bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing
Authors: Hu Junjie , Zhang Lele , Xia Haoran , Yan Yilv , Zhu Xinsheng , Sun Fenghuan , Sun Liangdong , Li Shuangyi , Li Dianke , Wang Jin , Han Ya , Zhang Jing , Bian Dongliang , Yu Huansha , Chen Yan , Fan Pengyu , Ma Qiang , Jiang Gening , Wang Chenfei , Zhang Peng 
Published: March 2023

Abstract
Background
Immunotherapy has revolutionized cancer treatment, but most patients are refractory to immunotherapy or acquire resistance, with the underlying mechanisms remaining to be explored.

Methods
We characterized the transcriptomes of ~92,000 single cells from 3 pre-treatment and 12 post-treatment patients with non-small cell lung cancer (NSCLC) who received neoadjuvant PD-1 blockade combined with chemotherapy. The 12 post-treatment samples were categorized into two groups based on pathologic response: major pathologic response (MPR; n = 4) and non-MPR (NMPR; n = 8).

Results
Distinct therapy-induced cancer cell transcriptomes were associated with clinical response. Cancer cells from MPR patients exhibited a signature of activated antigen presentation via major histocompatibility complex class II (MHC-II). Further, the transcriptional signatures of FCRL4+FCRL5+ memory B cells and CD16+CX3CR1+ monocytes were enriched in MPR patients and are predictors of immunotherapy response. Cancer cells from NMPR patients exhibited overexpression of estrogen metabolism enzymes and elevated serum estradiol. In all patients, therapy promoted expansion and activation of cytotoxic T cells and CD16+ NK cells, reduction of immunosuppressive Tregs, and activation of memory CD8+T cells into an effector phenotype. Tissue-resident macrophages were expanded after therapy, and tumor-associated macrophages (TAMs) were remodeled into a neutral instead of an anti-tumor phenotype. We revealed the heterogeneity of neutrophils during immunotherapy and identified an aged CCL3+ neutrophil subset was decreased in MPR patients. The aged CCL3+ neutrophils were predicted to interact with SPP1+ TAMs through a positive feedback loop to contribute to a poor therapy response.

Conclusions
Neoadjuvant PD-1 blockade combined with chemotherapy led to distinct NSCLC tumor microenvironment transcriptomes that correlated with therapy response. Although limited by a small patient sample size subjected to combination therapy, this study provides novel biomarkers to predict therapy response and suggests potential strategies to overcome immunotherapy resistance.
Epigenome-wide association study in Chinese monozygotic twins identifies DNA methylation loci associated with blood pressure
Authors: Wang Weijing , Yao Jie , Li Weilong , Wu Yili , Duan Haiping , Xu Chunsheng , Tian Xiaocao , Li Shuxia , Tan Qihua , Zhang Dongfeng 
Published: March 2023

AbstractBackgroundHypertension is a crucial risk factor for developing cardiovascular disease and reducing life expectancy. We aimed to detect DNA methylation (DNAm) variants potentially related to systolic blood pressure (SBP) and diastolic blood pressure (DBP) by conducting epigenome-wide association studies in 60 and 59 Chinese monozygotic twin pairs, respectively.MethodsGenome-wide DNA methylation profiling in whole blood of twins was performed using Reduced Representation Bisulfite Sequencing, yielding 551,447 raw CpGs. Association between DNAm of single CpG and blood pressure was tested by applying generalized estimation equation. Differentially methylated regions (DMRs) were identified bycomb-Papproach. Inference about Causation through Examination of Familial Confounding was utilized to perform the causal inference. Ontology enrichment analysis was performed using Genomic Regions Enrichment of Annotations Tool. Candidate CpGs were quantified using Sequenom MassARRAY platform in a community population. Weighted gene co-expression network analysis (WGCNA) was conducted using gene expression data.ResultsThe median age of twins was 52 years (95% range 40, 66). For SBP, 31 top CpGs (p < 1 × 10–4) and 8 DMRs were identified, with several DMRs withinNFATC1,CADM2,IRX1,COL5A1, andLRAT. For DBP, 43 top CpGs (p < 1 × 10–4) and 12 DMRs were identified, with several DMRs withinWNT3A,CNOT10, andDAB2IP. Important pathways, such as Notch signaling pathway, p53 pathway by glucose deprivation, and Wnt signaling pathway, were significantly enriched for SBP and DBP. Causal inference analysis suggested that DNAm at top CpGs withinNDE1,MYH11,SRRM1P2, andSMPD4influenced SBP, while SBP influenced DNAm at CpGs withinTNK2. DNAm at top CpGs withinWNT3Ainfluenced DBP, while DBP influenced DNAm at CpGs withinGNA14. Three CpGs mapped toWNT3Aand one CpG mapped toCOL5A1were validated in a community population, with a hypermethylated and hypomethylated direction in hypertension cases, respectively. Gene expression analysis by WGCNA further identified some common genes and enrichment terms.ConclusionWe detect many DNAm variants that may be associated with blood pressure in whole blood, particularly the loci withinWNT3AandCOL5A1. Our findings provide new clues to the epigenetic modification underlying hypertension pathogenesis.
Impact of a strategy based on unique blood culture sampling on contamination rate and detection of bloodstream infections in critically ill patients
Authors: Mahieu Rafael , Lemarié Carole , Douillet Delphine , Mercat Alain , Cormier Hélène , Eveillard Matthieu , Dubée Vincent , Riou Jérémie , Kouatchet Achille 
Published: March 2023

Abstract
Background
Unique blood culture (UBC) has been proposed to limit the number of venipuncture and to decrease the risk of BC contaminations (BCC) without affecting their yield. We hypothesized that a multi-faceted program based on UBC in the ICU may reduce the rate of contaminants with a similar performance for bloodstream infections (BSI) identification.

Methods
In a before and after design, we compared the proportion of BSI and BCC. A first 3-year period with multi-sampling (MS) strategy followed by a 4-month washout period, where staff received education and training for using UBC, and a 32-month period, where UBC was routinely used, while education and feedback were maintained. During the UBC period, a large volume of blood (40 mL) was sampled through a unique venipuncture with additional BC collections discouraged for 48 h.

Results
Of the 4,491 patients included (35% female patients, mean age 62 years) 17,466 BC were collected. The mean volume of blood per bottle collected increased from 2.8 ± 1.8 mL to 8.2 ± 3.9 mL between the MS and UBC periods, P < 0.01. A 59.6% reduction (95% CI 56.7–62.3; P < 0.001) of BC bottles collected per week was observed between the MS and UBC periods. The rate of BCC per patient decreased between the two periods from 11.2% to 3.8% (73.4% reduction; P < 0.001) for the MS and UBC periods, P < 0.001. Meanwhile, the rate of BSI per patient remained stable at 13.2% and 13.2% for the MS and UBC periods, P = 0.98.

Conclusions
In ICU patients, a strategy based on UBC reduces the contamination rate of cultures without affecting their yield.

Graphical Abstract
A congestion control scheme based on path recovery for smart grid communication
Authors: Ji Yanpeng , Zeng Siming , Zhao Jianli , Liu Liangshuai , Feng Haiyan , Shen Xingdi , Liu Deliang 
Published: March 2023

AbstractIn order to solve the problem that the original path forwarding traffic caused by congestion that cannot be recovered in time in Smart Grid Communication, a congestion control scheme RFCC (Router Forwarding Congestion Control) based on path recovery is proposed, which not only supports the receiving end combined with router nodes to relieve congestion, it can also solve the problem of low transmission performance caused by not being able to restore the original path in time after the traffic is transferred. Active queue management technology is used to detect congestion and notify downflow nodes (users and routers) in time, which trigger downflow users to adjust the request sending window and intermediate routers to transfer packets. In addition, the original path traffic is restored in time through the path recovery policy. Firstly, the path traffic is recovered according to the congestion mark carried by the subsequent content packets. Secondly, the transmission frequency of the probe packets is calculated according to the information such as the packet queue length of routers and the available bandwidth of the congested path, and the probe packets are periodically sent to the congested path, and the traffic is sent to the congested path in time. The alternate path is transferred back to the original path. This paper implements the scheme in NS-3, and extensive experiments show that the proposed scheme outperforms the comparison schemes, which not only higher and more stable throughput can be obtained, but also shorter and more stable transmission delay can be obtained. In addition, the optimal path transmission volume and link utilization are improved.
Novel advances in high-order numerical algorithm for evaluation of the shallow water wave equations
Authors: Poochinapan Kanyuta , Wongsaijai Ben 
Published: March 2023

AbstractIn this paper, we propose a high-order nonlinear algorithm based on a finite difference method modification to the regularized long wave equation and the Benjamin–Bona–Mahony–Burgers equation subject to the homogeneous boundary. The consequence system of nonlinear equations typically trades with high computation burden. This dilemma can be overcome by establishing a fast numerical algorithm procedure without a reduction of numerical accuracy. The proposed algorithm forms a linear system with constant coefficient matrix at each time step and produces numerical solutions, which remarkably gains many computational advantages. In terms of analysis, a priori estimation for the numerical solution is derived to obtain the convergence and stability analysis. Additionally, the algorithm is globally mass preserving to avoid nonphysical behavior. Two benchmarks, including a single solitary wave to both equations, are given to validate the applicability and accuracy of the proposed method. Numerical results are obtained and compared to other approaches available in the literature. From the comparisons it is clear that the proposed approach produces accurate and precise results at low computational cost. Besides, the proposed scheme is applied to study the effect of the viscous term on a single solitary wave. It is shown that the viscous term results in the amplitude and width of the initial condition but not in its velocities in the case of a single solitary wave. As a consequence, theoretical and numerical findings provide a new area to investigate and expand the high-order algorithm for the family of wave equations.
Podcasts’ effects on the EFL classroom: a socially relevant intervention
Authors: Chaves-Yuste Beatriz , de-la Peña Cristina 
Published: March 2023

AbstractICT tools have gained particular importance in the English as a foreign language classroom in order to promote students’ interaction, exchange of opinions, negotiation of meaning, or digital competence. Technological development and the impact of multimedia and virtual spaces on students’ lives make educational institutions and teachers explore new tools and strategies to learn the target language. Podcasts present content available on the Internet and can become an influential teaching strategy that may improve the teaching–learning process of EFL. This study aims to investigate the effect of audio podcasts, which deal with social inequality issues, on secondary education students’ EFL linguistic competence. A sample of seventy-eight students was randomly distributed into a control and an experimental group during a term in a high school in Madrid (Spain). As instruments for data collection, the grades obtained in the different skills in the pre and post-tests and the different task performance scores were analysed in both groups. The methodological framework is defined as a quasi-experimental design that provides quantitative data. The results confirm the hypothesis that the creation and use of podcasts are beneficial for improving EFL linguistic competence, especially speaking and listening skills. Practical implications aimed at organising English classes to improve EFL proficiency are discussed.Graphical Abstract
Statistical analysis for EUV dynamic spectra and their impact on the ionosphere during solar flares
Authors: Nishimoto Shohei , Watanabe Kyoko , Jin Hidekatsu , Kawai Toshiki , Imada Shinsuke , Kawate Tomoko , Otsuka Yuichi , Shinbori Atsuki , Tsugawa Takuya , Nishioka Michi 
Published: March 2023

AbstractThe X-rays and extreme ultraviolet (EUV) emitted during solar flares can rapidly change the physical composition of Earth’s ionosphere, causing space weather phenomena. It is important to develop an accurate understanding of solar flare emission spectra to understand how it affects the ionosphere. We reproduced the entire solar flare emission spectrum using an empirical model and physics-based model, and input it into the Earth’s atmospheric model, GAIA to calculate the total electron content (TEC) enhancement due to solar flare emission. We compared the statistics of nine solar flare events and calculated the TEC enhancements with the corresponding observed data. The model used in this study was able to estimate the TEC enhancement due to solar flare emission with a correlation coefficient greater than 0.9. The results of this study indicate that the TEC enhancement due to solar flare emission is determined by soft X-ray and EUV emission with wavelengths shorter than 35 nm. The TEC enhancement is found to be largely due to the change in the soft X-ray emission and EUV line emissions with wavelengths, such as Fe XVII 10.08 nm, Fe XIX 10.85 nm and He II 30.38 nm.
Graphical Abstract
Plasma bioactive adrenomedullin on intensive care unit admission is associated with acute respiratory distress syndrome: an observational study
Authors: Johnsson Patrik , Fredriksson Andrea , Tung Christer , Friberg Hans , Frigyesi Attila 
Published: March 2023

Abstract
Background
Bioactive adrenomedullin (bio-ADM) is a vasoactive peptide with a key role in reducing vascular hyperpermeability and improving endothelial stability during infection, but it also has vasodilatory properties. Bioactive ADM has not been studied in conjunction with acute respiratory distress syndrome (ARDS), but it has recently been shown to correlate with outcomes after severe COVID-19. Therefore, this study investigated the association between circulating bio-ADM on intensive care unit (ICU) admission and ARDS. The secondary aim was the association between bio-ADM and ARDS mortality.

Methods
We analysed bio-ADM levels and assessed the presence of ARDS in adult patients admitted to two general intensive care units in southern Sweden. Medical records were manually screened for the ARDS Berlin criteria. The association between bio-ADM levels and ARDS and mortality in ARDS patients was analysed using logistic regression and receiver-operating characteristics analysis. The primary outcome was an ARDS diagnosis within 72 h of ICU admission, and the secondary outcome was 30-day mortality.

Results
Out of 1224 admissions, 11% (n = 132) developed ARDS within 72 h. We found that elevated admission bio-ADM level was associated with ARDS independently of sepsis status and of organ dysfunction as measured by the Sequential organ failure assessment (SOFA) score. Both lower levels (< 38 pg/L) and high (> 90 pg/L) levels of bio-ADM were independently (of the Simplified acute physiology score, SAPS-3) predictive of mortality. Patients with indirect mechanisms of lung injury had higher bio-ADM levels than those with a direct mechanism of injury, and bio-ADM increased with increasing ARDS severity.

Conclusions
High levels of bio-ADM on admission are associated with ARDS, and bio-ADM levels significantly differ depending on the injury mechanism. In contrast, both high and low levels of bio-ADM are associated with mortality, possibly due to the dual action of bio-ADM in stabilising the endothelial barrier and causing vasodilation. These findings could lead to improved diagnostic accuracy of ARDS and potentially lead to new therapeutic strategies.
Successful resection of port site recurrence of pancreatic ductal adenocarcinoma after laparoscopic distal pancreatectomy
Authors: Aida Takashi , Iwase Ryota , Usuba Teruyuki , Kumagai Yu , Furukawa Kenei , Onda Shinji , Ogawa Masaichi , Ikegami Toru 
Published: March 2023

Abstract
Background
There are many reports of port site recurrence after laparoscopic surgery for various types of cancer. However, only two cases of port site recurrence after laparoscopic pancreatectomy have been reported to date. We herein report a case of port site recurrence after laparoscopic distal pancreatectomy.

Case presentation
A 73-year-old woman was diagnosed with pancreatic tail cancer and underwent laparoscopic distal pancreatectomy with splenectomy. Histopathological examination revealed pancreatic ductal carcinoma (pT1N0M0 pStage I). The patient was discharged on postoperative day 14 with no complications. However, 5 months after surgery, computed tomography showed a small tumor at the right abdominal wall. No distant metastasis had appeared after 7 months of follow-up. Under the diagnosis of port site recurrence without any other metastases, we resected this abdominal tumor. Histopathological examination showed port site recurrence of pancreatic ductal carcinoma. No recurrence was observed 15 months postoperatively.

Conclusions
This is the report of successful resection of port site recurrence of pancreatic cancer.
Degradation and restoration of Indigenous California black oak (Quercus kelloggii) stands in the northern Sierra Nevada
Authors: Stephens Scott L. , Hall Les , Stephens Connor W. , Bernal Alexis A. , Collins Brandon M. 
Published: March 2023

AbstractBackgroundThe cultural connections of the Maidu to the lands they inhabit are profound with burning being a major component of their culture. California black oak plays an important role in the lifeways of many Indigenous tribes and Native peoples tend black oaks. We used multiple lines of evidence to reconstruct Indigenous fire use in a mixed conifer forest in the northern Sierra Nevada. This includes summarizing oral traditions by the Mountain Maidu, quantifying current and historical forest structure, and characterizing fire effects in an area impacted by the 2021 Dixie Fire.ResultsThe promotion of fire, both lighting- and human-ignited, has always been part of Mountain Maidu land stewardship. The mixed conifer forests in our focal study site had very high tree densities that were dominated by small, shade-tolerant species and the historic mean fire return interval was 8.6 years. Twenty-three fire intervals of 10 years or less and 11 fire intervals of 5 years or less were recorded. Based on forest inventory data collected in 1924, a majority of the forests in the broader region surrounding our focal site (82%) did not experience high levels of conifer competition. This is a stark contrast to contemporary forest conditions which showed that 73% of forests either were experiencing full site occupancy or were within the zone of imminent mortality. Contemporary forests not experiencing high levels of conifer competition had the highest density of large California black oak while forests in the zone of imminent mortality had the lowest density of large California black oak.ConclusionsFire exclusion and suppression led to a slow, albeit catastrophic, shift for California black oaks. The mixed conifer forests sampled in the early 1920s had very low tree densities and were dominated by large ponderosa and sugar pine trees which would have allowed California black oak to thrive. The number of very short fire intervals recorded is difficult to explain by lightning alone, pointing to the management of this area for Indigenous purposes. The 2021 wildfire resulted in 100% mortality of all conifer trees in the area but 61% of the California black oaks resprouted. This provides an opportunity to remove the conifer snags and allow the California black oaks to regain dominance. It would take active stewardship to produce the oak dominance again but it is possible and could be co-led by the Maidu and federal managers.
Mass flows and characteristic of mercury emitted from coal-fired power plant equipped with seawater flue gas desulphurization
Authors: Huang Mao Hung , Chen Wei Huan , Trinh Minh Man , Chang Moo Been 
Published: March 2023

AbstractThis study investigated the characteristics of mercury emitted from a large-scale coal-fired power plant in Taiwan via intensive sampling campaigns. The air pollution control devices equipped in this coal-fired power plant include selective catalytic reduction, fabric filter and seawater flue gas desulfurization. During three sampling campaigns, mercury concentrations emitted from this large-scale coal fired power plant ranged from 0.04 to 0.35 μg Nm−3. In addition, solid and liquid samples including coal, bottom ash, fly ash and inlet/outlet seawater were collected and analyzed for mercury content to provide the mass flows of mercury in this plant. The results indicate that mercury emitted from this coal-fired power plant is dominated by Hg0, and the emission factor of mercury ranges from 0.37 to 3.37 mg Hg t−1coal, which is relatively lower than those reported in other studies. The relative enrichment factor of mercury in fly ash (0.23–1.22) is significantly higher than that of bottom ash (0.10 × 10–3–0.89 × 10–3). Although this coal-fired power plant has a relatively low mercury atmospheric emission which accounts for 6.4% of the total mercury output, it is essential to further control mercury released from fly ash (62.6% of the total mercury output) and discharged seawater (33.7% of the total mercury output) to reduce environmental damage and human health effects.
Securing DNN for smart vehicles: an overview of adversarial attacks, defenses, and frameworks
Authors: Almutairi Suzan , Barnawi Ahmed 
Published: March 2023

AbstractRecently, many applications have begun to employ deep neural networks (DNN), such as image recognition and safety-critical applications, for more accurate results. One of the most important critical applications of DNNs is in smart autonomous vehicles. The operative principles of autonomous vehicles depend heavily on their ability to collect data from the environment via integrated sensors, then employ DNN classification to interpret them and make operative decisions. The security and the reliability of DNNs raise many challenges and concerns for researchers. One of those challenges currently in the research domain is the threat of adversarial attacks on DNNs. In this survey, we present state-of-the-art research on DNN frameworks, adversarial attacks, and defenses. We discuss each work along with its advantages and limitations and present our thoughts on and future directions for adversarial attacks and defenses.