bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards Probabilistic Robust and Sparsity-Free Compressive Sampling in Civil Engineering: A Review
Authors: Zhang Haoyu , Xue Shicheng , Huang Yong , Li Hui
Published: July 2023

Compressive sampling (CS) is a novel signal processing paradigm whereby the data compression is performed simultaneously with the sampling, by measuring some linear functionals of original signals in the analog domain. Once the signal is sparse sufficiently under some bases, it is strictly guaranteed to stably decompress/reconstruct the original one from significantly fewer measurements than that required by the sampling theorem, bringing considerable practical convenience. In the field of civil engineering, there are massive application scenarios for CS, as many civil engineering problems can be formulated as sparse inverse problems with linear measurements. In recent years, CS has gained extensive theoretical developments and many practical applications in civil engineering. Inevitable modelling and measurement uncertainties have motivated the Bayesian probabilistic perspective into the inverse problem of CS reconstruction. Furthermore, the advancement of deep learning techniques for efficient representation has also contributed to the elimination of the strict assumption of sparsity in CS. This paper reviews the advancements and applications of CS in civil engineering, focusing on challenges arising from data acquisition and analysis. The reviewed theories also have applicability to inverse problems in broader scientific fields.
Seismic Response Reduction of Liquid Storage Tank Using a Passive System Based on Improved Tuned Mass Damper
Authors: Jing Wei , Feng Jie , Cheng Xuansheng , Yang Wenwei
Published: July 2023

Liquid storage tanks are widely used in the industrial and the agricultural production, the earthquake damage of the liquid storage tanks will not only lead to economic losses, but also may cause environmental pollution, fire and explosion. Considering the fluid–structure interaction, the liquid sloshing and the material nonlinearity, the three-dimensional numerical calculation models of nondamping and tuned mass damper (TMD) liquid storage tanks are established, respectively. The earthquake waves with different characteristics are selected to investigate the dynamic responses of the liquid storage tank, the control effects of the TMD on the seismic responses of the liquid storage tank are analyzed, and the influence law of the change of the spring stiffness on the damping effect is discussed. The results show that the TMD has a significant damping effect on the liquid storage tank, and the element damping has significant influence on the dynamic responses in the subsequent stage of the earthquake action. Under the action of Darfield–New Zealand wave, the damping ratio corresponding to the acceleration of the tank wall is 69.6%. When the element damping is not considered, the small change of the spring stiffness has significant influence on the damping effect, but after the element damping being considered, the influence of the spring stiffness change on the damping effect is small. The TMD provides a high performance system to the damping control of the liquid storage tank under the action of earthquakes with different intensity.
Bifurcation analysis and global sensitivity index for malaria disease transmission dynamics: Information and treated bed nets control
Authors: Adeniyi Michael O. , Amalare Asimi A. , Oke Segun I. , Salawu Sulyman O.
Published: July 2023

Malaria is known globally as the foremost cause of death in children and adults. Several intervention strategies and controls have been implemented and proposed, among which is Long Lasting Insecticide Treated Nets (LLINs). Malaria cases have been reported to reduce by [Formula: see text] due to the use of LLINs. However, the laid-back behaviors of humans negatively impact its effective use through improper handling and exposure to direct sunlight. To this end, a mathematical model is formulated to investigate the influence of individual response to information on the transmission dynamics of malaria infection in both human and mosquito populations. The threshold for the effective reduction of the prevalence of malaria through a behavioral change in the use of LLINs in response to the created awareness is determined in this study. The point of departure of this study from other studies is that it incorporates information/awareness as a dynamic variable to investigate the impact of LLINs on malaria. The equilibrium points of the model are analyzed using stability theory and the associated basic reproduction number [Formula: see text]. The implicit function theorem is used to determine the direction of bifurcation. We use Latin hypercube sampling (LHS) to test the most sensitive parameters in the basic reproduction number. The correlation between the [Formula: see text] and parameters is displayed using Scatter plots. The mathematical analysis shows that the direction of bifurcation is supercritical, which suggests that we only need to bring [Formula: see text] below unity for disease eradication. The study also revealed that an increase in awareness of the use of LLINs has an impact on reducing malaria transmission.
Stationary distribution and density function analysis of stochastic SIQS epidemic model with Markov chain
Authors: Cao Yusi , Fu Jing
Published: July 2023

In this paper, a stochastic SIQS epidemic model perturbed by both white and telephone noises is investigated. By constructing several suitable Lyapunov functions, we obtain sufficient conditions for the existence of ergodic stationary distribution of the positive solution. Moreover, by solving the Fokker–Planck equation, we obtain the exact expression of probability density function around the quasi-equilibrium of the stochastic model. In addition, sufficient conditions for the extinction are established. Finally, the results of this paper are further verified by numerical simulation.
L-Alanine Supported Autogenous Eruption Combustion Synthesis of Ni/NiO@RuO2 Heterostructure for Electrochemical Glucose and pH Sensor
Authors: Padmanathan N. , Sasikumar R. , Thayanithi V. , Razeeb Kafil M.
Published: July 2023

Safety and quality control are important for long-term storage and preservation of food. Glucose and food pH are the two most common markers for evaluating food quality. Herein, we constructed a Ni/NiO@RuO2 heterostructure-based two-way sensor via a novel eruption combustion pattern (ECP) using non-conventional amino acid as a propellant. This approach has the unique points of interests of in situ doping of oxides and the formation of heterojunctions, providing well-developed pores and high surface areas to enhance the material performance. The Ni/NiO@RuO2 heterostructures have been tested as a bi-functional catalyst for glucose and pH sensing. The sensor exhibits a fast response time of <0.1 ± 0.02 s, a sensitivity of 641.95 ± 0.5 μA mM−1 cm−2 towards glucose with a 0.4 ± 0.08 μM detection limit and a linear response of 0.1 to 5 mM. As a pH sensor, it exhibits an acceptable sensitivity of −41.6 mV pH−1 with a response time of <50 s over a pH range of 2–12. Moreover, this bi-functional sensor based on Ni/NiO@RuO2 performs well when applied to a selection of beverage samples. This study provides a new scalable and low-cost approach to fabricating hetero-oxide nanostructures with controllable heterojunctions for various sensor applications.
Table S8 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Comparisons in cell type proportions predicted by RCTD between LG and HGPDAC epilesional, jutxalesional, and perilesional spots.
Table S5 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Differentially expressed genes between LG and HGPDAC juxtalesional spots.
Table S4 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Differentially expressed genes between LG and HGPDAC epilesional spots.
Table S22 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Differentially expressed genes between NKX6-2 overexpressing and control KPC cell lines.
Table S21 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Overlap between genes differentially expressed in the NKX6-2 overexpressing and control Kras;Gnas cell line and genes differentially expressed in NKX6-2 positive and negative epilesional spots from the human LG IPMN dataset.
Table S20 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Overlap between genes differentially expressed in the NKX6-2 overexpressing and control Kras;Gnas cell line and genes differentially expressed in Nkx6-2 positive and negative spots from the Kras;Gnas ST epithelial spots.
Table S2 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Gene markers per each of the scMC clusters from the IPMN dataset
Table S18 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Differentially expressed genes between Nkx6-2 positive and negative spots in the Kras;Gnas STepithelial spots.
Table S11 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Counts and percentage of NKX6-2 positive nuclei in HG vs LG IPMN samples as determined by quantification of the COMET images.
Supplementary Figures S1-S13 from Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential
Authors: Sans Marta , Makino Yuki , Min Jimin , Rajapakshe Kimal I. , Yip-Schneider Michele , Schmidt C. Max , Hurd Mark W. , Burks Jared K. , Gomez Javier A. , Thege Fredrik I. , Fahrmann Johannes F. , Wolff Robert A. , Kim Michael P. , Guerrero Paola A. , Maitra Anirban
Published: July 2023

Figure S1. Spatial maps showing number of genes detected per spot in the 13 samples used for spatial transcriptomics analyses. Figure S2. A) Uniform Manifold Approximation and Projection (UMAP) of all spots collected from the 13 samples by ST. Figure S3. A) Violin plot showing expression of CDX2 and MUC2 in the epilesional compartments of IPMN and PDAC samples. Figure S4. Cell type proportions in LG and HR IPMN compartments determined by RCTD deconvolution. Figure S5. COMET cyclic IF imaging of IPMN. Figure S6. NKX6-2 levels determined by ST and COMET analyses conducted on tissue samples from the same patient. Figure S7. NKX6-2 expression in LG IPMN samples and its associated signature. Figure S8. A) Enrichment plots for gastric REG3A positive cells, main fetal acinar cells, pancreas acinar cells, and ductal cells obtained via GSEA analyses. Figure S9. Spatial transcriptomic analyses of a murine model of IPMN. Figure S10. A) Gene set enrichment analyses (GSEA) of differentially expressed cell type signatures between Nkx6-2+ and Nkx6-2 – spots in the Gnas;Kras mice samples. Figure S11. Nkx6-2 overexpression in a Kras;Gnas cell line. Figure S12. Nkx6-2 overexpression in KPC cell lines. Figure S13. Quantification of the percentage of glandular structures in the tumors derived from Kras;GnasNkx6-2 or control cell lines in littermate (Kras;Gnas, left) mice or immunodeficient nude mice (NuJ, right).
Supplementary_Table1 from Effectors Enabling Adaptation to Mitochondrial Complex I Loss in Hürthle Cell Carcinoma
Authors: Gopal Raj K. , Vantaku Venkata R. , Panda Apekshya , Reimer Bryn , Rath Sneha , To Tsz-Leung , Fisch Adam S. , Cetinbas Murat , Livneh Maia , Calcaterra Michael J. , Gigliotti Benjamin J. , Pierce Kerry A. , Clish Clary B. , Dias-Santagata Dora , Sadow Peter M. , Wirth Lori J. , Daniels Gilbert H. , Sadreyev Ruslan I. , Calvo Sarah E. , Parangi Sareh , Mootha Vamsi K.
Published: July 2023

Supplementary Table 1 describes the HCC clinical cohort
Table S4 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Supplementary Table S4 shows the publicly validated RCC-associated motifs, together with their antigen-specificities with TCRGP, and motifs found in the REP TILs using GLIPH2.
Supplementary Figure S3 from Sequential Chromogenic IHC: Spatial Analysis of Lymph Nodes Identifies Contact Interactions between Plasmacytoid Dendritic Cells and Plasmablasts
Authors: Claudio Natalie , Nguyen My-Tien , Wanner Adrian , Pucci Ferdinando
Published: July 2023

Trained networks detected artifacts and tissue of interest limits, and excluded them from the analysis.
Table S2 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Supplementary Table S2 shows the list of all markers, antibodies and their catalog numbers used for multi-parameter flow cytometry immunophenotyping, co-culture and T-cell activation assays.
Supplementary Figure S2 from Sequential Chromogenic IHC: Spatial Analysis of Lymph Nodes Identifies Contact Interactions between Plasmacytoid Dendritic Cells and Plasmablasts
Authors: Claudio Natalie , Nguyen My-Tien , Wanner Adrian , Pucci Ferdinando
Published: July 2023

Alignment results. Comparison of before and after alignment for CD3 (red, top) and CD20 (red, bottom) superimposed with hematoxylin (green).
Supplementary Figure S1 from Sequential Chromogenic IHC: Spatial Analysis of Lymph Nodes Identifies Contact Interactions between Plasmacytoid Dendritic Cells and Plasmablasts
Authors: Claudio Natalie , Nguyen My-Tien , Wanner Adrian , Pucci Ferdinando
Published: July 2023

Distortion maps. In order to align all the biomarker images for a given sample, each image needs to be corrected for distortions that happen during the staining procedure. This step aims to rectify micro- and macro-anatomical shifts in the tissue sections. Two examples of the calculated shifts (dx, dy and amplitude) and support points for CD3 and CD20.
Movie M1 from Sequential Chromogenic IHC: Spatial Analysis of Lymph Nodes Identifies Contact Interactions between Plasmacytoid Dendritic Cells and Plasmablasts
Authors: Claudio Natalie , Nguyen My-Tien , Wanner Adrian , Pucci Ferdinando
Published: July 2023

Cell segmentation of hematoxylin-stained tissue. Example of segmented cells in the sub-capsular region, showing both small round nuclei in lymphocyte-rich areas (B cell follicle, top left) and elongated nuclei in macrophage-rich areas (sub-capsular sinus, middle).
Figure S4 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Figure S4 shows representative gating strategies for the different marker expressions in the CD4+ and CD8+ T-cells for the different samples (healthy kidney, tumor, pre-REP TIL and REP TIL).
Figure S15 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Figure S15 shows pathway enrichment analyses for the pre-REP TILs and REP TILs, as well as the abundance of the RCC-associated motifs found in the UMAP T-cell clusters for each tumor sample.
Figure S13 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Figure S13 shows analyses from the scRNA+TCRab-seq data, including the different UMAP clusters, differentially expressed genes and canonical marker gene expressions.
Figure S1 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Figure S1 shows a schematic of the TIL expansion protocol.
FIGURE 6 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Expanded clonotypes between the pre-REP TILs and REP TILs show distinct phenotypic differences within the tumor. A, UMAPs comparing the size of the T cell clonotypes found in the sc-RNAseq+TCRαβ-seq and TCRβ-seq data from 2 patients (pt115 and pt616). Each dot represents a clone in which the color corresponds to the size of the clone in the sc-RNAseq+TCRαβ-seq (left column), TCRβ-seq data from the pre-REP TILs (middle column), and TCRβ-seq data from the REP TILs (right column). Representations for all samples, including the available tumor and healthy kidney samples are found in Supplementary Fig. S10C). B, UMAPs showing the expanded pre-REP TIL and REP TIL clones in pt115 and pt616 (Benjamini-Hochberg–corrected two-sided Fisher’s exact test, Padjusted < 0.05). In both patients, more pre-REP TIL clonotypes were expanded in the CD8+ TPRE-EXH (pt115) and CD8+ TEXH (pt616) phenotypes, whereas expanded REP TIL clonotypes were mainly characterized by the CD4+ TCYTOTOXIC cell phenotype. C, Volcano plots showing the DEGs in the expanded REP TIL samples (right) compared with those in the pre-REP TILs (left) in pt115 and pt616. In pt115, genes that were most upregulated (right) in the expanded REP TIL clonotypes were NKG7, CCL5, and CD8A, together with those related to cytotoxicity, such as GZMB, GZMH, and GZMK. In pt616, genes related to activation such as HLA-DRB1, HLA-DRA, chemokines such as CCL3 and CCL4L2, as well as LAG-3 were upregulated in the expanded REP TIL clonotypes. In both patients, IL7R was among the DEGs in the expanded pre-REP TIL clonotypes. D, UMAP showing T cells carrying the RCC-associated motifs found in the sc-RNAseq+TCRαβ-seq tumor patients (n = 3). T cells carrying the RCC-associated motifs showed distinct T cell phenotypes in each individual sample.
FIGURE 5 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Distinct origins of pre-REP TIL and REP TIL TCR clonotypes in RCC tumors. A, Dissociated tumor samples that were enriched for lymphocytes and flow-sorted for CD45+ cells (n = 3) were analyzed with sc-RNAseq+TCRαβ-seq. The UMAP shows separately clustered T cells, and the UMAP including all cell types can be found in the Supplementary Fig. S9A. Eight different T cell clusters present in the tumor were annotated on the basis of the canonical marker genes, DEGs, and different gene module scores [from Tirosh and colleagues (41)], where each color indicates a distinct T cell cluster. Cluster 0: cytotoxic CD4+ T (TCYTOTOXIC), cluster 1: exhausted CD8+ T cell (TEXH), cluster 2: pre-exhausted CD8+ T (TPRE-EXH), cluster 3: CD8+ T effector (TEFF), cluster 4: CD4+ TREG, cluster 5: CD8+ tissue resident memory (TTRM), cluster 6: CD8+ TEFF), cluster 7: CD4+ T follicular helper (TFH). B, UMAP showing all clusters present in each patient sample (pt115, pt423, and pt616), with distinct T cell phenotypes. The CD8+ TPRE-EXH and CD4+ TFH phenotypes were dominant in pt115, pt423 encompassed a more CD8+ TEFF and CD4+ TCYTOTOXIC phenotype, and pt616 was characterized by CD8+ TEXH and CD8+ TTRM phenotypes. C, Mapped expanded and singlet TCRαβ clonotypes on the tumor UMAP show that the clonotypes lie on distinct parts of the UMAP. Most of the non-expanded (singlet) clonotypes have a CD4+ TCYTOTOXIC phenotype (cluster 0), whereas expanded clonotypes are dominant in the CD8+ TEFF, TPRE-EXH and TEXH phenotypes (cluster 3, 2, and 1, respectively). The relative proportion of the different clonotypes in each of the UMAP clusters is found in Supplementary Fig. S9B. D, Scaled expression of selected canonical markers related to stemness, tissue residency, cytotoxicity, and exhaustion in the T cell UMAP representation as in A. E, Dot plot showing the scaled average (scale) and percentage (dot size) of expression between the selected DEGs for each UMAP cluster. The full list of the top 10 DEGs and their scaled expressions are found in Supplementary Fig. S9C and S9D).
FIGURE 3 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

T cell repertoire differences between the tumor and TIL T cells. A, Healthy kidney (n = 24), tumor (n = 36), pre-REP TIL (n = 7), and REP TIL (n = 7) samples were sequenced with bulk TCRβ-seq. The clonality of the TCR repertoire was analyzed with the Gini index (values closer to 1 denote increased clonality). The pre-REP TILs were observed to be the most clonal out of the different samples, suggesting the loss of TCR repertoire diversity during the REP protocol. P < 0.0001, Kruskal–Wallis nonparametric test. B, Two representative cases (pt081 and pt115) showing the relative abundance of clonotypes in the tumor, pre-REP TILs, and REP TILs. The pre-REP TILs were dominated by the top 10 clones of the entire repertoire. Clonotype indices represent the rank of the clone (i.e., 1:10 indicates the top 10 most expanded clonotypes). Comparisons between the rest of the samples are found in Supplementary Fig. S4A. C, The top 20 most abundant REP TIL clonotypes were tracked to the corresponding tumor and pre-REP TIL samples in the same representative cases (pt081 and pt115). Overall, the clonotypes ending up in the REP TILs were very small clonotypes in the other sample types. Comparisons between the rest of the samples are found in Supplementary Fig. S4B. D, The frequencies of the overlapping T cell clonotypes in one representative case (pt115) between the REP TIL and pre-REP TIL samples (left), as well as between the tumor and pre-REP TILs (right). Spearman correlation was used to compare the frequencies of the clonotypes in the samples. The x- and y-axes are logarithmically transformed. R and P values refer to the log-transformed frequencies of the clonotypes. The frequencies for the rest of the samples are found in Supplementary Fig. S5 and S6). E, Treemaps showing the size of the T cell clonotypes in each sample type (tumor, pre-REP TIL, and REP TIL) in one representative case (pt081). The size of each box indicates the size of one clonotype in the TCR repertoire. Colored boxes indicate TCRs matched to viral-specific TCRs found in VDJdb (45). Few matches were discovered and represented as small T cell clonotypes, indicating that expanded clones in the tumor, pre-REP TILs and REP TILs do not target common viruses. Treemaps for all the samples are found in Supplementary Fig. S7.
FIGURE 1 from Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma
Authors: Lee Moon Hee , Theodoropoulos Jason , Huuhtanen Jani , Bhattacharya Dipabarna , Järvinen Petrus , Tornberg Sara , Nísen Harry , Mirtti Tuomas , Uski Ilona , Kumari Anita , Peltonen Karita , Draghi Arianna , Donia Marco , Kreutzman Anna , Mustjoki Satu
Published: July 2023

Immunophenotypic differences between tumor, healthy kidney tissue, pre-REP TILs, and REP TILs. A, Matching healthy kidney tissue (n = 30), tumor (n = 58), pre-REP TIL (n = 15), and REP TIL (n = 25) samples were used for flow cytometry immunophenotypic analysis. The median positive expression levels were compared between each sample type. The pre-REP TILs and REP TILs had a greater abundance of CD4+ T cells (median 46.8% and 68.4% out of lymphocytes, respectively) than CD8+ T cells (4.8% and 10.5%), compared with the tumor CD4+ (34%) and CD8+ (19.5%) T cells. In contrast, an increased proportion of cells in the tumor (14.4%), healthy kidney (14.4%), and pre-REP TIL (13.5%) samples were NK cells. B, The CD4+ and CD8+ T cell immunophenotypes were analyzed using CCR7 and CD45RO markers. Most of the pre-REP TIL CD4+ T cells were of the central memory (TCM; CCR7+ CD45RO+) phenotype (median 64%), and the pre-REP TIL CD8+ T cells were either TCM (37.7%) or effector memory (TEM; CCR7-CD45RO+, median 40.8%) cells. REP TIL CD4+ T cells were TCM (37%), but more TEM (55.8%) cells, whereas more than half (61.5%) of the REP TIL CD8+ T cells were TEM cells. TNAIVE = naïve T cells, TCM = central memory T cells, TEM = effector memory T cells, TEMRA = terminally differentiated effector memory T cells. C, The greatest LAG-3 expression was observed in the REP TIL CD8+ T cells (median 70.7%) compared with healthy kidney (1.6%), tumor (3.5%), and pre-REP TIL (30%) samples. D, PD-1 expression was greatest in the tumor CD4+ (41.6%) and CD8+ (54%) T cells, suggesting an exhausted phenotype compared with the healthy tissue, pre-REP TILs and REP TILs. E, CD25 expression was highest in both pre-REP TIL (36.5%) and REP TIL (30.1%) CD4+ T cells compared with the tumor and healthy kidney. F, The highest HLA-DR expression was observed in the pre-REP TILs and REP TILs in both CD4+ (67.6% and 91.9%, respectively) and CD8+ T cell compartments (69.3% and 82.8%). For all immunophenotypic analyses, Kruskal–Wallis nonparametric test with Dunn’s post hoc test was used for all analyses. ns, not significant; *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.
Understanding the contribution of lifestyle in breast cancer risk prediction: a systematic review of models applicable to Europe
Authors: Mertens Elly , Barrenechea-Pulache Antonio , Sagastume Diana , Vasquez Maria Salve , Vandevijvere Stefanie , Peñalvo José L.
Published: July 2023

Background

Breast cancer (BC) is a significant health concern among European women, with the highest prevalence rates among all cancers. Existing BC prediction models account for major risks such as hereditary, hormonal and reproductive factors, but research suggests that adherence to a healthy lifestyle can reduce the risk of developing BC to some extent. Understanding the influence and predictive role of lifestyle variables in current risk prediction models could help identify actionable, modifiable, targets among high-risk population groups.

Purpose

To systematically review population-based BC risk prediction models applicable to European populations and identify lifestyle predictors and their corresponding parameter values for a better understanding of their relative contribution to the prediction of incident BC.

Methods

A systematic review was conducted in PubMed, Embase and Web of Science from January 2000 to August 2021. Risk prediction models were included if (i) developed and/or validated in adult cancer-free women in Europe, (ii) based on easily ascertained information, and (iii) reported models’ final predictors. To investigate further the comparability of lifestyle predictors across models, estimates were standardised into risk ratios and visualised using forest plots.

Results

From a total of 49 studies, 33 models were developed and 22 different existing models, mostly from Gail (22 studies) and Tyrer-Cuzick and co-workers (12 studies) were validated or modified for European populations. Family history of BC was the most frequently included predictor (31 models), while body mass index (BMI) and alcohol consumption (26 and 21 models, respectively) were the lifestyle predictors most often included, followed by smoking and physical activity (7 and 6 models respectively). Overall, for lifestyle predictors, their modest predictive contribution was greater for riskier lifestyle levels, though highly variable model estimates across different models.

Conclusions

Given the increasing BC incidence rates in Europe, risk models utilising readily available risk factors could greatly aid in widening the population coverage of screening efforts, while the addition of lifestyle factors could help improving model performance and serve as intervention targets of prevention programmes.
Comparative study on the selection of drainage methods in posterior lumbar interbody fusion
Authors: Wang Chaoran , Wang Xuewei , Yang Zongqiang , Shi Jiandang , Niu Ningkui
Published: July 2023

Objective

To compare and analyze the clinical effects of bilateral natural pressure drainage and negative pressure drainage after posterior lumbar interbody fusion (PLIF) to provide a reference for selecting drainage methods after lumbar surgery.

Methods

A retrospective cohort study, 281 patients who underwent single-segment PLIF in our hospital from January 2017 to December 2020 and met the inclusion and exclusion criteria were included in the study, including 132 males and 149 females, aged 22–85 years, with an average of (53.62 ± 11.23) years. According to different postoperative incision drainage methods determined by the random number table method before surgery, they were divided into the natural pressure drainage group and negative pressure drainage group, both of which were bilateral drainage. The general observation indexes and perioperative-related indexes were recorded and analyzed.

Results

There were 143 cases in the natural pressure drainage group and 138 cases in the negative pressure drainage group. There was no significant difference in age, gender, body mass index, disease type, blood pressure on the day of surgery, preoperative albumin, hemoglobin, platelet, prothrombin time, and intraoperative bleeding between the two groups (P > 0.05). The albumin on the first postoperative day in the natural pressure drainage group was higher than that in the negative pressure drainage group [(33.24 ± 3.52) vs. (32.17 ± 5.03), P < 0.05]; The hemoglobin on the first postoperative day in the natural pressure drainage group was higher than that in the negative pressure drainage group [(126.01 ± 15.03) vs. (115.19 ± 16.25), P < 0.01]; The drainage volume on the first postoperative day in the natural pressure drainage group was lower than that in the negative pressure drainage group [(93.25 ± 63.58) ml vs. (119.46 ± 54.48) ml, P < 0.01]; The total postoperative drainage volume in the natural pressure drainage group was lower than that in the negative pressure drainage group [(355.60 ± 189.69) ml vs. (434.37 ± 149.12) ml, P < 0.01]; The indwelling time of drainage tube in the natural pressure drainage group was lower than that in the negative pressure drainage group [(3.29 ± 1.17) d vs. (3.45 ± 0.97) d, P < 0.05]. There was no significant difference in platelet count on the first postoperative day, postoperative hospital stays, and complications (incision infection and hematoma) between the two groups (P > 0.05).

Conclusion

Bilateral natural pressure drainage and negative pressure drainage can achieve good drainage effects after PLIF, but patients with natural pressure drainage have less loss of albumin and hemoglobin, less drainage volume, and shorter drainage tube indwelling time, which is worthy of clinical application.
Dietary Antioxidant Quality Score (DAQS), serum lipids, markers of glucose homeostasis, blood pressure and anthropometric features among apparently metabolically healthy obese adults in two metropolises of Iran (Tabriz and Tehran): a cross-sectional study
Authors: Nikrad Negin , Shakarami Amir , Tousi Ayda Zahiri , Farhangi Mahdieh Abbasalizad , Ardekani Abnoos Mokhtari , Jafarzadeh Faria
Published: July 2023

Background

Oxidative stress (OS) is associated with a variety of non-communicable diseases, including MetS, diabetes mellitus, metabolic syndrome, and cardiovascular disease through increased production of reactive oxygen species (ROS) and impairment of antioxidant defense mechanisms. Antioxidants can protect cells against free radical damage, so it seems important to determine the relationship between the quality of dietary antioxidants intake and chronic diseases. The Dietary Antioxidant Quality Score (DAQS) is obtained by adding the daily intake of known dietary vitamins and minerals, including selenium, zinc, vitamin A, vitamin C, and vitamin E, compared to the recommended daily intake (RDI). Therefore, this study aims to determine the relationship between DAQS, serum lipids, markers of glucose homeostasis, blood pressure and anthropometric features among obese adults.

Methods

In the present cross-sectional study, 338 individuals who were obese (BMI ≥ 30 kg/m2) aged 20-50 years were recruited from Tabriz and Tehran, Iran. A validated semi-quantitative Food Frequency Questionnaire (FFQ) with 168 food items was used to quantify dietary consumption; accordingly, DAQS was computed. Blood biomarkers were measured using enzyme-linked immunosorbent assay (ELISA) kits. A standard mercury sphygmomanometer was used to assess blood pressure, and bioelectrical impedance analysis (BIA) was performed to determine body composition. The association between the DAQS tertiles and biochemical variables was investigated using multinomial logistic regression.

Results

Participants in the highest tertile of DAQS have a lower diastolic blood pressure (DBP) values in all of the adjusted models [odds ratio (OR) = 0.920; confidence interval (CI)= 0.852-0.993, P-value = 0.03] in the analysis of co-variance (ANCOVA) model. Similarly, subjects at the second tertile of DAQS had lower DBP compared with the first tertile in age and sex-adjusted model [OR= 0.937; CI= 0.882-0.997]. There was no statistically significant difference for other metabolic parameters in different DAQS tertiles.

Conclusion

According to our findings, higher DAQS was associated with lower DBP among obese adults with obesity in two major cities of Iran (Tehran and Tabriz). Other studies with interventional design are needed to better elucidate these associations and underlying mechanisms.
Key aspects of psychosocial needs in palliative care - a qualitative analysis within the setting of a palliative care unit in comparison with specialised palliative home care
Authors: Michel Cathrin , Seipp Hannah , Kuss Katrin , Hach Michaela , Kussin Andrea , Riera-Knorrenschild Jorge , Bösner Stefan
Published: July 2023

Background

The number of palliative care patients with complex needs is increasing in developed countries. In addition to physical aspects and symptom control, psychosocial aspects are of great importance for palliative care patients. The aim of this study was to understand which psychosocial aspects are important to patients, relatives and health professionals within the setting of a palliative care unit in comparison with specialised palliative home-care (SPHC).

Methods

We used a qualitative design based on semistructured interviews, which were coded via qualitative content analysis. The study took place in the state of Hesse, Germany, and data collection was conducted in 2017 (interviews from the ELSAH study, which was conducted in a SPHC) and 2018 (supplementary interviews conducted in a palliative care unit). The results from both settings were compared.

Results

In the palliative care unit, 10 health professionals, 11 patients and 8 relatives were interviewed. In the outpatient setting, we interviewed 30 health professionals, 14 patients and 14 relatives. We identified four key psychosocial issues related to palliative care that were relevant in both the inpatient and outpatient settings: care planning, patient-centred care, a protected environment with feelings of safety, and psychological well-being. In addition, immediate availability of medical staff, greater relief of the relatives and better accessibility of psychological care were more important in the inpatient setting than in the specialised palliative home care setting.

Conclusions

Knowledge and application of the identified key issues may improve patient-centred palliative care. Accessibility of psychological care and immediate availability of medical staff may be important factors for enhancing psychological well-being in the inpatient palliative care setting. Consideration of the identified key issues may help to develop more collaborative transitions between the palliative care unit and the SPHC and may help to provide palliative care patients and their families with care that is appropriate and feasible for them.

Trial registration

The underlying comparative study of the outpatient setting of specialised palliative home-care (ELSAH) was registered within the German Clinical Trials Register DRKS-ID: DRKS00012421, (https://drks.de/search/de/trial/DRKS00012421) on 19th May 2017.
Multisystem inflammatory syndrome in children and Kawasaki disease; comparison of their clinical findings and one-year follow-up—a cross-sectional study
Authors: Mehrban Saghar , Tahghighi Fatemeh , Aghaei Moghadam Ehsan , Ziaee Vahid
Published: July 2023

Background

Studies on Multisystem Inflammatory Syndrome in Children (MIS-C) and Kawasaki Disease (KD) have yielded inconsistent results and are lacking in Asian and African countries. This study aimed to compare the laboratory and clinical features, short-term outcomes, and one-year follow-ups of a large cohort of MIS-C and KD patients.

Methods

Data from 176 MIS-C and 56 KD patients admitted to Tehran Children's Medical Center between January 2021 and January 2022 were collected. Patients were followed up until January 2023.

Results

While lymphopenia and thrombocytopenia were more prevalent in MIS-C (73.2% vs. 20% in KD, p < 0.001), KD patients exhibited a higher median white blood cell count and prevalence of anemia, along with higher fibrinogen and erythrocyte sedimentation rate levels (p < 0.001, p < 0.001, p = 0.005, p < 0.001, respectively). MIS-C patients also exhibited lower ejection fraction, a greater occurrence of pericardial effusion, and a higher incidence of coronary aneurysms and ectasia, and ascites. Echocardiography after seven days of treatment showed a reduction in pathologies for both groups, but it was significant only for MIS-C. After one year, coronary artery abnormalities remained in only six cases.

Conclusions

In conclusion, this study highlights differences between MIS-C and KD, including laboratory indices as well as echocardiographic and abdominal ultrasound findings. These findings contribute valuable data on Iranian patients to the existing literature on this topic and have significant implications for accurate diagnosis and improved management of pediatric patients presenting with these conditions.
A simple and high-efficiency viscoacoustic reverse time migration calculated by finite difference
Authors: Mu Xinru , Huang Jianping
Published: July 2023

The viscoacoustic wave equation with decoupled amplitude attenuation and phase dispersion terms is convenient for implementing reverse time migration (RTM) in attenuating media. However, the traditional viscoacoustic wave equations are expressed by the fractional Laplacian, which requires computationally expensive fast Fourier transforms to perform numerical solutions. This is not conducive for commercial applications with seismic data in terabyte, particularly in three dimensions. Based on the memory-variable-represented viscoacoustic wave equation, the new dispersion- and dissipation-dominated wavefield extrapolation operators that can be solved using the economical finite-difference method (FDM) are developed. In numerical simulation, the staggered-grid FDM is used to solve the temporal and spatial derivatives. The computational efficiency analysis indicates that, compared to the traditional viscoacoustic wave equation, the new viscoacoustic wave equation has an efficiency improvement of approximately more than two times. The accuracy of simulations of amplitude attenuation and phase dispersion is evaluated in viscoacoustic media with varying Q values. The proposed viscoacoustic wave equation is also extended to Q-compensated RTM. Two synthetic tests and one field data test indicate that the Q-compensated RTM can produce high-resolution images by correcting phase dispersion and compensating amplitude loss.
Study of Patient and Physician Attitudes Toward Automated Prognostic Models for Patients With Metastatic Cancer
Authors: Hildebrand Rachel D. , Chang Daniel T. , Ewongwoo Agnes N. , Ramchandran Kavitha J. , Gensheimer Michael F.
Published: July 2023

PURPOSE

For patients with cancer and their doctors, prognosis is important for choosing treatments and supportive care. Oncologists' life expectancy estimates are often inaccurate, and many patients are not aware of their general prognosis. Machine learning (ML) survival models could be useful in the clinic, but there are potential concerns involving accuracy, provider training, and patient involvement. We conducted a qualitative study to learn about patient and oncologist views on potentially using a ML model for patient care.

METHODS

Patients with metastatic cancer (n = 15) and their family members (n = 5), radiation oncologists (n = 5), and medical oncologists (n = 5) were recruited from a single academic health system. Participants were shown an anonymized report from a validated ML survival model for another patient, which included a predicted survival curve and a list of variables influencing predicted survival. Semistructured interviews were conducted using a script.

RESULTS

Every physician and patient who completed their interview said that they would want the option for the model to be used in their practice or care. Physicians stated that they would use an AI prognosis model for patient triage and increasing patient understanding, but had concerns about accuracy and explainability. Patients generally said that they would trust model results completely if presented by their physician but wanted to know if the model was being used in their care. Some reacted negatively to being shown a median survival prediction.

CONCLUSION

Patients and physicians were supportive of use of the model in the clinic, but had various concerns, which should be addressed as predictive models are increasingly deployed in practice.
Cross-sensitivity immune SPR sensor based on fan-shaped microstructured optical fiber for temperature and refractive index sensing
Authors: Zhang Wandi , Luan Nannan
Published: July 2023

To avoid coating and filling into the fiber holes, facilitate the phase-matching and eliminate cross-sensitivity problems, we propose a surface plasmon resonance sensor based on a fan-shaped microstructured optical fiber (MOF) for the simultaneous sensing of temperature and refractive index (RI). The fan-shaped structure is fabricated by polishing two sides of MOF with an angle of 120°. One side is coated with the gold film and polydimethylsiloxane layer for temperature sensing, and the other side is only coated with the gold film for RI sensing. The two sensing sides can support resonance peaks with two polarized directions at the angle of 120°, which are independent without cross-sensitivity. By monitoring the shifts of the two polarized peaks, our numerical results show that the temperature sensitivity is 2.932 nm/°C in the range of 30 °C to 40 °C, and RI sensitivity is 4235 nm/RIU in the range of 1.38 to 1.39, respectively.