bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forest Biomass Feedstock Availability and Economic Contribution of Biopower Facilities in the Lake States Region
Authors: Pokharel Raju , Poudel Jagdish , Dahal Ram , GC Shivan 
Published: July 2023

Abstract
The Lake States (MI, MN, WI) region holds 54.8 million acres of forest and offers the potential to meet the increasing demand for sustainable energy through forest biomass. The objective of this study is to estimate the annual availability of biomass, after considering the sustainability threshold, for a wood price and its economic impact in the Lake States region. This study identified twenty-seven active power facilities using biomass in addition to oil, gas, and coal, with a total capacity of 3.85 million MWh per year. They consumed 2.80 million dry tons of biomass in 2019. At the current delivered wood price, an additional 9.72 million dry tons of biomass is economically available, which, if used, would generate an additional 11,112 jobs (1,583 direct and 9,529 indirect and induced), $1.54 billion in value added ($803 million direct and $733 million indirect and induced), and $2.71 billion ($1.46 billion direct and $1.25 billion indirect and induced) in total output. Operating at least one-third of the existing capacity for biomass-based power generation would add 1,969 jobs, $293 million in value added, and $413 million in total output. The expansion of the biomass biopower industry has the potential to significantly increase economic impact, especially in rural areas.
Study Implications: Mapping procurement zones for resource allocation using delivered wood prices for biomass helps identify the economic availability of biomass for electric power production in the Lake States. Our results establish the market extent for biomass and identify potential areas where investment in biopower production or capacity upgrade is feasible. This study also provides insight into the economic impacts of additional biomass utilization to produce power. Most of these impacts would come about in rural areas, improving economic growth in these communities. A combined analysis estimating the potential supply and demand and the economic effects of biopower industry expansion provides valuable insight into decision-making for state forest action plans and private sector forest management plans. Furthermore, the findings from this study will help inform effective regional policy and investment decisions on biomass power industries. The method used can also be tailored to a specific facility to estimate its procurement zone, feedstock availability, and economic impacts.
The benefit of complete resection of contrast enhancing tumor in glioblastoma patients: A population-based study
Authors: Mendoza Mireles Eduardo Erasmo , Skaga Erlend , Server Andres , Leske Henning , Brandal Petter , Helseth Eirik , Rønning Pål A , Vik-Mo Einar O 
Published: July 2023

Abstract

Background
New treatment modalities have not been widely adopted for patients with glioblastoma (GBM) after the addition of temozolomide to radiotherapy. We hypothesize that increased extent of resection (EOR) has resulted in improved survival for surgically treated patients with glioblastoma at the population level.

Methods
Retrospective analysis of adult patients operated for glioblastoma in the population of South–Eastern Norway. Patients were stratified into Pre-temozolomide- (2003–2005), temozolomide- (2006–2012), and resection-focused period (2013–2019) and evaluated according to age and EOR.

Results
The study included 1657 adult patients operated on for supratentorial glioblastoma. The incidence of histologically confirmed glioblastoma increased from 3.7 in 2003 to 5.3 per 100 000 in 2019. The median survival was 11.4 months. Complete resection of contrast-enhancing tumor (CRCET) was achieved in 386 patients, and this fraction increased from 13% to 32% across the periods. Significant improvement in median survival was found between the first 2 periods and the last (10.5 and 10.6 vs. 12.3 months; P &lt; .01), with a significant increase in 3- and 5-year survival probability to 12% and 6% (P &lt; .01). Patients with CRCET survived longer than patients with non-CRCET (16.1 vs. 10.8 months; P &lt; .001). The median survival doubled in patients ≥70 years and (12.1 months). Survival was similar between the time periods in patients where CRCET was achieved.

Conclusions
We demonstrate an improved survival of GBM patients at the population level associated with an increased fraction of patients with CRCET. The data support the importance of CRCET to improve glioblastoma patient outcomes.
Microalbuminuria in Perinatally HIV-Infected Children and Adolescents in the United States
Authors: Al Hammoud Roukaya , Kalaskar Anupama , Rodriguez Gilhen , Del Bianco Gabriela , Bell Cynthia , Murphy James R , Heresi Gloria P 
Published: July 2023

Abstract

Background
The kidney is a common target for human immunodeficiency virus (HIV), making renal disease a common noninfectious complication of HIV. Microalbuminuria is an important marker that can detect early renal damage. Timely detection of microalbuminuria is important to initiate renal management and stop the progression of renal dysfunction in people with HIV. Limited data are available about renal abnormalities in people with perinatal HIV infection. The objective of this study was to determine the prevalence of microalbuminuria in a cohort of perinatally HIV-infected children and young adults receiving combination antiretroviral therapy and investigate correlations between microalbuminuria and clinical and laboratory findings.

Methods
This was a retrospective study of 71 patients with HIV followed in an urban pediatric HIV clinic in Houston, Texas, between October 2007 and August 2016. Demographic, clinical, and laboratory data were compared between subjects with persistent microalbuminuria (PM) and those without. PM is defined as a microalbumin-to-creatinine ratio ≥30 mg/g on at least 2 occasions separated by at least 1 month.

Results
Sixteen of 71 patients (23%) met the definition of PM. In univariate analysis, patients with PM had significantly higher CD8+ T-cell activation and lower CD4+ T-cell nadir. Multivariate analysis demonstrated increased microalbuminuria to be independently associated with older age and CD8+ T-cell activation measured as CD8+HLA-DR+ T-cell percentage.

Conclusions
Older age and increased activation of CD8+HLA-DR+ on T cells correlate with presence of microalbuminuria in this cohort of HIV-infected patients.
Long-term Safety and Tolerability of Omadacycline for the Treatment of Mycobacterium abscessus Infections
Authors: Mingora Christina M , Bullington Wendy , Faasuamalie Paige E , Levin Adrah , Porter Gabriella , Stadnik Ryan , Varley Cara D , Addrizzo-Harris Doreen , Daley Charles L , Olivier Kenneth N , Winthrop Kevin L , Dorman Susan E , Flume Patrick A 
Published: July 2023

Abstract

Background
Mycobacterium abscessus is a virulent human pathogen. Treatment is complex and often poorly tolerated with suboptimal rates of eradication, highlighting the need for improved therapeutics. This study reports clinical experience with omadacycline for treatment of M abscessus infections at five large nontuberculous mycobacterial (NTM) disease clinics across the United States to better understand long-term safety and tolerability.

Methods
We conducted a multicenter retrospective chart review of adults with M abscessus infections. All patients treated with omadacycline as part of a multidrug therapeutic regimen through December 2021 were included. Clinical data from time of omadacycline initiation and up to 12 months of follow-up were collected. Descriptive statistics were performed.

Results
Analysis included 117 patients. Among patients with M abscessus isolate subspeciation, 58 of 71 (81.7%) were M abscessus spp abscessus. In isolates with reported drug susceptibility testing, 15 of 70 (21.4%) had confirmed susceptibility to macrolides. The most common site of infection was lungs. Median duration omadacycline treatment was 8 months (range, 0.25–33 months; interquartile range, 4–15 months). Omadacycline was discontinued in 60 patients (51.3%); 20 completed planned treatment course, 23 experienced intolerance or adverse event leading to drug cessation, and 17 stopped due to cost, death (unrelated to NTM infection or therapy), or another reason. In those with pulmonary disease, 44 of 95 (46%) had 1 or more negative cultures at time of final microbiological assessment, with 17 of 95 (18%) achieving culture conversion.

Conclusions
This study reports data supporting long-term safety and tolerability of omadacycline along with signal of effectiveness in treatment of M abscessus infections.
Identification of Immune Subtypes and Candidate mRNA Vaccine Antigens in Small Cell Lung Cancer
Authors: Wei Yuanfeng , Zheng Lingnan , Yang Xi , Luo Yong , Yi Cheng , Gou Hongfeng 
Published: July 2023

Abstract

Background
Immune checkpoint inhibitors (ICIs) have demonstrated promising outcomes in small cell lung cancer (SCLC), but not all patients benefit from it. Thus, developing precise treatments for SCLC is a particularly urgent need. In our study, we constructed a novel phenotype for SCLC based on immune signatures.

Methods
We clustered patients with SCLC hierarchically in 3 publicly available datasets according to the immune signatures. ESTIMATE and CIBERSORT algorithm were used to evaluate the components of the tumor microenvironment. Moreover, we identified potential mRNA vaccine antigens for patients with SCLC, and qRT-PCR were performed to detect the gene expression.

Results
We identified 2 SCLC subtypes and named Immunity High (Immunity_H) and Immunity Low (Immunity_L). Meanwhile, we obtained generally consistent results by analyzing different datasets, suggesting that this classification was reliable. Immunity_H contained the higher number of immune cells and a better prognosis compared to Immunity_L. Gene-set enrichment analysis revealed that several immune-related pathways such as cytokine-cytokine receptor interaction, programmed cell death-Ligand 1 expression and programmed cell death-1 checkpoint pathway in cancer were hyperactivated in the Immunity_H. However, most of the pathways enriched in the Immunity_L were not associated with immunity. Furthermore, we identified 5 potential mRNA vaccine antigens of SCLC (NEK2, NOL4, RALYL, SH3GL2, and ZIC2), and they were expressed higher in Immunity_L, it indicated that Immunity_L maybe more suitable for tumor vaccine development.

Conclusions
SCLC can be divided into Immunity_H and Immunity_L subtypes. Immunity_H may be more suitable for treatment with ICIs. NEK2, NOL4, RALYL, SH3GL2, and ZIC2 may be act as potential antigens for SCLC.
Application of new breeding techniques in fruit trees
Authors: Campa Manuela , Miranda Simón , Licciardello Concetta , Lashbrooke Justin Graham , Dalla Costa Lorenza , Guan Qingmei , Spök Armin , Malnoy Mickael 
Published: July 2023

Abstract
Climate change and rapid adaption of invasive pathogens pose a constant pressure on the fruit industry to develop improved varieties. Aiming to accelerate the development of better-adapted cultivars, new breeding techniques have emerged as a promising alternative to meet the demand of a growing global population. Accelerated breeding, cisgenesis, and CRISPR/Cas genome editing hold significant potential for crop trait improvement and have proven to be useful in several plant species. This review focuses on the successful application of these technologies in fruit trees to confer pathogen resistance and tolerance to abiotic stress and improve quality traits. In addition, we review the optimization and diversification of CRISPR/Cas genome editing tools applied to fruit trees, such as multiplexing, CRISPR/Cas-mediated base editing and site-specific recombination systems. Advances in protoplast regeneration and delivery techniques, including the use of nanoparticles and viral-derived replicons, are described for the obtention of exogenous DNA-free fruit tree species. The regulatory landscape and broader social acceptability for cisgenesis and CRISPR/Cas genome editing are also discussed. Altogether, this review provides an overview of the versatility of applications for fruit crop improvement, as well as current challenges that deserve attention for further optimization and potential implementation of new breeding techniques.
Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus
Authors: Zhang Jin , Wang Xiaqin , Wang Hsin-Tzu , Qiao Zhenzhen , Yao Tao , Xie Meng , Urbanowicz Breeanna R , Zeng Wei , Jawdy Sara S , Gunter Lee E , Yang Xiaohan , Czarnecki Olaf , Regan Sharon , Seguin Armand , Rottmann William , Winkeler Kimberly A , Sykes Robert , Lipzen Anna , Daum Chris , Barry Kerrie , Lu Meng-Zhu , Tuskan Gerald A , Muchero Wellington , Chen Jin-Gui 
Published: July 2023

Abstract
Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation of xylan in secondary cell walls impedes the conversion of biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved in the acetylation of xylan but the regulatory mechanism of RWAs is not fully understood. In this study, we demonstrate that overexpression of a Populus trichocarpa PtRWA-C gene increases the level of xylan acetylation and increases the lignin content and S/G ratio, ultimately yielding poplar woody biomass with reduced saccharification efficiency. Furthermore, through gene coexpression network and expression quantitative trait loci (eQTL) analysis, we found that PtRWA-C was regulated not only by the secondary cell wall hierarchical regulatory network but also by an AP2 family transcription factor HARDY (HRD). Specifically, HRD activates PtRWA-C expression by directly binding to the PtRWA-C promoter, which is also the cis-eQTL for PtRWA-C. Taken together, our findings provide insights into the functional roles of PtRWA-C in xylan acetylation and consequently saccharification and shed light on synthetic biology approaches to manipulate this gene and alter cell wall properties. These findings have substantial implications for genetic engineering of woody species, which could be used as a sustainable source of biofuels, valuable biochemicals, and biomaterials.
Online data resource for exploring transposon insertion polymorphisms in public soybean germplasm accessions
Authors: Yin Zhiyuan , Yang Qingjie , Shen Danyu , Liu Jinding , Huang Wen , Dou Daolong 
Published: July 2023

Abstract
Soybean (Glycine max L. Merrill) is one of the most important economical crops. A large number of whole-genome resequencing datasets have been generated and are increasingly expanded for exploring genetic diversity and mining important quantitative trait loci. Most genome-wide association studies have focused on single-nucleotide polymorphisms, short insertions, and deletions. Nevertheless, structure variants mainly caused by transposon element mobilization are not fully considered. To fill this gap, we uniformly processed the publicly available whole-genome resequencing data from 5,521 soybean germplasm accessions and built an online soybean transposon insertion polymorphisms database named Soybean Transposon Insertion Polymorphisms Database (SoyTIPdb) (https://biotec.njau.edu.cn/soytipdb). The collected germplasm accessions derived from more than 45 countries and 160 regions representing the most comprehensive genetic diversity of soybean. SoyTIPdb implements easy-to-use query, analysis, and browse functions to help understand and find meaningful structural variations from TE insertions. In conclusion, SoyTIPdb is a valuable data resource and will help soybean breeders/researchers take advantage of the whole-genome sequencing datasets available in the public depositories.
Identification of blood metabolites linked to the risk of intervertebral disc diseases: a comprehensive Mendelian randomization study
Authors: Ji Linsong , Wang Yanping , Lu Tingsheng , Yang Jianwen , Luo Chunshan , Qiu Bing 
Published: July 2023

Abstract

Background
Intervertebral disc degeneration (IVDD) has affected millions of people worldwide and dramatically affects human beings’ quality of life. Observational studies hypothesize that metabolites play key roles as markers and effectors of IVDD, but their causality has not yet been illustrated.

Methods
We conducted comprehensive Mendelian randomization (MR) to determine the causal relationship between 249 plasma metabolites and IVDD. Inverse-variance weighting was used as the primary estimate, whereas MR-Egger and weighed median were used to detect robustness. A series of sensitivity analyses including Cochran Q test, leave one out, and MR-Egger intercept analysis were also conducted.

Results
In total, we found 13 blood metabolites significantly associated with IVDD, including phospholipids in very large high-density lipoprotein (HDL), free cholesterol to total lipids ratio in very large HDL, average diameter for HDL particles, cholesteryl esters to total lipids ratio in large HDL, free cholesterol to total lipids ratio in medium HDL, creatinine, free cholesterol to total lipids ratio in large HDL, phospholipids to total lipids ratio in very large HDL, cholesterol to total lipids ratio in very large HDL, cholesteryl esters to total lipids ratio in large HDL, phospholipids in large HDL, total lipids in very large HDL, and total lipids in large HDL. No pleiotropy was detected. Heterogeneity existed in several estimates and random-effect inverse-variance weighting was applied.

Conclusions
Our study highlighted the causal association of blood metabolites with the risk of IVDD. Our results provide new insights into possible treatment protocols controlling the concentration of specific blood metabolites in IVDD patients.
Key messages What is already known on this topic Low back pain is the most common symptom for patients with intervertebral disc degeneration (IVDD) and influences the quality of life of large populations. Observational studies have indicated the association between metabolites and IVDD. However, causality has not been determined yet. What this study adds We conducted a comprehensive Mendelian randomization study to reveal the causal effect from 249 blood metabolites on low back pain. A total of 13 metabolites were found to causally affect the risk of IVDD, among which 11 were negatively associated and 2 were positively asscociated. How this study might affect research, practice, or policy These 13 significant metabolites could serve as biomarkers for IVDD and our results provide new insights into possible treatment protocols for IVDD patients.
Development of a method of evaluating PuO2 particle diameters using an alpha-particle imaging detector
Authors: Morishita Yuki , Sagawa Naoki , Takada Chie , Momose Takumaro , Takasaki Koji 
Published: July 2023

Abstract
It is very important to evaluate the diameters (activity median aerodynamic diameter) of plutonium dioxide (PuO2) particles for internal exposure dose evaluation. In this study, a method of evaluating PuO2 particle diameters using an alpha-particle imaging detector was developed. PuO2 particles with different diameters were modeled by Monte Carlo simulation, and the change in the shape of the energy spectrum for each particle diameter was evaluated. Two different patterns were modeled, namely, the case of 239PuO2 and the case of PuO2 (including isotopic composition of Pu). Multiple regression analysis was performed to determine the PuO2 particle diameter from the obtained parameters. The simulated diameters and the diameters obtained with the regression model were in good agreement. The advantage of using the alpha-particle imaging detector is to measure the alpha energy spectrum for individual particle, and this allows accurate measurement of particle diameter distribution.
The study of virtual source position with the geometric convergent ratio errors prevention management method of spot scanning beam in carbon ion therapy
Authors: Zhang Wen-Hua , Luo Bing-Zhi , Ye Yan-Cheng , Wu Jia-Ming 
Published: July 2023

Abstract
Introduction: We developed a technique including preventing errors management method capable of dealing with the virtual source position delivered by different carbon ion energies from the pattern of spot scanning beam in this study. Materials and Methods: A homemade large-format complementary metal-oxide-semiconductor (CMOS) sensor and Gaf Chromic EBT3 films were used for the virtual source position measurement. The Gaf films were embedded in a self-designed rectangular plastic frame to tighten the films and set up on a treatment couch for irradiation in the air with the film perpendicular to the carbon ion beam at the nominal source-axis-distance (SAD) as well as upstream and downstream from the SAD. The horizontal carbon ion beam with five energies at a machine opening field size was carried out in this study. The virtual source position was determined mainly with a linear regression by back projecting the full width half maximum (FWHM) to zero at a distance upstream from the various source-film-distance and double checks additionally with a geometric convergent method to avoid any mistakes caused by manual measurement on FWHM. Results: The virtual source position for higher carbon ion energy has an obvious longer distance from the SAD since the more carbon ion beam energy, the less spreading affected by the horizontal and vertical magnetism, therefore, the distance of virtual source positions is decreased from SAD with high to low energy. Conclusion: The method for investigating the virtual source position in the carbon ion beam in this study can also be used for electrons and the proton. We have developed a technique capable of dealing with the virtual source position with a geometric convergent method to avoid any mistakes in spot scanning carbon ion beam.
IL33-mediated NPM1 promotes fibroblast-to-myofibroblast transition via ERK/AP-1 signaling in silica-induced pulmonary fibrosis
Authors: Wang Yue , Cheng Demin , Li Ziwei , Sun Wenqing , Zhou Siyun , Peng Lan , Xiong Haojie , Jia Xinying , Li Wei , Han Lei , Liu Yi , Ni Chunhui 
Published: July 2023

Abstract
Silicosis is a global occupational pulmonary disease due to the accumulation of silica dust in the lung. Lacking effective clinical drugs makes the treatment of this disease quite challenging in clinics largely because the pathogenic mechanisms remain obscure. Interleukin 33 (IL33), a pleiotropic cytokine, could promote wound healing and tissue repair via the receptor ST2. However, the mechanisms governing the involvement of IL33 in silicosis progression remain to be further explored. Here, we demonstrated that the IL33 levels in the lung sections were significantly overexpressed after bleomycin and silica treatment. Chromatin immunoprecipitation assay, knockdown, and reverse experiments were performed in lung fibroblasts to prove gene interaction following exogenous IL33 treatment or cocultured with silica-treated lung epithelial cells. Mechanistically, we illustrated that silica-stimulated lung epithelial cells secreted IL33 and further promoted the activation, proliferation, and migration of pulmonary fibroblasts by activating the ERK/AP-1/NPM1 signaling pathway in vitro. And more, treatment with NPM1 siRNA-loaded liposomes markedly protected mice from silica-induced pulmonary fibrosis in vivo. In conclusion, the involvement of NPM1 in the progression of silicosis is regulated by the IL33/ERK/AP-1 signaling axis, which is the potential therapeutic target candidate in developing novel antifibrotic strategies for pulmonary fibrosis.