review using the revised A Measurement Tool to Assess Systematic Reviews appraisal tool. Results The search yielded 1506 articles, of which 13 met inclusion. It was found that 46.2% (6/13) of the articles contained spin within the abstract. Of the nine most severe types, type 5 was found to be the most prevalent (4/13, 30.8%), followed by types 9 (2/13, 15.4%), 3 (1/13, 7.7%), 4 (1/13, 7.7%), and 6 (1/13, 7.7%). Spin types 1, 2, 7 and 8 were not found. According to AMSTAR-2, 53.8% (7/13) of the studies were appraised as “critically low” quality and 46.2% (6/13) as “low” quality. Conclusion This study demonstrated the presence of spin in 46.2% of abstracts pertaining to the treatment for spinal stenosis with degenerative spondylolisthesis. Spine surgeons should learn to recognize spin as they review articles before implementing them into practice.
Postoperative Opioid Usage and Disposal Strategies After Arthroscopic Procedures in a Young Cohort: A Prospective Observational Study
Authors: Johns William L. , Johnson Emma E. , Brutico Joseph , Sherman Matthew B. , Freedman Kevin B. , Emper William , Salvo John P. , Hammoud Sommer 
Published: May 2024

Background: Although several studies have noted that patients are routinely overprescribed opioids, few have reported usage after arthroscopic surgery. Purpose: To determine opioid consumption and allocation for unused opioids after common arthroscopic surgeries. Study Design: Case series; Level of evidence, 4. Methods: Patients between the ages of 15 and 40 years who were scheduled to undergo anterior cruciate ligament reconstruction (ACLR), labral repair of the hip or shoulder, meniscectomy, or meniscal repair were prospectively enrolled. Patients were prescribed either 5 mg hydrocodone-325 mg acetaminophen or 5 mg oxycodone-325 mg acetaminophen based on surgeon preference. Patients completed a daily opioid usage survey during the 2-week postoperative period. In addition, patients completed a survey on postoperative day 21 inquiring about continued opioid use and medication disposal, if applicable. Opioid medication consumption was converted to morphine milligram equivalents (MMEs). Results: Of the 200 patients who were enrolled in the study, 176 patients had sufficient follow-up after undergoing 85 (48%) ACLR, 26 (14.8%) hip labral repair, 34 (19.3%) shoulder labral repair, 18 (10.2%) meniscectomy, and 13 (7.4%) meniscal repair procedures. Mean age was 26.1 years (SD, 7.38); surgeons prescribed a mean of 26.6 pills whereas patients reported consuming a mean of 15.5 pills. The mean MME consumption in the 14 days after each procedure was calculated: ACLR (95.7; 44% of prescription), hip labral repair (84.8; 37%), shoulder labral repair (57.2; 35%), meniscectomy (18.4; 27%), and meniscal repair (32.1; 42%). This corresponded to approximately 39% of the total opioid prescription being utilized across all procedures. Mean MME consumption was greatest on postoperative day 1 in hip, shoulder, and meniscal procedures and on postoperative day 2 in ACLR. Only 7.04% of patients reported continued opioid use in the third postoperative week. Patients had a mean of 11 unused pills or 77.7 MMEs remaining. Of the patients with remaining medication, 24.7% intended to keep their medication for future use. Conclusion: The results of our study indicate that patients who undergo the aforementioned arthroscopic procedures consume <75 MMEs in the 2-week postoperative period, translating into a mean of 10 to 15 pills consumed. Approximately 60% of total opioids prescribed went unused, and one-fourth of patients intended to keep their remaining medication for future usage. We have provided general prescribing guidelines and recommend that surgeons carefully consider customizing their opioid prescriptions on the basis of procedure site to balance optimal postoperative analgesia with avoidance of dissemination of excess opioids.
Real-Time Co-optimization of Gear Shifting and Engine Torque for Predictive Cruise Control of Heavy-Duty Trucks
Authors: Chu Hongqing , Na Xiaoxiang , Liu Huan , Wang Yuhai , Yang Zhuo , Zhang Lin , Chen Hong 
Published: May 2024

AbstractFuel consumption is one of the main concerns for heavy-duty trucks. Predictive cruise control (PCC) provides an intriguing opportunity to reduce fuel consumption by using the upcoming road information. In this study, a real-time implementable PCC, which simultaneously optimizes engine torque and gear shifting, is proposed for heavy-duty trucks. To minimize fuel consumption, the problem of the PCC is formulated as a nonlinear model predictive control (MPC), in which the upcoming road elevation information is used. Finding the solution of the nonlinear MPC is time consuming; thus, a real-time implementable solver is developed based on Pontryagin’s maximum principle and indirect shooting method. Dynamic programming (DP) algorithm, as a global optimization algorithm, is used as a performance benchmark for the proposed solver. Simulation, hardware-in-the-loop and real-truck experiments are conducted to verify the performance of the proposed controller. The results demonstrate that the MPC-based solution performs nearly as well as the DP-based solution, with less than 1% deviation for testing roads. Moreover, the proposed co-optimization controller is implementable in a real-truck, and the proposed MPC-based PCC algorithm achieves a fuel-saving rate of 7.9% without compromising the truck’s travel time.
Association between urinary phthalate metabolites and renal function in late pregnant women
Authors: Hong Qifu , Pu Tao , Li Maojie , Chen Zhongbao , Liu Xingyan , Zeng Rong , Zhang Mingzhe , Dai Lulu , An Songlin , Shen Xubo , Shang Xuejun , Zhou Yuanzhong , Tian Kunming 
Published: May 2024

AbstractEvidence about associations of phthalates metabolites with increased serum uric acid (SUA) levels in pregnant women remains unknown. To address this, we conducted a cross-sectional population-based study including 851 pregnant women from Zunyi birth cohort in southwest China. Multiple linear regression models were used to explore single relationships between ten urinary phthalate metabolites with SUA and estimated glomerular filtration rate (eGFR). And then, the overall relationship of phthalate mixture with SUA and eGFR were determined by principal component analysis (PCA) and quantile g-computation (Q-g) analysis. The multivariable linear regression showed that mono-butyl phthalate (MBP), mono-octyl phthalate (MOP) and mono-benzyl phthalate (MBzP) were positively associated with SUA, while mono (2-ethylhexyl) phthalate (MEHP) and mono (2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) were associated with increased eGFR level. Moreover, PCA analysis suggested that phthalate mixture was positively associated with SUA, and MOP, MBzP and MEHP appeared to be the major contributors. Furthermore, Q-g regression showed that each quantile increase in phthalate mixture was associated with 3.27% higher SUA (95% CI 0.21%, 6.41%). Our results imply that phthalate metabolites were associated with higher SUA in late pregnant women, and MBP, MBzP and MOP might be the major drivers. So, a health perinatal duration should be seriously taken to counteract the environment-related dysregulated kidney function.
Accuracy of genomic prediction using multiple Atlantic salmon populations
Authors: Ajasa Afees A. , Boison Solomon A. , Gjøen Hans M. , Lillehammer Marie 
Published: May 2024

Abstract
Background
The accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four parallel populations often exist, thus offering the opportunity to increase the size of the reference set by combining these populations. By allowing a reduction in the number of records per population, multi-population prediction can potentially reduce cost and welfare issues related to the recording of traits, particularly for diseases. In this study, we evaluated the accuracy of multi- and across-population prediction of breeding values for resistance to amoebic gill disease (AGD) using all single nucleotide polymorphisms (SNPs) on a 55K chip or a selected subset of SNPs based on the signs of allele substitution effect estimates across populations, using both linear and nonlinear genomic prediction (GP) models in Atlantic salmon populations. In addition, we investigated genetic distance, genetic correlation estimated based on genomic relationships, and persistency of linkage disequilibrium (LD) phase across these populations.

Results
The genetic distance between populations ranged from 0.03 to 0.07, while the genetic correlation ranged from 0.19 to 0.99. Nonetheless, compared to within-population prediction, there was limited or no impact of combining populations for multi-population prediction across the various models used or when using the selected subset of SNPs. The estimates of across-population prediction accuracy were low and to some extent proportional to the genetic correlation estimates. The persistency of LD phase between adjacent markers across populations using all SNP data ranged from 0.51 to 0.65, indicating that LD is poorly conserved across the studied populations.

Conclusions
Our results show that a high genetic correlation and a high genetic relationship between populations do not guarantee a higher prediction accuracy from multi-population genomic prediction in Atlantic salmon.
Identification and expression analysis of the Xyloglucan transglycosylase/hydrolase (XTH) gene family under abiotic stress in oilseed (Brassica napus L.)
Authors: Chen Jingdong , Wan Heping , Zhao Huixia , Dai Xigang , Wu Wanjin , Liu Jin , Xu Jinsong , Yang Rui , Xu Benbo , Zeng Changli , Zhang Xuekun 
Published: May 2024

AbstractXTH genes are key genes that regulate the hydrolysis and recombination of XG components and plays role in the structure and composition of plant cell walls. Therefore, clarifying the changes that occur in XTHs during plant defense against abiotic stresses is informative for the study of the plant stress regulatory mechanism mediated by plant cell wall signals. XTH proteins in Arabidopsis thaliana was selected as the seed sequences in combination with its protein structural domains, 80 members of the BnXTH gene family were jointly identified from the whole genome of the Brassica napus ZS11, and analyzed for their encoded protein physicochemical properties, phylogenetic relationships, covariance relationships, and interoperating miRNAs. Based on the transcriptome data, the expression patterns of BnXTHs were analyzed in response to different abiotic stress treatments. The relative expression levels of some BnXTH genes under Al, alkali, salt, and drought treatments after 0, 6, 12 and 24 h were analyzed by using qRT-PCR to explore their roles in abiotic stress tolerance in B. napus. BnXTHs showed different expression patterns in response to different abiotic stress signals, indicating that the response mechanisms of oilseed rape against different abiotic stresses are also different. This paper provides a theoretical basis for clarifying the function and molecular genetic mechanism of the BnXTH gene family in abiotic stress tolerance in rapeseed.
Unravelling the metabolomic diversity of pigmented and non-pigmented traditional rice from Tamil Nadu, India
Authors: Subramanian Venkatesan , Dhandayuthapani Udhaya Nandhini , Kandasamy Senthilraja , Sivaprakasam Jidhu Vaishnavi , Balasubramaniam Prabha , Shanmugam Mohan Kumar , Nagappan Sriram , Elangovan Subramanian , Subramani Umesh Kanna , Palaniyappan Kumaresan , Vellingiri Geethalakshmi , Muthurajan Raveendran 
Published: May 2024

AbstractRice metabolomics is widely used for biomarker research in the fields of pharmacology. As a consequence, characterization of the variations of the pigmented and non-pigmented traditional rice varieties of Tamil Nadu is crucial. These varieties possess fatty acids, sugars, terpenoids, plant sterols, phenols, carotenoids and other compounds that plays a major role in achieving sustainable development goal 2 (SDG 2). Gas-chromatography coupled with mass spectrometry was used to profile complete untargeted metabolomics of Kullkar (red colour) and Milagu Samba (white colour) for the first time and a total of 168 metabolites were identified. The metabolite profiles were subjected to data mining processes, including principal component analysis (PCA), Orthogonal Partial Least Square Discrimination Analysis (OPLS-DA) and Heat map analysis. OPLS-DA identified 144 differential metabolites between the 2 rice groups, variable importance in projection (VIP) ≥ 1 and fold change (FC) ≥ 2 or FC ≤ 0.5. Volcano plot (64 down regulated, 80 up regulated) was used to illustrate the differential metabolites. OPLS-DA predictive model showed good fit (R2X = 0.687) and predictability (Q2 = 0.977). The pathway enrichment analysis revealed the presence of three distinct pathways that were enriched. These findings serve as a foundation for further investigation into the function and nutritional significance of both pigmented and non-pigmented rice grains thereby can achieve the SDG 2.