bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome sequencing and analysis of the symbiotic Armillaria gallica M3 with Gastrodia elata
Authors: Luo Chengying , Lu Yao , Su Lei , Li Xindong , Liu Jiajia , Miao Jiayun , Lin Yicen , Lin Lianbing 
Published: March 2024

Abstract
Background
Armillariaare phytopathogens that cause severe root rot of trees in forests, but at the same time, some Armillaria are important symbiotic fungi of the valuable Chinese herb Gastrodia elata. Currently, the whole genome database of Armillaria is relatively limited, and it is expected that a more comprehensive understanding of the symbiotic interactions between Armillaria and G. elata can be achieved through genome-wide comparisons and functional annotations. Whole genome sequencing of Armillaria gallica M3 strain was performed using Oxford Nanopore Technologies sequencing platform, and the sequencing data were used to perform genome assembly, gene prediction and functional annotation, carbohydrate-active enzymes, and host-pathogen interactions using bioinformatics methods.
Results
In this study, we obtained an 83.33 M genome of A. gallicaM3 strain, which consisted of 38 overlapping clusters with an N50 of 6,065,498 bp and a GC content of 47.43 %. A total of 12,557 genes were identified in the genome of A. gallica M3, and the repetitive sequences accounted for about 44.36 % of the genome. 42.26 % of the genome was composed of glycoside hydrolases (GHs), 16.15 % of the genome was composed of glycosyltransferases (GTs), and 16.15 % of the genome was composed of glycoside hydrolases (GHs). GHs accounted for 42.26 % and glycosyltransferases (GTs) for 16.15 %. In addition, 3412 genes in A. gallica M3 were involved in the host-pathogen interaction mechanism.
Conclusions
These results have elucidated the characteristics of A. gallica M3 from a genomic perspective to a certain extent. They help to analyze the inner mechanism of A. gallicaM3 being able to symbiosis with G. elataat the genomic level, which is of great significance to the next related research of A. gallica M3.
Biomechanical effects of different approaches and titanium mesh in combined anterior cervical corpectomy decompression and fusion：a finite element study
Authors: Li Dan , Yu Yuting , Dong Chao , Zhou Bo , Gu Lin 
Published: March 2024

Abstract

Background: Anterior Cervical Corpectomy and Fusion(ACCF), which is one of the common surgeries used to treat cervical spine diseases, has been widely applied in clinical practice. The commonly used internal fixation forms in ACCF surgery include the traditional anterior vertebral body screw-plate (AVBSP) structure and the anterior cervical pedicle screw-plate (APSP) structure, both of which are combined with titanium mesh to achieve support and bone fusion.
Objetives: The purpose was to investigate the effects of different surgical plans on cervical spine biomechanics and the interplay between internal fixation instruments after surgery.
Methods: In this study, a finite element model of the human lower cervical spine (C3-C7) after ACCF surgery was established. The surgical plan consisted of two internal fixation forms (AVBSP and APSP) and two titanium mesh forms (linear and curved), combined in different ways.
Results: The mechanical sensitivity of adjacent intervertebral disc nuclei to different surgical plans was significantly different. The stress concentration areas on the vertebral body entry surface varied with different entry methods, and the stress values were greatly affected by cervical movements. The related instrument studies showed that the choice of anterior fixation method would affect the stress level and distribution of the titanium mesh. Theoretically, the combination of curved titanium mesh and AVBSP is beneficial to reducing the overall stress level of the internal fixation instruments and titanium mesh.
Conclusion:The research provides theoretical basis for the selection of clinical surgical plans. It is advantageous in enhancing postoperative stability of cervical vertebrae while reducing the risk of recurrence or other complications such as adjacent segment disease. Clinically, when selecting the excision fusion surgical plan based on the condition of the patient's cervical lesion, consideration should also be given to the matching characteristics between internal fixation methods and titanium mesh forms, as well as their effects on the biomechanics of adjacent segments.
A simple structure and high sensitivity side-polished micro-structured fiber RI sensor based on open-loop channel gold-coated
Authors: Wang Yujun , Li Peng , Liu Yundong , Tang Chunjuan , Liu Lina , Shan Feng 
Published: March 2024

Abstract

A highly sensitive and simple structure side-polished micro-structured fiber (MOF) refractive index (RI) sensor based on surface plasmon resonance (SPR) is proposed and studied by the finite element method (FEM). The gold nanofilm used to stimulate plasmons is directly deposited on the inner wall of the open-loop channel of a MOF consisting of an arrangement of six cladding air-holes. The sample analyte is arranged on the outer surface of the optical fiber to improve the utilization rate of the sensor and reduce the tediousness of operation. Meanwhile, in order to increase the leakage intensity of evanescent field, three large air-holes were introduced near the fiber core. Research has shown that the proposed sensor can achieve sensing detection in the range of 1.19–1.37 RI. The maximum sensitivity in the x-polarized direction can reach 12,500 nm/RIU, and its corresponding resolution is 3.64 × 10− 5 RIU. Moreover, it has a high linear response of 0.9944 within the RI detection range of 1.19–1.33. Obviously, the proposed sensor has a simple structure, wide RI detection range, and high sensitivity, which can make it widely used in biomedical and analytical chemistry.
Historical contingencies linked to past drought-wetting cycles as a driver of bacterial–not fungal–community assembly processes in an arid desert
Authors: Maurice Kenji , Boukcim Hassan , Selosse Marc-André , Ducousso Marc 
Published: March 2024

Abstract
Soil microbial communities are complex and dynamic, and their composition is jointly driven by niche and neutral processes. Otherwise, the assembly processes of these communities are known to be influenced by both biotic and abiotic factors, yet the extent to which past events could explain their contemporary composition remains unclear, particularly in natural desert environments. We used a phylogenetic framework to quantify the deterministic and stochastic community assembly processes of bacteria and fungi facing historical contingencies linked to past short- and long-term drought-wetting cycles. We found that deterministic and stochastic processes underpinned bacterial community assembly, while fungal communities were mainly assembled via stochastic processes. Abundant bacterial species were at the origin of the differences in phylodiversity noted between natural sites and those facing historical contingencies, while rare fungal species were at the origin of these differences. Furthermore, we showed that historical contingencies increased selection while decreasing dispersal limitation and homogeneous dispersal of bacterial communities. Yet fungal communities were found to be unaffected by past events and their assembly was constantly supported by stochastic processes. These results shed light on the differential impacts of historical contingencies on both bacteria and fungi. They also provide crucial information that could contribute to enhancing desert ecosystem resilience and conservation, and improving our comprehension of soil microbial community assembly in desert ecosystems.
Validation of the Molecular International Prognostic Scoring System (IPSS-M) for myelodysplastic neoplasms (MDS) and comparison with the revised International Prognostic Scoring System (IPSS-R) in Chinese Population: A Multicenter Retrospective Study.
Authors: Hu Mengmeng , Zhou Ming , Shen Yingying , He Guangsheng , Huang Li , Zhou Shujuan , Fu Jiaping , Jiang Huifang , Chen Sai , Ye Xiujin , Zheng Zhiyin , Wu Liqiang , Wang Bo , Wu Gongqiang , Lin Shengyun , Ye Baodong , Yu Qinghong 
Published: March 2024

Abstract

Objectives The Revised international prognostic scoring system (IPSS-R) is now commonly being used clinically to guide the treatment of myelodysplastic neoplasms (MDS). Recently, the Molecular International Prognostic Scoring System (IPSS-M)was proposed. In this study, we have validated the potential predictive value of the comparative IPSS-M in Chinese MDS patients.
Design Retrospective multicenter observational study.
Setting and participants 113 MDS patients(April 2019 - June 2022) from 10 distinct centers in Jiangnan region of China, grouped by IPSS-R and IPSS-M was obtained and the scoring criteria were retrospectively analyzed to compare the prognostic assessment efficacy of the different prognostic assessment systems.
Main outcome measures The prognostic indicators of MDS patients are main outcome measures.
Results 72 (63.7%) patients were reclassified after regrouping from IPSS-R to IPSS-M, and 52 of them were transferred to a higher risk group, with a higher percentage of patients aged ≥ 60 years in the higher risk group. Survival analysis confirmed that overall survival(OS) was variable in the different risk strata, with shorter survival time in the higher risk group and lower OS in the older(≥ 60 years) than in the younger group; whereas in univariate and multifactorial analysis, age ≥ 60 years, percentage of bone marrow blasts, chromosomal classification of IPSS-R, TP53, RUNX1, DNMT3A, NRAS, CBL, GNAS, and FLT3_ITD gene mutation were associated with OS. Leukemia-free survival(LFS)analysis revealed that higher IPSS-R and IPSS-M risk stratification was linked with shorter LFS time. Receiver operating characteristic (ROC) curves were drawn according to OS displaying AUC = 0.629 for IPSS-R and AUC = 0.705 for IPSS-M; AUC = 0.635 for IPSS-M younger group and AUC = 0.691 for older group.
Conclusions Our study confirmed that the IPSS-M prognostic scoring system could be applicable to Chinese patients and that IPSS-M was significantly better than IPSS-R for the prognostic assessment of MDS patients. Moreover, IPSS-M appeared to have better predictive validity in older patients compared to younger patients.
Research on Applying Machine Learning Models to Predict and Assess Return on Assets (Roa)
Authors: Pham Vu Hong Son , Le Tung Duong 
Published: March 2024

Abstract
Return on Assets (ROA), a profitability measure, is crucial in corporate finance for assessing how efficiently a company uses assets to generate profit. Currently, the prediction of the ROA index at present is a tedious, manual process. It usually involves making educated guesses or waiting for the accurate data, which becomes available only after financial reports have been compiled. This paper introduces a machine learning model for predicting the ROA index. The model draws data from 78 companies listed on the Vietnam Stock Exchanges (HOSE and HNX) over the span of 2012 to 2022.The Random Forest (RF) model was put to the test using datasets from selected Vietnamese businesses in 2023. The results demonstrated a high level of precision, with an error rate of less than 1%, an R2 value of 0.9762, and a Root Mean Square Error (RMSE) of 0.5826. These findings indicate potential real-world uses in predicting and boosting business performance. In conclusion, the integration of machine learning in financial analysis and prediction represents substantial progress. It enhances both accuracy and efficiency and holds promise for future advancements in financial management practices. This study aims to encourage more research and development in this area, leading to more advanced and efficient financial management tools.
The Association Between County Ordinances Allowing Off-Road Vehicles on Public Roads and Crash Rates
Authors: Monson Christopher D. , Vakkalanka J. Priyanka , Denning Gerene M. , Stange Nicholas R. , Jennissen Charles A. 
Published: March 2024

Abstract

Background
Legislative bodies across the country have increasingly allowed off-road vehicles (ORVs) including all-terrain vehicles (ATVs) and utility task vehicles (UTVs) on public roads, an environment for which they are not designed. In 2009, Iowa gave individual counties the discretion to pass ordinances allowing ORVs on public roadways. The objective of this study was to evaluate the relationship between the passage of ORV ordinances and ORV crash rates, especially on public roads.
Methods
An Iowa ORV roadway ordinance database and an Iowa ORV crash database (2002-2018) for all 99 counties were compiled. Crashes for which county location could not be determined were excluded. Utilizing a zero-inflated Poisson model, correcting for background crash frequency trends and population, investigators compared the relative rates of crashes after ordinance passage to time points before ordinance implementation and to counties without such ordinances. Sub-analyses, including that focused on more recent years (2008-2018), were also performed.
Results
Forty-five county ORV roadway ordinances went into effect between 2011-2018 and 2,347 crashes (69%) met inclusion criteria. Adjusted for year, there was a 58% greater ORV crash rate in counties after passing an ORV roadway ordinance (incidence rate ratio (IRR) 1.58, 95% CI 1.32-1.90). Roadway crashes (n=834) increased 48% after ordinance passage (IRR 1.48, 95% CI 1.14-1.94). This roadway crash association remained statistically significant when analysis was limited to the years 2008-2018 (IRR 1.39, CI 1.06-1.83, n=544); to ATV crashes only (IRR 1.70, CI 1.20-2.40, n=683); and to ATV crashes excluding counties with UTV-only ordinances (IRR 1.74, CI 1.40-2.15, n=2,011).
Conclusions
ORV roadway and total crashes increased significantly after implementation of county ordinances allowing ORVs on public roadways and when compared to counties without such ordinances. It is likely that these increased crashes have resulted in more deaths and serious injuries. Results from this study may help inform policymakers as they consider legislation regarding ORV usage on public roads.
Dapagliflozin Reduces Systemic Inflammation in Patients with Type 2 Diabetes Without Known Heart Failure
Authors: Wang Dennis , Naumova Anna , Isquith Daniel , Sapp Jaime , Huynh Kim Anh , Tucker Isabella , Balu Niranjan , Voronyuk Anna , Chu Baocheng , Ordovas Karen , Maynard Charles , Tian Rong , Zhao Xue-Qiao , Kim Francis 
Published: March 2024

Abstract

Objective: Sodium glucose cotransporter 2 (SGLT2) inhibitors significantly improve cardiovascular outcomes in diabetic patients; however, the mechanism is unclear. We hypothesized that dapagliflozin improves cardiac outcomes via beneficial effects on systemic and cardiac inflammation and cardiac fibrosis.
Research and Design Methods: This randomized placebo-controlled clinical trial enrolled 62 adult patients (mean age 62, 17% female) with type 2 diabetes (T2D) without known heart failure. Subjects were randomized to 12 months of daily 10 mg dapagliflozin or placebo. For all patients, blood/plasma samples and cardiac magnetic resonance imaging (CMRI) were obtained at time of randomization and at the end of 12 months. Systemic inflammation was assessed by plasma IL-1B, TNFα, IL-6 and ketone levels and PBMC mitochondrial respiration, an emerging marker of sterile inflammation. Cardiac fibrosis was assessed by T1 mapping to calculate extracellular volume fraction (ECV); cardiac tissue inflammation was assessed by T2 mapping.
Results: Between the baseline and 12-month time point, plasma IL-1B was reduced (-1.8 pg/mL, P=0.003) while ketones were increased (0.26 mM, P=0.0001) in patients randomized to dapagliflozin. PBMC maximal oxygen consumption rate (OCR) decreased over the 12-month period in the placebo group but did not change in patients receiving dapagliflozin (-158.9 pmole/min/106cells, P=0.0497 vs -45.2 pmole/min/106cells, P=0.41), a finding consistent with an anti-inflammatory effect of SGLT2i. ECV and T2 relaxation time did not change in both study groups.
Conclusion: This study demonstrates that 12 months of dapagliflozin reduces IL-1B mediated systemic inflammation but affect cardiac fibrosis in T2D.
Clinical Trial.gov Registration NCT03782259
Why models underestimate West African tropical forest productivity
Authors: Zhang-Zheng Huanyuan , Deng Xiongjie , Stocker Benjamin , Ding Ruijie , Thomson Eleanor , Gutiérrez Jesús Aguirre , Adu-Bredu Stephen , Duah-Gyamfi Akwasi , Gvozdevaite Agne , Moore Sam , Menor Imma Oliveras , Prentice Iain , Malhi Yadvinder 
Published: March 2024

Abstract

Tropical forests dominate terrestrial photosynthesis, yet there are major contradictions in our understanding due to a lack of field studies, especially outside the tropical Americas. A recent field study indicated that West African forests have among the highest forests gross primary productivity (GPP) yet observed, contradicting models that rank them lower than Amazonian forests. Here, we explore possible reasons for this data-model mismatch. We found the in situ GPP measurements higher than multiple global GPP products at the studied sites in Ghana. The underestimation of GPP by models largely disappears when a standard photosynthesis model is informed by local field-measured values of (a) fractional absorbed photosynthetic radiation (fAPAR), and (b) photosynthetic traits. Satellites systematically underestimate fAPAR in the tropics due to cloud contamination issues. The study highlights the potential widespread underestimation of tropical forests GPP and carbon cycling and hints at the ways forward for model and input data improvement.
INTERGEN: a computational package applied to large-scale animal and plant genetic analysis
Authors: Junqueira Vinícius Silva , Campos Gabriel Soares , Cardoso Fernando Flores 
Published: March 2024

Abstract
Background
Genomic selection has become the standard genetic evaluation approach for estimating the genetic merit of animal and plant populations. That trend is mainly driven by the cost reduction for obtaining genomic data, such as single-nucleotide polymorphism (SNP) cost as novel genotyping and sequencing becomes more efficient and worldwide accessible. Although several software options are available for efficient estimation of non-genomic (i.e., traditional) genetic evaluations, the constant increase in genomic data availability requires new software that handles this data efficiently. The INTERGEN package has been constantly developing using Fortran programming language over the last two decades. The most recent of INTERGEN contains three different binaries (intergen, intergeniod, intergenacc). The initial developments in intergen were focused on Bayesian modeling with reaction norms, multiple-breed, and parentage uncertainty allowing for Gaussian and heavier-tailed alternatives such as Student’s t or Slash densities for variance component estimation. More recently, intergen has been constantly expanded to include the Best Linear Unbiased Prediction (BLUP), genomic module. The intergeniod and intergenacc are new binary and it intends to estimate genetic merit using iteration on data (IOD), and approximate accuracy, respectively.
Results
Several single-step GBLUP (ssGBLUP) single- and multi-trait models were implemented for running validations with benchmarking software (intergen and BLUPF90). The software produced reliable estimates for both genetic merit and accuracy in all IOD and approximate accuracy analyses. Rank correlation for the genetic merit for all bivariate ssGBLUP analyses in intergeniod was equal to intergen solutions. The approximate accuracies were compared with the exact accuracies estimated in BLUPF90. The rank correlation, regression slopes, and bias in intergenacc varied based on the amount of information (i.e., genotypes and phenotypes) for each animal across the different analyses.
Conclusions
The INTERGEN package can be applied to the genetic analysis of large-scale datasets using Bayesian and BLUP analysis. For traditional methods such as BLUP, intergen is a flexible tool. The package allows users to adopt IOD and approximate accuracy using intergeniod and intergenacc, respectively.
Distribution of EGFR fusions in 35,023 Chinese patients with solid tumors-the frequency, fusion partners and clinical outcome
Authors: Zhang Haiping , Wang Julei , Li Xiaoxiao , Zhang Dongfeng , Qi Yingxue , Zhang Qin , Luo Ningning , Wang Xiaoou , Wang Tuo 
Published: March 2024

Abstract

Background
Epidermal growth factor receptor (EGFR) fusions are rare but potentially actionable oncogenic drivers across multiple solid tumors. However, the distribution and molecular characteristics of EGFR fusions in Chinese patients with solid malignancies have not been explored.
Methods
Panel-based next-generation sequencing (NGS) data of 35,023 patients with various types of solid tumors were collected and analyzed from the Simcere Diagnostics (Nanjing, China) database. A 9563-patient cohort was derived from The Cancer Genome Atlas (TCGA) to explore the relationship between EGFR fusion status and overall survival (OS).
Results
In this study, prevalence of functional EGFR fusions was 0.303% (106/35016) in total across solid tumors, which occur more commonly in gastroesophageal junction cancer (1.613%), followed by medatloblastoma (1.515%) and glioma (1.370%). Analysis showed a prevalence for fusion partners in different tumor types. The top 3 co-mutant genes with EGFR fusion were TP53 (mutation frequency, MF: 65%), BRCA2 (MF: 43%), and ALK (MF: 41%). Furthermore, patients in the EGFR fusion group had a significantly shorter OS than those in the non-EGFR fusion group (p < 0.0001) in the TCGA cohort,, suggesting that EGFR fusion might be a high-risk factor for poor prognosis.
Conclusions
Our study is the first retrospective analysis of EGFR fusions in a large-scale solid tumor population, which may provide a reference for future EGFR-TKI clinical trials with EGFR fusions.
Seismic activity characteristics of the Chinese continent based on a ‘hybrid’ probability forecasting model
Authors: Ma Yong , Bi Jinmeng , Dong Demiao 
Published: March 2024

Abstract

In the research on Operational Earthquake Forecasting (OEF), a crucial aspect involves constructing a predictive model capable of assessing its efficacy while aligning with the regional seismic activity characteristics. This study delineates Chinese continent, characterized by complex seismotectonic, into six distinct zones: Northeast, North China, South China, North-South Zone, Xinjiang, and Xizang. Three earthquake probability forecasting models-namely, the relative intensity (RI) model, the moment ratio (MR) model, and the simple smoothing (Triple-S) model are employed. Utilizing seismic catalog data from the China Earthquake Networks Center dating back to 1970, with a ‘anomaly learning period’ spanning 10 years and a step length of 1 year, a retrospective sliding forecasting analysis is conducted for earthquakes of magnitude Ms5.0 or greater over varying intervals, such as 3 years and 5 years. The efficacy of the forecasting models is assessed through the Molchan chart method and T-test method. Model parameters are fine-tuned, determining the optimal computational parameters for the three forecasting models. A composite probability forecasting model, adaptable across different time scales and tailored to the seismic activity characteristics of Chinese continent, is developed. An analysis of seismic activity over the past decade provides insights into the current landscape. This analysis highlights that the high-risk areas identified through the composite model closely align with previous findings and correlate well with actual earthquake occurrences in Chinese continent in 2023.