bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic value of genomic mutation signature associated with immune microenvironment in southern Chinese patients with esophageal squamous cell carcinoma
Authors: Zhou Yue , Chu Li , Li Shuyan , Chu Xiao , Ni Jianjiao , Jiang Shanshan , Pang Yechun , Zheng Danru , Lu Yujuan , Lan Fangcen , Cai Xiuyu , Yang Xi , Zhu Zhengfei 
Published: June 2024

AbstractThe genomic landscape of esophageal squamous cell cancer (ESCC), as well as its impact on the regulation of immune microenvironment, is not well understood. Thus, tumor samples from 92 patients were collected from two centers and subjected to targeted-gene sequencing. We identified frequently mutated genes, including TP53, KMT2C, KMT2D, LRP1B, and FAT1. The most frequent mutation sites were ALOX12B (c.1565C > T), SLX4 (c.2786C > T), LRIG1 (c.746A > G), and SPEN (c.6915_6917del) (6.5%). Pathway analysis revealed dysregulation of cell cycle regulation, epigenetic regulation, PI3K/AKT signaling, and NOTCH signaling. A 17-mutated gene-related risk model was constructed using random survival forest analysis and showed significant prognostic value in both our cohort and the validation cohort. Based on the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression (ESTIMATE) algorithm, the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm, and the MCPcounter algorithm, we found that the risk score calculated by the risk model was significantly correlated with stimulatory immune checkpoints (TNFSF4, ITGB2, CXCL10, CXCL9, and BTN3A1; p < 0.05). Additionally, it was significantly associated with markers that are important in predicting response to immunotherapy (CD274, IFNG, and TAMM2; p < 0.05). Furthermore, the results of immunofluorescence double staining showed that patients with high risk scores had a significantly higher level of M2 macrophage than those with low risk scores (p < 0.05). In conclusion, our study provides insights into the genomic landscape of ESCC and highlights the prognostic value of a genomic mutation signature associated with the immune microenvironment in southern Chinese patients with ESCC.
Comprehensive analysis of the relationship between ubiquitin-specific protease 21 (USP21) and prognosis, tumor microenvironment infiltration, and therapy response in colorectal cancer
Authors: Nie Haihang , Yu Yali , Wang Fan , Huang Xing , Wang Haizhou , Wang Jing , Tao Mi , Ning Yumei , Zhou JingKai , Zhao Qiu , Xu Fei , Fang Jun 
Published: June 2024

Abstract
Background
Ubiquitin-specific proteases family is crucial to host immunity against pathogens. However, the correlations between USP21 and immunosurveillance and immunotherapy for colorectal cancer (CRC) have not been reported.

Methods
The differential expression of USP21 between CRC tissues and normal tissues was analyzed using multiple public databases. Validation was carried out in clinical samples through qRT-PCR and IHC. The correlation between USP21 and the prognosis, as well as clinical pathological characteristics of CRC patients, was investigated. Moreover, cell models were established to assess the influence of USP21 on CRC growth and progression, employing CCK-8 assays, colony formation assays, and wound-healing assays. Subsequently, gene set variation analysis (GSVA) was used to explore the potential biological functions of USP21 in CRC. The study also examined the impact of USP21 on cytokine levels and immune cell infiltration in the tumor microenvironment (TME). Finally, the effect of USP21 on the response to immunotherapy and chemotherapy in CRC was analyzed.

Results
The expression of USP21 was significantly upregulated in CRC. High USP21 is correlated with poor prognosis in CRC patients and facilitates the proliferation and migration capacities of CRC cells. GSVA indicated an association between low USP21 and immune activation. Moreover, low USP21 was linked to an immune-activated TME, characterized by high immune cell infiltration. Importantly, CRC with low USP21 exhibited higher tumor mutational burden, high PD-L1 expression, and better responsiveness to immunotherapy and chemotherapeutic drugs.

Conclusion
This study revealed the role of USP21 in TME, response to therapy, and clinical prognosis in CRC, which provided novel insights for the therapeutic application in CRC.
SIRPG expression positively associates with an inflamed tumor microenvironment and response to PD-1 blockade
Authors: Luo Libo , Jiang Minlin , Wu Hong , Liu Yiqiang , Wang Haowei , Zhou Caicun , Ren Shengxiang , Chen Xiaoxia , Jiang Tao , Xu Chuan 
Published: June 2024

Abstract
Background
This study aimed to investigate the relationship between signal regulatory protein gamma (SIRPG) and tumor immune microenvironment phenotypes or T cell mediated-adaptive antitumor immunity, and its predictive value for response to PD-1 blockade in cancers.

Methods
Pan-cancer analysis of SIRPG expression and immune deconvolution was performed using transcriptomic data across 33 tumor types. Transcriptomic and clinical data from 157 patients with non-small-cell lung cancer (NSCLC) and melanoma received PD-1 blockade were analyzed. Expression characteristics of SIRPG were investigated using single-cell RNA sequencing (scRNA-seq) data of 103,599 cells. The effect of SIRPG expression was evaluated via SIRPG knockdown or overexpression in Jurkat T cells.

Results
The results showed that most cancers with high SIRPG expression had significantly higher abundance of T cells, B cells, NK cells, M1 macrophages and cytotoxic lymphocytes and increased expression level of immunomodulatory factors regulating immune cell recruitment, antigen presentation, T cell activation and cytotoxicity, but markedly lower abundance of neutrophils, M2 macrophages, and myeloid-derived suppressor cells. High SIRPG expression was associated with favorable response to PD-1 blockade in both NSCLC and melanoma. scRNA-seq data suggested SIRPG was mainly expressed in CD8+ exhausted T and CD4+ regulatory T cells, and positively associated with immune checkpoint expression including PDCD1 and CTLA4. In vitro test showed SIRPG expression in T cells could facilitate expression of PDCD1 and CTLA4.

Conclusion
High SIRPG expression is associated with an inflamed immune phenotype in cancers and favorable response to PD-1 blockade, suggesting it would be a promising predictive biomarker for PD-1 blockade and novel immunotherapeutic target.
Combinational zimberelimab plus lenvatinib and chemotherapy for alpha-fetoprotein elevated, advanced gastric cancer patients (AFPGC): a phase 1 dose-escalation study
Authors: Deng Ting , Wang Feixue , Zhang Le , Ning Tao , Sun Yansha , Ge Shaohua , Bai Ming , Lu Yao , Li Hongli , Ba Yi 
Published: June 2024

Abstract
Background
Alpha-fetoprotein elevated gastric cancer (AFPGC) got growing interests for its aggressive nature and unfavorable prognosis. Here, a phase 1 dose escalation study was conducted to evaluate safety and efficacy of zimberelimab (GLS-010, anti-PD-1) plus lenvatinib and chemotherapy (XELOX) as the first-line treatment for AFPGC.

Methods
Histologically confirmed HER2-negative, advanced GC patients with elevated serum AFP level (≥ 20 ng/ml) were screened. Using a 3 + 3 dose escalation design, patients were administered varying doses of lenvatinib (12, 16, 20 mg) with GLS-010 and XELOX. The primary endpoints were safety and determination of recommended phase II dose (RP2D). Secondary endpoints included overall response rate (ORR), progression-free survival (PFS) and disease control rate.

Results
Nine patients were enrolled with no dose-limiting toxicities observed. Most frequent treatment-related AEs were fatigue (55.6%), hand-foot syndrome (55.6%) and rash (55.6%), and no grade ≥ 4 AEs were reported. All patients exhibited disease control with ORR reaching 33.3%. The median PFS and OS reached 7.67 months (95% CI 4.07–11.27) and 13.17 months (95% CI 2.78–23.56), respectively. Serum AFP level was found correlated with therapeutic responses. Further 16s rRNA sequencing analysis demonstrated altered gut microbiota with elevated abundance of Lachnospiraceae bacterium-GAM79 and Roseburia hominis A2-183.

Conclusions
GLS-010 plus lenvatinib and XELOX demonstrated a manageable safety profile with promising efficacy for AFPGC. With RP2D of lenvatinib determined as 16 mg, further expansion cohort is now ongoing. Translational investigation suggested that serum AFP can be indictive for therapeutic responses and certain microbiota species indicating favorable responses to immunotherapy was elevated after the combinational treatment.
Functional LSMO foams for magneto-caloric applications
Authors: Koblischka Michael R. , Koblischka-Veneva Anjela , Schmauch Jörg 
Published: June 2024

AbstractThe ferromagnetic La$$_{1-x}$$

1
-
x

Sr$$_{x}$$

x

MnO$$_3$$

3

(LSMO) manganites are ideal materials for magneto-caloric applications due to their high Curie temperature. Here, we prepare open-cell, porous LSMO foams starting from a commercial polyurethane (PU) foam and commercial LSMO powder with $$x = 0.3.$$

x
=
0.3
.

The cut PU foams are then covered by a slurry of LSMO powder mixed with PVA and water, and then, the foams are subjected to a heat-treatment with two steps at 600 $$^\circ$$

∘

C (burn-off organic material) and 1200 $$^\circ$$

∘

C (sintering/compacting). The resulting ceramic LSMO foams are then characterized by X-ray, SEM, electron backscatter diffraction (EBSD) orientation mapping and magnetic measurements. The foam sample consists of randomly-oriented LSMO grains with an average grain size of 188 nm, being distinctly smaller than bulk samples of the same composition, but considerably larger than LSMO nanowires prepared by electrospinning. The magnetic data reveal a high Curie temperature like the bulk samples, and an entropy change, $$-\Delta S_{\text{M}}$$

-
Δ

S
M

slightly higher than that of the bulk samples, which points to a strong influence of the LSMO grain size. Thus, the resulting LSMO foam material is well suited for magneto-caloric applications at room temperature.
Shadow-aware image colorization
Authors: Duan Xin , Cao Yu , Zhang Renjie , Wang Xin , Li Ping 
Published: June 2024

AbstractSignificant advancements have been made in colorization in recent years, especially with the introduction of deep learning technology. However, challenges remain in accurately colorizing images under certain lighting conditions, such as shadow. Shadows often cause distortions and inaccuracies in object recognition and visual data interpretation, impacting the reliability and effectiveness of colorization techniques. These problems often lead to unsaturated colors in shadowed images and incorrect colorization of shadows as objects. Our research proposes the first shadow-aware image colorization method, addressing two key challenges that previous studies have overlooked: integrating shadow information with general semantic understanding and preserving saturated colors while accurately colorizing shadow areas. To tackle these challenges, we develop a dual-branch shadow-aware colorization network. Additionally, we introduce our shadow-aware block, an innovative mechanism that seamlessly integrates shadow-specific information into the colorization process, distinguishing between shadow and non-shadow areas. This research significantly improves the accuracy and realism of image colorization, particularly in shadow scenarios, thereby enhancing the practical application of colorization in real-world scenarios.
Use of coronary physiology to guide revascularization in clinical practice: results of the F(FR)2 registry
Authors: Altstidl J. Michael , Achenbach Stephan , Feyrer Johannes , Nazli J. Benedikt , Marwan Mohamed , Gaede Luise , Möllmann Helge , Giesler Tom , Rittger Harald , Pauschinger Matthias , Rudolph Tanja K. , Moshage Werner , Brück Martin , Tröbs Monique 
Published: June 2024

Abstract
Background
Despite the recommendation of coronary physiology to guide revascularization in angiographically intermediate stenoses without established correlation to ischemia, its uptake in clinical practice is slow.

Aims
This study aimed to analyze the use of coronary physiology in clinical practice.

Methods
Based on a multicenter registry (Fractional Flow Reserve Fax Registry, F(FR)2, ClinicalTrials.gov identifier NCT03055910), clinical use, consequences, and complications of coronary physiology were systematically analyzed.

Results
F(FR)2 enrolled 2,000 patients with 3,378 intracoronary pressure measurements. Most measurements (96.8%) were performed in angiographically intermediate stenoses. Out of 3,238 lesions in which coronary physiology was used to guide revascularization, revascularization was deferred in 2,643 (78.2%) cases.
Fractional flow reserve (FFR) was the most common pressure index used (87.6%), with hyperemia induced by an intracoronary bolus of adenosine in 2,556 lesions (86.4%) and intravenous adenosine used for 384 measurements (13.0%). The route of adenosine administration did not influence FFR results (change-in-estimate -3.1% for regression model predicting FFR from diameter stenosis). Agreement with the subsequent revascularization decision was 93.4% for intravenous and 95.0% for intracoronary adenosine (p = 0.261).
Coronary artery occlusion caused by the pressure wire was reported in two cases (0.1%) and dissection in three cases (0.2%), which was fatal once (0.1%).

Conclusions
In clinical practice, intracoronary pressure measurements are mostly used to guide revascularization decisions in angiographically intermediate stenoses. Intracoronary and intravenous administration of adenosine seem equally suited. While the rate of serious complications of wire-based intracoronary pressure measurements in clinical practice seems to be low, it is not negligible.

Graphical abstract
Effect of the porous structure on the hygrothermal vibration analysis of functional graded nanoplates using nonlocal high-order continuum plate model
Authors: Yıldırım E. , Esen I. 
Published: June 2024

AbstractThis study delves into the thermomechanical vibration behavior of functionally graded porous nanoplates under extreme thermal temperature and humidity conditions. The equation of motion of the nanoplate was derived using advanced theories in elasticity and deformation. The nanoplate consists of metal (SUS304) on the bottom surface and ceramic (Ni3S4) on the top surface, with the material distribution changing according to the power law across the plate thickness. The nanoplate was modeled with uniform and symmetric distributions of porosity reaching as high as 60%. Upon incorporating the thermal and moisture loads from the humid surroundings into the equations of motion derived from Hamilton's principle, the equations were solved using Navier's method and simplified to the eigenvalue equation. Analyzed within a broad framework are the thermomechanical vibration behavior of the nanoplate, temperature impact, humidity influence, porosity and its distribution, material grading parameter effects, and nonlocal integral elasticity effects. Observations indicate that variations in thermal temperature, humidity, and nonlocal parameters can lower the thermomechanical vibration frequency of the nanoplate, whereas porosity has the opposite effect. The effects mentioned are influenced by factors, such as the porosity ratio, porosity distribution, material ratios, and the size of the nonlocal parameter in the plate. The primary objective of this work is to uncover the nonlinear frequency response of nanoplates with high porosity in conditions characterized by high temperature and humidity.
Including validation of process control systems’ engineering into the technical debt classification
Authors: Dong Quang Huan , Vogel-Heuser Birgit , Neumann Eva-Maria 
Published: June 2024

AbstractThe Technical Debt (TD) concept depicts a situation in which a technical compromise is selected despite a better solution available. The associated risks to TD may be critical if TD is overlooked or not fixed properly. For instance, the product might not be used safely (in the healthcare supplies industry) or be contaminated (in the food & beverage sector) due to a design fault not adequately addressed. This work extends the TD classification for process automation systems that need to undergo a validation process according to Good Automated Manufacturing Practice (GAMP), which is required for pharmaceutical production or food processing, for example. The approach analysed industrial engineering documents to identify such TD types and sub-types. Three selected TD use cases confirmed by industry experts are reported. The presented meta-analysis approach on engineering documents can be employed as a TD identification method for such process control systems. The TD classification for process automation was thereby enlarged for an especially critical type of machine that may harm the health of many humans.
When the diagnosis is in the patient’s hand and in the neurologist’s eye
Authors: Bertini Alessandro , Lenti Sveva , Libelli Giorgia , Ronco Riccardo , Oliveri Serena , Montemagno Kora , Priori Alberto , Bocci Tommaso 
Published: June 2024

AbstractThe objective of this study was to encompass current knowledge about pathophysiological mechanisms of those specific hand postures or deformities caused by central nervous system disorders. In the era of high-resolution neuroimaging and molecular biology, clinicians are progressively losing confidence with neurological examination. Careful hand observation is of key importance in order to differentiate neurological from non-neurological conditions, central from peripheral aetiologies, and organic from functional disorders. Localizing the potential anatomical site is essential to properly conduct subsequent exams. We provided a practical guide for clinicians to recognize hand patterns caused by central nervous system disorders, avoiding mimicking conditions, thus optimizing and prompting the diagnostic pathway.
Managing and treating COVID-19 in patients with hematological malignancies: a narrative review and expert insights
Authors: Ng Heng Joo , Alata Maaz Kamal , Nguyen Quang The , Huynh Duc Vinh Phu , Tan Jing Yuan , Wong Chieh Lee 
Published: June 2024

AbstractPatients with hematologic malignancies (HMs) are at a significantly higher risk of contracting COVID-19 and experiencing severe outcomes compared to individuals without HMs. This heightened risk is influenced by various factors, including the underlying malignancy, immunosuppressive treatments, and patient-related factors. Notably, immunosuppressive regimens commonly used for HM treatment can lead to the depletion of B cells and T cells, which is associated with increased COVID-19-related complications and mortality in these patients. As the pandemic transitions into an endemic state, it remains crucial to acknowledge and address the ongoing risk for individuals with HMs. In this review, we aim to summarize the current evidence to enhance our understanding of the impact of HMs on COVID-19 risks and outcomes, identify particularly vulnerable individuals, and emphasize the need for specialized clinical attention and management. Furthermore, the impaired immune response to COVID-19 vaccination observed in these patients underscores the importance of implementing additional mitigation strategies. This may include targeted prophylaxis and treatment with antivirals and monoclonal antibodies as indicated. To provide practical guidance and considerations, we present two illustrative cases to highlight the real-life challenges faced by physicians caring for patients with HMs, emphasizing the need for individualized management based on disease severity, type, and the unique circumstances of each patient.
Vitamin D receptor gene polymorphisms and multiple myeloma: a meta-analysis
Authors: Lyu Chunyi , Yin Xuewei , Li Zonghong , Wang Teng , Xu Ruirong 
Published: June 2024

AbstractVitamin D acts through the vitamin D receptor (VDR), and vitamin D level decreases in multiple myeloma (MM) patients. Single nucleotide polymorphisms in VDR alter its functions to affect the vitamin D status. This raises the question of whether VDR gene polymorphisms are associated with MM risk, which has been investigated in case‒control studies, but the results have been inconsistent. This meta-analysis aimed to investigate the relationship between VDR gene polymorphisms and MM risk. The PubMed, Web of Science, Medline, Embase, Chinese National Knowledge Infrastructure (CNKI), Chinese Scientific Journal (VIP), Wanfang Databases (WANFANG) were searched from inception to June 1, 2023, without language restriction or publication preference. Pooled odds ratio (OR) and 95% confidence interval (CI) for each variable were calculated. Leave-one-out sensitivity analysis was performed to determine the source of heterogeneity. Publication bias was assessed using Begg’ and Egger’s tests, and the trim-and-fill method was used to compensate for publication bias. The correlation meta‐analysis was conducted using Comprehensive Meta‐Analysis 3.0 and STATA 12.0 software. All the included studies were based on Asian populations and involved four VDR gene polymorphisms, TaqI (rs731236), ApaI (rs7975232), BsmI (rs1544410) and FokI (rs2228570). The results showed that TaqI (C vs. T: OR = 1.487, 95% CI 1.052, 2.104, P = 0.025; CC + CT vs. TT: OR = 1.830, 95% CI 1.138, 2.944, P = 0.013), ApaI (T vs. G: OR = 1.292, 95% CI 1.101, 1.517, P = 0.002; TT vs. GG: OR = 1.600, 95% CI 1.106, 2.314, P = 0.013; TG vs. GG: OR 1.305, 95% CI 1.050, 1.622; P = 0.016; TT + TG vs. GG: OR = 1.353, 95% CI 1.103, 1.662, P = 0.004), BsmI (GG vs. AA: OR = 1.918, 95% CI 1.293, 2.844, P = 0.001; GA vs. AA: OR = 1.333, 95% CI 1.058, 1.679, P = 0.015; G vs. A: OR = 1.398, 95% CI 1.180, 1.657, P = 0.000; GG vs. AA + GA: OR = 1.686, 95% CI 1.174, 2.423, P = 0.005), and FokI (T vs. C: OR = 1.687, 95% CI 1.474, 1.931, P = 0.000; TT vs. CC: OR = 2.829, 95% CI 2.066, 3.872, P = 0.000; TC vs. CC: OR = 1.579, 95% CI 1.304, 1.913, P = 0.000, TT + TC vs. CC: OR = 1.771, 95% CI 1.477, 2.125, P = 0.000; TT vs. CC + TC: OR = 2.409, 95% CI 1.814, 3.200, P = 0.000) are associated with MM risk. VDR gene polymorphisms including ApaI, BsmI, TaqI, and FokI are associated with MM risk in Asian populations. Additional studies with large sample sizes and different ethnicities are needed.
Phosphorus recycling by mineral-catalyzed ribonucleotide cleavage on iron and manganese oxides
Authors: Klein Annaleise R. , Basinski Jade J. , Niyitanga Manzi Aurore , Cheng Cynthia X. , Sanchez Marcos , Thongsomboon Wiriya , Aristilde Ludmilla 
Published: June 2024

AbstractPhosphorus is an essential element influencing both food security via plant fertilization, and water pollution through excessive phosphorus use, yet the phosphorus cycle in ecosystems is poorly known. In particular, beyond adsorption, the role of iron and manganese oxides in catalyzing the abiotic dephosphorylation of biomolecules is debated. Here, we studied the reactions of ribonucleotides, containing different phosphate bonding, with goethite, hematite, and birnessite. We employed both high-resolution mass spectrometry of solution species and molecular modeling simulations of ribonucleotide-mineral complexes. Results disclose an up to fivefold preferential hydrolytic cleavage of a phosphoanhydride bond over a phosphoester bond, indicating that mineral-catalyzed reactions reflect the hierarchy reported for the activity of phosphatase enzymes. The fourfold higher catalytic reactivity of goethite and birnessite versus hematite is explained by mineral-specific binding rather than surface area differences. Corresponding simulated adsorbate conformations at the water–mineral interfaces are proposed. Overall, our findings provide new insights on the catalytic recycling of organic phosphorus species by mineral oxides.