bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular characterization and pathogenicity evaluation of enterovirus G isolated from diarrheic piglets
Authors: Ibrahim Yassein M. , Zhang Wenli , Wang Xinrong , Werid Gebremeskel Mamu , Fu Lizhi , Yu Haidong , Wang Yue
Published: October 2023

Four enterovirus G (EV-G) strains were isolated from diarrheic piglets that were negative for common swine enteric viruses. The spherical enterovirus particles of roughly 30-nm diameter were observed under transmission electron microscopy by using plaque-purified enterovirus. The complete genome sequence analysis revealed that each of four enteroviruses contained a papain-like cysteine protease (PLCP) gene between the 2C and 3A junction regions of the viral genome. This insertion encoded a predicted protease similar to the PLCP of porcine torovirus. The phylogenetic analysis based on complete genome with and without
PLCP
gene revealed that the four isolated EV-G strains were grouped together with global enterovirus G1-PLCP strains, and more closely related to EV-G/PLCP strains previously detected in China, Japan, and Korea (90.3%–92.2% similarities based on nucleotides). The cell susceptibility test demonstrated that the isolated EV-G could infect and replicate in cell lines from various host species. Furthermore, pathogenicity evaluation showed that the isolated EV-Gs induced mild diarrhea, pyrexia, and reduced body weight in infected piglets. The epidemiological investigation revealed a high prevalence of EV-G in swine herds. Together, our findings demonstrate that the isolated EV-G is pathogenic in piglets and may be advantageous in providing more trustworthy data on the evolution and pathological properties of EV-G.

IMPORTANCE

Enterovirus G is a species of positive-sense single-stranded RNA viruses associated with several mammalian diseases. The porcine enterovirus strains isolated here were chimeric viruses with the
PLCP
gene of porcine torovirus, which grouped together with global EV-G1 strains. The isolated EV-G strain could infect various cell types from different species, suggesting its potential cross-species infection risk. Animal experiment showed the pathogenic ability of the isolated EV-G to piglets. Additionally, the EV-Gs were widely distributed in the swine herds. Our findings suggest that EV-G may have evolved a novel mechanism for broad tropism, which has important implications for disease control and prevention.
Anti-topoisomerase 1 Antibody Level Changes after B Cell Depletion Therapy in Systemic Sclerosis
Authors: Ananyeva L. P. , Garzanova L. A. , Koneva O. A. , Starovoytova M. N. , Desinova O. V. , Ovsyannikova O. B. , Shayakhmetova R. U. , Cherkasova M. V. , Aleksankin A. P. , Nasonov E. L.
Published: October 2023

The aim of our study was to assess the relationship between the changes of antinuclear autoantibodies (ANAs) and autoantibodies to topoisomerase 1 (anti-Topo 1) in systemic sclerosis (SSs) patients on rituximab (RTX) therapy. The prospective study included 88 patients (73 women) with a mean age of 47 (17–71) years. The mean disease duration was 5.9 ± 4.8 years. The mean follow-up period was more than 2 years (27 (12–42) months). We documented a statistically significant change in skin score, the disease activity index, improvement of pulmonary function and reduction of mean dose of prednisolone after RTX treatment. There was a significant decrease in the number of patients with high levels of ANA and overall decrease of the ANA and anti-Topo 1 levels. A moderate positive statistically significant correlation was found between ANA and anti-Topo 1 (r = 0.403). In the group of patients positive for anti-Topo 1 there were a more pronounced depletion of B lymphocytes, significantly higher increase in forced vital capacity and diffusion capacity, decrease in the disease activity index, compared with patients negative for anti-Topo 1. We observed the decline in the level of ANA and anti-Topo 1 in SSc patients after RTX therapy, and it was correlated by an improvement of the main outcome parameters of the disease. Therefore, anti-Topo 1 positivity could be considered as a predictor of a better response to RTX treatment, especially in SSc patients with hyperproduction of anti-Topo 1.
Culture, diversity and inclusion: a survey of British Hip Society members
Authors: Dayananda K , Gill K , Grove A , Parr J , Hook S , Howell J R , Maggs J
Published: October 2023

Aim

To explore the perceptions and experiences of members of the British Hip Society (BHS) as they relate to culture, diversity and inclusion in the professional sphere.

Method

BHS members participated in an anonymised online survey in 2021. Quantitative and qualitative data were collected on demographics, professional experiences and perceptions of workplace culture. Members provided suggestions for improving working culture and supporting inclusivity.

Results

A 45% response rate (n=217) was achieved. Most respondents were male consultant surgeons, of white ethnicity. Almost a quarter of respondents reported experiencing barriers to career progression within the hip subspecialty. Experience of barriers was more common among women and those of non-white ethnicity. Several members experienced an elitist, exclusive culture in the BHS which is closed to outsiders. Thematic analysis of textual data revealed narratives which portray the perception of the society as a closed-door society, and described a clique culture in orthopaedics, and the pervasiveness of discrimination and banter.

Conclusion

We found that barriers to inclusion and diversity exist within the professional society. Exploring the narratives around these has informed strategies to overcome them and has shaped future BHS initiatives. To ensure our patients receive the best possible surgical care, it is vital that those with the skills and expertise to deliver it, are supported by the Society and feel a sense of belonging and representation.
National examination of occupational hazards in emergency medical services
Authors: Powell Jonathan R , Cash Rebecca E , Kurth Jordan D , Gage Christopher B , Mercer Christopher B , Panchal Ashish R
Published: October 2023

Objective

Emergency medical services (EMS) clinicians operate in environments that predispose them to occupational hazards. Our objective was to evaluate the frequency of occupational hazards and associations with mitigation strategies in a national dataset.

Methods

We performed a cross-sectional analysis of currently working, nationally certified civilian EMS clinicians aged 18–85 in the USA. After recertifying their National EMS Certification, respondents were invited to complete a survey with questions regarding demographics, work experience and occupational hazards. Three multivariable logistic regression models (OR, 95% CI) were used to describe associations between these hazards and demographics, work characteristics and mitigation strategies. Models were adjusted for age, sex, minority status, years of experience, EMS agency type, service type and EMS role.

Results

A total of 13 218 respondents met inclusion criteria (response rate=12%). A high percentage of EMS clinicians reported occupational injuries (27%), exposures (38%) and violence (64%) in the past 12 months. Odds of injury were lower with the presence of a lifting policy (0.73, 0.67–0.80), lift training (0.74, 0.67–0.81) and always using a powered stretcher (0.87, 0.78–0.97). Odds of exposure decreased with chemical, biological and nuclear exposure protection training (0.75, 0.69–0.80). Training in de-escalation techniques was associated with lower odds of experiencing violence (0.87, 0.79–0.96).

Conclusions

Occupational hazards are commonly experienced among EMS clinicians. Common mitigation efforts are associated with lower odds of reporting these hazards. Mitigation strategies were not widespread and associated with lower odds of occupational hazards. These findings may present actionable items to reduce occupational hazards for EMS clinicians.
Incidence and predictors of futile recanalisation after endovascular therapy in acute vertebrobasilar artery occlusion patients: insight from the ANGEL-ACT registry
Authors: Sun Dapeng , Yang Xinguang , Huo Xiaochuan , ‑ Raynald , Jia Baixue , Tong Xu , Wang Anxin , Ma Ning , Gao Feng , Mo Dapeng , Miao Zhongrong
Published: October 2023

Objectives

To identify the occurrence rate and predictors of futile recanalisation after endovascular therapy (EVT) for acute vertebrobasilar artery occlusion (VBAO).

Methods

Participants of the Endovascular Treatment Key Technique and Emergency Workflow Improvement of Acute Ischaemic Stroke (ANGEL-ACT) registry were selected for the analysis. Futile recanalisation was defined as patients did not achieve a 90-day good outcome (modified Rankin Scale ≤3) despite successful recanalisation (modified Treatment in Cerebral Ischaemia Scale ≥2b) after the procedure. Multivariable logistic regression analysis was conducted to find independent predictors of futile recanalisation in VBAO patients undergoing EVT.

Results

Three hundred and fifteen patients with VBAO who achieved successful recanalisation after EVT were included in current analysis, of whom, 155 (49.2%) suffered futile recanalisation, and 160 achieved effective recanalisation. After the multivariable analysis, we found admission National Institutes of Health Stroke Scale (NIHSS) ≥19 (OR 4.81, 95% CI 2.76 to 8.39, p<0.001), platelet-lymphocyte ratio (PLR) ≥162.2 (OR 1.93, 95% CI 1.14 to 3.27, p=0.001), onset-to-puncture time (OTP) ≥334 min (OR 2.15, 95% CI 1.25 to 3.68, p=0.005) and use of general anesthesia (GA) (OR 1.87, 95% CI 1.09 to 3.22, p=0.024) were associated with futile recanalisation.

Conclusions

Futile recanalisation after EVT occurred 49.2% of VBAO patients in the ANGEL-ACT registry. NIHSS≥19, PLR≥162.2, OTP≥334 min and use of GA were independent predictors of futile recanalisation.
Explanation of the nuclear structure of even–even 76–82Se nuclei
Authors: Abdulsahib Saja A. , Kassim Huda H. , Sharrad Fadhil I. , Hossain M. I.
Published: October 2023

In this paper, the interacting boson model (IBM-1) with intrinsic coherent state is used to study the O(6) shapes in Se isotopes. The Hamiltonian is written in the annihilation and creation form with one and two body terms. For each nucleus, a fitting procedure is adopted to get the best model parameters by fitting selected experimental energy levels, B(E2), B(M1) transition rates and mixing ratio with the calculated ones. The O(6) IBM potential energy surfaces (PESs) are analyzed.
Parametric Information Geometry with the Package Geomstats
Authors: Le Brigant Alice , Deschamps Jules , Collas Antoine , Miolane Nina
Published: October 2023

We introduce the information geometry module of the Python package Geomstats. The module first implements Fisher–Rao Riemannian manifolds of widely used parametric families of probability distributions, such as normal, gamma, beta, Dirichlet distributions, and more. The module further gives the Fisher–Rao Riemannian geometry of any parametric family of distributions of interest, given a parameterized probability density function as input. The implemented Riemannian geometry tools allow users to compare, average, interpolate between distributions inside a given family. Importantly, such capabilities open the door to statistics and machine learning on probability distributions. We present the object-oriented implementation of the module along with illustrative examples and show how it can be used to perform learning on manifolds of parametric probability distributions.
Layout-aware Single-image Document Flattening
Authors: Li Pu , Quan Weize , Guo Jianwei , Yan Dong-Ming
Published: October 2023

Single image rectification of document deformation is a challenging task. Although some recent deep learning-based methods have attempted to solve this problem, they cannot achieve satisfactory results when dealing with document images with complex deformations. In this article, we propose a new efficient framework for document flattening. Our main insight is that most layout primitives in a document have rectangular outline shapes, making unwarping local layout primitives essentially homogeneous with unwarping the entire document. The former task is clearly more straightforward to solve than the latter due to the more consistent texture and relatively smooth deformation. On this basis, we propose a layout-aware deep model working in a divide-and-conquer manner. First, we employ a transformer-based segmentation module to obtain the layout information of the input document. Then a new regression module is applied to predict the global and local UV maps. Finally, we design an effective merging algorithm to correct the global prediction with local details. Both quantitative and qualitative experimental results demonstrate that our framework achieves favorable performance against state-of-the-art methods. In addition, the current publicly available document flattening datasets have limited 3D paper shapes without layout annotation and also lack a general geometric correction metric. Therefore, we build a new large-scale synthetic dataset by utilizing a fully automatic rendering method to generate deformed documents with diverse shapes and exact layout segmentation labels. We also propose a new geometric correction metric based on our paired document UV maps. Code and dataset will be released athttps://github.com/BunnySoCrazy/LA-DocFlatten.
Epigenomic Characterization of Lymphoid Neoplasms
Authors: Duran-Ferrer Martí , Martín-Subero José Ignacio
Published: October 2023

Lymphoid neoplasms represent a heterogeneous group of disease entities and subtypes with markedly different molecular and clinical features. Beyond genetic alterations, lymphoid tumors also show widespread epigenomic changes. These severely affect the levels and distribution of DNA methylation, histone modifications, chromatin accessibility, and three-dimensional genome interactions. DNA methylation stands out as a tracer of cell identity and memory, as B cell neoplasms show epigenetic imprints of their cellular origin and proliferative history, which can be quantified by an epigenetic mitotic clock. Chromatin-associated marks are informative to uncover altered regulatory regions and transcription factor networks contributing to the development of distinct lymphoid tumors. Tumor-intrinsic epigenetic and genetic aberrations cooperate and interact with microenvironmental cells to shape the transcriptome at different phases of lymphoma evolution, and intraclonal heterogeneity can now be characterized by single-cell profiling. Finally, epigenetics offers multiple clinical applications, including powerful diagnostic and prognostic biomarkers as well as therapeutic targets.
SLIT3-mediated fibroblast signaling: a promising target for antifibrotic therapies
Authors: Gong Lianghui , Si Ming-Sing
Published: October 2023

The SLIT family (SLIT1-3) of highly conserved glycoproteins was originally identified as ligands for the Roundabout (ROBO) family of single-pass transmembrane receptors, serving to provide repulsive axon guidance cues in the nervous system. Intriguingly, studies involving SLIT3 mutant mice suggest that SLIT3 might have crucial biological functions outside the neural context. Although these mutant mice display no noticeable neurological abnormalities, they present pronounced connective tissue defects, including congenital central diaphragmatic hernia, membranous ventricular septal defect, and osteopenia. We recently hypothesized that the phenotype observed in SLIT3-deficient mice may be tied to abnormalities in fibrillar collagen-rich connective tissue. Further research by our group indicates that both SLIT3 and its primary receptor, ROBO1, are expressed in fibrillar collagen-producing cells across various nonneural tissues. Global and constitutive SLIT3 deficiency not only reduces the synthesis and content of fibrillar collagen in various organs but also alleviates pressure overload-induced fibrosis in both the left and right ventricles. This review delves into the known phenotypes of SLIT3 mutants and the debated role of SLIT3 in vasculature and bone. Present evidence hints at SLIT3 acting as an autocrine regulator of fibrillar collagen synthesis, suggesting it as a potential antifibrotic treatment. However, the precise pathway and mechanisms through which SLIT3 regulates fibrillar collagen synthesis remain uncertain, presenting an intriguing avenue for future research.
Evaluation of Potential Peptide‐Based Inhibitors against SARS‐CoV‐2 and Variants of Concern
Authors: Boshah Hattan , Samkari Faris , Valle-Pérez Alexander U. , Alsawaf Sarah M. , Aldoukhi Ali H. , Bilalis Panayiotis , Alshehri Salwa A. , Susapto Hepi H. , Hauser Charlotte A. E.
Published: October 2023

The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic has greatly affected all aspect of life. Although several vaccines and pharmaceuticals have been developed against SARS‐CoV‐2, the emergence of mutated variants has raised several concerns. The angiotensin‐converting enzyme (ACE2) receptor cell entry mechanism of this virus has not changed despite the vast mutation in emerging variants. Inhibiting the spike protein by which the virus identifies the host ACE2 receptor is a promising therapeutic countermeasure to keep pace with rapidly emerging variants. Here, we synthesized two ACE2‐derived peptides, P1 and P25, to target and potentially inhibit SARS‐CoV‐2 cell entry. These peptides were evaluated in vitro using pseudoviruses that contained the SARS‐CoV‐2 original spike protein, the Delta‐mutated spike protein, or the Omicron spike protein. An in silico investigation was also done for these peptides to evaluate the interaction of the synthesized peptides and the SARS‐CoV‐2 variants. The P25 peptide showed a promising inhibition potency against the tested pseudoviruses and an even higher inhibition against the Omicron variant. The IC50 of the Omicron variant was 60.8 μM, while the IC50s of the SARS‐CoV‐2 original strain and the Delta variant were 455.2 μM and 546.4 μM, respectively. The in silico experiments also showed that the amino acid composition design and structure of P25 boosted the interaction with the spike protein. These findings suggest that ACE2‐derived peptides, such as P25, have the potential to inhibit SARS‐CoV‐2 cell entry in vitro. However, further in vivo studies are needed to confirm their therapeutic efficacy against emerging variants.
Prevalence of Clostridium Difficile Infection (CDI) among Inflammatory Bowel Disease (IBD) Patients in Comparison to Non-IBD Patients in King Abdulaziz Medical City in Jeddah
Authors: Sukkar Ghassan Abdulrahman , Aga Syed Sameer , Alsamadani Abdulrahman Hamid , Almalki Faisal Ghazi , Alsudais Ali Saleh , Alquzi Abdulrahman Sulaiman , Ahmed Mohamed Eldigire , Mir Mushtaq Ahmad , Alasmari Moudi M.
Published: October 2023

Background. The prevalence of Clostridium difficile infection (CDI) as a common complication among inflammatory bowel disease (IBD) has been reported to increase worldwide and has been associated with a poor IBD outcome. Objectives. In this study, our aim was to report on the prevalence of CDI among IBD vs. non-IBD patients in King Abdulaziz Medical City (KAMC). Methods. This retrospective descriptive study was carried out between 2016 and 2020. Data of 89 patients reported with CDI in KAMC were analyzed for demographics and correlations between various characteristics such as BMI, personal/family history of IBD, infection with CDI, diagnosis, method of diagnosis, and treatment modalities. Results. Of the total 89 CDI patients, 59 (66.3%) were adults and 30 (33.7%) were pediatric, of which 36 (40.4%) were females and 53 (59.6%) were males. PCR was the main method of choice for the diagnosis of CDI (89.9%) followed by a positive-culture result (10.0%). Seventy-eight (87.6%) CDI patients were found to be immunocompromised, with two patients diagnosed with IBDs, one with UC, and one with CD. The recurrence rate was 38.4 (30 patients) among the immunocompromised group in comparison to 27.2 (3 patients) in the immunocompetent group (

p
=
0.584

). Conclusion. In this study, we found that adults were more prone to CDI infection, especially within hospital settings, and most of the CDI infections occurred in immunocompromised individuals, with cancer as the most common cause of it.
Supplementary Data from Fatty Acids Support the Fitness and Functionality of Tumor-Resident CD8+ T Cells by Maintaining SCML4 Expression
Authors: Feng Maoxiao , Liu Xiaoyan , Hao Xiaodong , Ren Yidan , Dong Guoying , Tian Jie , Wang Yuli , Du Lutao , Wang Yunshan , Wang Chuanxin
Published: October 2023

Supplementary figure and table
Figure S6 from Targeting the Immunoglobulin IGSF9 Enhances Antitumor T-cell Activity and Sensitivity to Anti–PD-1 Immunotherapy
Authors: Liu Yifan , Wang Hongying , Zhao Xinyu , Zhang Jiashen , Zhao Zhiling , Lian Xia , Zhang Juan , Kong Feng , Hu Tao , Wang Ting , Li Xiaohua , Wang Lei , Wang Dapeng , Li Chunling , Luan Huiwen , Liu Xiaoli , Wang Chunyan , Jiang Yun , Li Xiaomin , Li Fangmin , Ji Shuhao , Wang Yaopeng , Li Zunling
Published: October 2023

THP-1-igsf9-WT not -igsf9-KO cells inhibited T cell proliferation in vitro.
Supplementary Table 1 from Spatial Profiling of Circular RNAs in Cancer Reveals High Expression in Muscle and Stromal Cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedichte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: October 2023

List of primers designed for Sanger sequencing across the back splicing junctions.
Figure S4 from Targeting the Immunoglobulin IGSF9 Enhances Antitumor T-cell Activity and Sensitivity to Anti–PD-1 Immunotherapy
Authors: Liu Yifan , Wang Hongying , Zhao Xinyu , Zhang Jiashen , Zhao Zhiling , Lian Xia , Zhang Juan , Kong Feng , Hu Tao , Wang Ting , Li Xiaohua , Wang Lei , Wang Dapeng , Li Chunling , Luan Huiwen , Liu Xiaoli , Wang Chunyan , Jiang Yun , Li Xiaomin , Li Fangmin , Ji Shuhao , Wang Yaopeng , Li Zunling
Published: October 2023

Mouse IGSF9 was detected before and after MC38 implantation.
Supplementary Fig. 9 from Spatial Profiling of Circular RNAs in Cancer Reveals High Expression in Muscle and Stromal Cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedichte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: October 2023

Single molecule in situ hybridization for circSLC8A1 in prostate adenocarcinoma. Brightfield microscopy image at 200X magnification of DESMIN immunohistochemical staining (left panel). Brightfield and fluorescent microscopy images of circSLC8A1 at 200X magnification. A signal from circSLC8A1 can be observed in muscle cells, whereas the cancer cells were negative (right panel).
Figure S2 from Targeting the Immunoglobulin IGSF9 Enhances Antitumor T-cell Activity and Sensitivity to Anti–PD-1 Immunotherapy
Authors: Liu Yifan , Wang Hongying , Zhao Xinyu , Zhang Jiashen , Zhao Zhiling , Lian Xia , Zhang Juan , Kong Feng , Hu Tao , Wang Ting , Li Xiaohua , Wang Lei , Wang Dapeng , Li Chunling , Luan Huiwen , Liu Xiaoli , Wang Chunyan , Jiang Yun , Li Xiaomin , Li Fangmin , Ji Shuhao , Wang Yaopeng , Li Zunling
Published: October 2023

IGSF9 expression was detected in normal tissue array.
Supplementary Fig. 6 from Spatial Profiling of Circular RNAs in Cancer Reveals High Expression in Muscle and Stromal Cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedichte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: October 2023

Expression levels of MKI67. Measurement of levels of MKI67 by RT-qPCR normalized to MRPL19.
Supplementary Fig. 5 from Spatial Profiling of Circular RNAs in Cancer Reveals High Expression in Muscle and Stromal Cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedichte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: October 2023

Analysis of Ki67 staining on colon adenocarcinoma and adjacent normal tissue sections.
Representative Ki67 staining from tumor (left) and adjacent normal (right) tissues from the five patients’
samples subjected to the analysis. Positive staining is visible as brown color. In the tumor tissues, Ki67 is clearly present in the cancer cells and in some cells in the tumor stroma. In the normal tissue sections, the positive staining is found at the bottom of the crypts in the epithelium whereas no staining is detected in the mucosa and muscle sub-compartments.
Tables S1-S3 from Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: October 2023

Table S1: TARGET clinical sample and RNA-sequencing characteristics, Table S2: Genomic loci for lncRNA and protein coding genes in this study, Table S3: Number and types of genes expressed per cancer
Supplementary Information from Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: October 2023

Supplementary Methods, Index for Tables S1-S17, Index for Figures S1-S8
Supplementary Data from The Ratio of Key Metabolic Transcripts Is a Predictive Biomarker of Breast Cancer Metastasis to the Lung
Authors: Mathur Deepti , Liao Chen , Lin Wendy , La Ferlita Alessandro , Alaimo Salvatore , Taylor Samuel , Zhong Yi , Iacobuzio-Donahue Christine , Ferro Alfredo , Xavier Joao B.
Published: October 2023

Supplementary figures and figure legends
Supplementary Table S2 from Histone Methyltransferase NSD2 Activates PKCα to Drive Metabolic Reprogramming and Lenalidomide Resistance in Multiple Myeloma
Authors: Chong Phyllis S.Y. , Chooi Jing-Yuan , Lim Julia S.L. , Leow Aaron C.Y. , Toh Sabrina Hui Min , Azaman Irfan , Koh Mun Yee , Teoh Phaik Ju , Tan Tuan Zea , Chung Tae-Hoon , Chng Wee Joo
Published: October 2023

Supplementary Table S2
Figure S6 from Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: October 2023

Figure S6: Defining mesenchymal vs adrenergic lncRNAs in two NBL cohorts
Figure S5 from Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: October 2023

Figure S5: Characteristics of lncMod analysis and results
Supplementary Data from Histone Methyltransferase NSD2 Activates PKCα to Drive Metabolic Reprogramming and Lenalidomide Resistance in Multiple Myeloma
Authors: Chong Phyllis S.Y. , Chooi Jing-Yuan , Lim Julia S.L. , Leow Aaron C.Y. , Toh Sabrina Hui Min , Azaman Irfan , Koh Mun Yee , Teoh Phaik Ju , Tan Tuan Zea , Chung Tae-Hoon , Chng Wee Joo
Published: October 2023

Figure S1-9 and Supplementary Materials
Figure S3 from Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: October 2023

Figure S3: Regions of somatic copy number aberration across cancers and genes dysregulated due to copy number
Figure S1 from Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: October 2023

Figure S1: Workflow for RNA-seq gene mapping and quantification
Supplementary Figure S6 from Radiotherapy-Induced Neurocognitive Impairment Is Driven by Heightened Apoptotic Priming in Early Life and Prevented by Blocking BAX
Authors: Singh Rumani , Yu Stacey , Osman Marwa , Inde Zintis , Fraser Cameron , Cleveland Abigail H. , Almanzar Nicole , Lim Chuan Bian , Joshi Gaurav N. , Spetz Johan , Qin Xingping , Toprani Sneh M. , Nagel Zachary , Hocking Matthew C. , Cormack Robert A. , Yock Torunn I. , Miller Jeffrey W. , Yuan Zhi-Min , Gershon Timothy , Sarosiek Kristopher A.
Published: October 2023

Supplementary Figure S6
Supplementary Figure S1 from Radiotherapy-Induced Neurocognitive Impairment Is Driven by Heightened Apoptotic Priming in Early Life and Prevented by Blocking BAX
Authors: Singh Rumani , Yu Stacey , Osman Marwa , Inde Zintis , Fraser Cameron , Cleveland Abigail H. , Almanzar Nicole , Lim Chuan Bian , Joshi Gaurav N. , Spetz Johan , Qin Xingping , Toprani Sneh M. , Nagel Zachary , Hocking Matthew C. , Cormack Robert A. , Yock Torunn I. , Miller Jeffrey W. , Yuan Zhi-Min , Gershon Timothy , Sarosiek Kristopher A.
Published: October 2023

Supplementary Figure S1
Supplementary Figures from GTP Cyclohydrolase Drives Breast Cancer Development and Promotes EMT in an Enzyme-Independent Manner
Authors: Wang Zijing , Zhang Nan , Zhang Miao , Jiang Yao , Ng Aik Seng , Bridges Esther , Zhang Wei , Zeng Xin , Luo Qi , Liang Jiabien , Győrffy Balázs , Hublitz Philip , Liang Zhu , Fischer Roman , Kerr David , Harris Adrian L. , Cai Shijie
Published: October 2023

Supplementary Figures S1-S11
Figure S2 from Breast Cancer–Secreted Factors Promote Lung Metastasis by Signaling Systemically to Induce a Fibrotic Premetastatic Niche
Authors: Cohen Noam , Mundhe Dhanashree , Deasy Sarah K. , Adler Omer , Ershaid Nour , Shami Tamar , Levi-Galibov Oshrat , Wassermann Rina , Scherz-Shouval Ruth , Erez Neta
Published: October 2023

Supplementary data to Figure 4
Figure S1 from Breast Cancer–Secreted Factors Promote Lung Metastasis by Signaling Systemically to Induce a Fibrotic Premetastatic Niche
Authors: Cohen Noam , Mundhe Dhanashree , Deasy Sarah K. , Adler Omer , Ershaid Nour , Shami Tamar , Levi-Galibov Oshrat , Wassermann Rina , Scherz-Shouval Ruth , Erez Neta
Published: October 2023

Supplementary data to Figure 1
Data from Development of a rare earth nanoprobe enables in vivo real-time detection of sentinel lymph node metastasis of breast cancer using NIR-IIb imaging
Authors: Zhu Yuan-Yuan , Song Liang , Zhang Yong-Qu , Liu Wan-Ling , Chen Wei-Ling , Gao Wen-Liang , Zhang Li-Xin , Wang Jia-Zheng , Ming Zi-He , Zhang Yun , Zhang Guo-Jun
Published: October 2023

Abstract
Sentinel lymph node (SLN) biopsy plays a critical role in axillary staging of breast cancer. However, traditional SLN mapping does not accurately discern the presence or absence of metastatic disease. Detection of SLN metastasis largely hinges on examination of frozen sections or paraffin-embedded tissues post-SLN biopsy. To improve detection of SLN metastasis, we developed a second near-infrared (NIR-II) in vivo fluorescence imaging system, pairing erbium-based rare-earth nanoparticles (ErNPs) with bright down-conversion fluorescence at 1556 nm. To visualize SLNs bearing breast cancer, ErNPs were modified by balixafortide (ErNPs@POL6326), a peptide antagonist of the chemokine receptor CXCR4. The ErNPs@POL6326 probes readily drained into SLNs when delivered subcutaneously, entering metastatic breast tumor cells specifically via CXCR4-mediated endocytosis. NIR fluorescence signals increased significantly in tumor-positive versus tumor-negative SLNs, enabling accurate determination of SLN breast cancer metastasis. In a syngeneic mouse mammary tumor model and a human breast cancer xenograft model, sensitivity for SLN metastasis detection was 92.86% and 93.33%, respectively, and specificity was 96.15% and 96.08%, respectively. Of note, the probes accurately detected both macrometastases and micrometastases in SLNs. These results overall underscore the potential of ErNPs@POL6326 for real-time visualization of SLNs and in vivo screening for SLN metastasis.
Data from Development of a Rare Earth Nanoprobe Enables In Vivo Real-Time Detection of Sentinel Lymph Node Metastasis of Breast Cancer Using NIR-IIb Imaging
Authors: Zhu Yuan-Yuan , Song Liang , Zhang Yong-Qu , Liu Wan-Ling , Chen Wei-Ling , Gao Wen-Liang , Zhang Li-Xin , Wang Jia-Zheng , Ming Zi-He , Zhang Yun , Zhang Guo-Jun
Published: October 2023

Abstract
Sentinel lymph node (SLN) biopsy plays a critical role in axillary staging of breast cancer. However, traditional SLN mapping does not accurately discern the presence or absence of metastatic disease. Detection of SLN metastasis largely hinges on examination of frozen sections or paraffin-embedded tissues post-SLN biopsy. To improve detection of SLN metastasis, we developed a second near-infrared (NIR-II) in vivo fluorescence imaging system, pairing erbium-based rare-earth nanoparticles (ErNP) with bright down-conversion fluorescence at 1,556 nm. To visualize SLNs bearing breast cancer, ErNPs were modified by balixafortide (ErNPs@POL6326), a peptide antagonist of the chemokine receptor CXCR4. The ErNPs@POL6326 probes readily drained into SLNs when delivered subcutaneously, entering metastatic breast tumor cells specifically via CXCR4-mediated endocytosis. NIR fluorescence signals increased significantly in tumor-positive versus tumor-negative SLNs, enabling accurate determination of SLN breast cancer metastasis. In a syngeneic mouse mammary tumor model and a human breast cancer xenograft model, sensitivity for SLN metastasis detection was 92.86% and 93.33%, respectively, and specificity was 96.15% and 96.08%, respectively. Of note, the probes accurately detected both macrometastases and micrometastases in SLNs. These results overall underscore the potential of ErNPs@POL6326 for real-time visualization of SLNs and in vivo screening for SLN metastasis.
Significance:
NIR-IIb imaging of a rare-earth nanoprobe that is specifically taken up by breast cancer cells can accurately detect breast cancer macrometastases and micrometastases in sentinel lymph nodes.
Data from Spatial Profiling of Circular RNAs in Cancer Reveals High Expression in Muscle and Stromal Cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedichte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: October 2023

Abstract
Circular RNAs (circRNA) are covalently closed molecules that can play important roles in cancer development and progression. Hundreds of differentially expressed circRNAs between tumors and adjacent normal tissues have been identified in studies using RNA sequencing or microarrays, emphasizing a strong translational potential. Most previous studies have been performed using RNA from bulk tissues and lack information on the spatial expression patterns of circRNAs. Here, we showed that the majority of differentially expressed circRNAs from bulk tissue analyses of colon tumors relative to adjacent normal tissues were surprisingly not differentially expressed when comparing cancer cells directly with normal epithelial cells. Manipulating the proliferation rates of cells grown in culture revealed that these discrepancies were explained by circRNAs accumulating to high levels in quiescent muscle cells due to their high stability; on the contrary, circRNAs were diluted to low levels in the fast-proliferating cancer cells due to their slow biogenesis rates. Thus, different subcompartments of colon tumors and adjacent normal tissues exhibited striking differences in circRNA expression patterns. Likewise, the high circRNA content in muscle cells was also a strong confounding factor in bulk analyses of circRNAs in bladder and prostate cancers. Together, these findings emphasize the limitations of using bulk tissues for studying differential circRNA expression in cancer and highlight a particular need for spatial analysis in this field of research.
Significance:
The abundance of circRNAs varies systematically between subcompartments of solid tumors and adjacent tissues, implying that differentially expressed circRNAs discovered in bulk tissue analyses may reflect differences in cell type composition between samples.
Data from The ratio of key metabolic transcripts is a predictive biomarker of breast cancer metastasis to the lung
Authors: Mathur Deepti , Liao Chen , Lin Wendy , La Ferlita Alessandro , Alaimo Salvatore , Taylor Samuel , Zhong Yi , Iacobuzio-Donahue Christine , Ferro Alfredo , Xavier Joao B.
Published: October 2023

Abstract
Understanding the rewired metabolism underlying organ-specific metastasis in breast cancer could help identify strategies to improve the treatment and prevention of metastatic disease. Here, we used a systems biology approach to compare metabolic fluxes used by parental breast cancer cells and their brain- and lung-homing derivatives. Divergent lineages had distinct, heritable metabolic fluxes. Lung-homing cells maintained high glycolytic flux despite low levels of glycolytic intermediates, constitutively activating a pathway sink into lactate. This strong Warburg effect was associated with a high ratio of lactate dehydrogenase (LDH) to pyruvate dehydrogenase (PDH) expression, which correlated with lung metastasis in patients with breast cancer. While feature classification models trained on clinical characteristics alone were unable to predict tropism, the LDH/PDH ratio was a significant predictor of metastasis to the lung but not to other organs, independent of other transcriptomic signatures. High lactate efflux was also a trait in lung-homing metastatic pancreatic cancer cells, suggesting that lactate production may be a convergent phenotype in lung metastasis. Together, these analyses highlight the essential role that metabolism plays in organ-specific cancer metastasis and identify a putative biomarker for predicting lung metastasis in breast cancer patients.
Data from Breast Cancer–Secreted Factors Promote Lung Metastasis by Signaling Systemically to Induce a Fibrotic Premetastatic Niche
Authors: Cohen Noam , Mundhe Dhanashree , Deasy Sarah K. , Adler Omer , Ershaid Nour , Shami Tamar , Levi-Galibov Oshrat , Wassermann Rina , Scherz-Shouval Ruth , Erez Neta
Published: October 2023

Abstract
Metastatic cancer is largely incurable and is the main cause of cancer-related deaths. The metastatic microenvironment facilitates formation of metastases. Cancer-associated fibroblasts (CAF) are crucial players in generating a hospitable metastatic niche by mediating an inflammatory microenvironment. Fibroblasts also play a central role in modifying the architecture and stiffness of the extracellular matrix (ECM). Resolving the early changes in the metastatic niche could help identify approaches to inhibit metastatic progression. Here, we demonstrate in mouse models of spontaneous breast cancer pulmonary metastasis that fibrotic changes and rewiring of lung fibroblasts occurred at premetastatic stages, suggesting systemic influence by the primary tumor. Activin A (ActA), a TGFβ superfamily member, was secreted from breast tumors and its levels in the blood were highly elevated in tumor-bearing mice. ActA upregulated the expression of profibrotic factors in lung fibroblasts, leading to enhanced collagen deposition in the lung premetastatic niche. ActA signaling was functionally important for lung metastasis, as genetic targeting of ActA in breast cancer cells significantly attenuated lung metastasis and improved survival. Moreover, high levels of ActA in human patients with breast cancer were associated with lung metastatic relapse and poor survival. This study uncovers a novel mechanism by which breast cancer cells systemically rewire the stromal microenvironment in the metastatic niche to facilitate pulmonary metastasis.
Significance:
ActA mediates cross-talk between breast cancer cells and cancer-associated fibroblasts in the lung metastatic niche that enhances fibrosis and metastasis, implicating ActA as a potential therapeutic target to inhibit metastatic relapse.
Supplementary Figure S1 from Negative Predictive Value of Circulating Tumor Tissue Modified Viral (TTMV)-HPV DNA for HPV-driven Oropharyngeal Cancer Surveillance
Authors: Hanna Glenn J. , Roof Scott A. , Jabalee Jamie , Rettig Eleni M. , Ferrandino Rocco , Chen Sida , Posner Marshall R. , Misiukiewicz Krzysztof J. , Genden Eric M. , Chai Raymond L. , Sims John , Thrash Elaine , Stern Scott J. , Kalman Noah S. , Yarlagadda Sreenija , Raben Adam , Clements Lydia , Mendelsohn Abie , Kaczmar John M. , Pandey Yadav , Bhayani Mihir , Gupta Piyush , Kuperwasser Charlotte , Del Vecchio Fitz Catherine , Berger Barry M.
Published: October 2023

Supplementary Figure S1: Case examples of false negative TTMV-HPV DNA results identified during surveillance
Teee vs Treg Clusters DEGs DS3 from A Population of Tumor-Infiltrating CD4+ T Cells Co-Expressing CD38 and CD39 Is Associated with Checkpoint Inhibitor Resistance
Authors: Mitra Ankita , Thompson Brian , Strange Ann , Amato Carol M. , Vassallo Melinda , Dolgalev Igor , Hester-McCullough Jonathan , Muramatsu Tomoaki , Kimono Diana , Puranik Amrutesh S. , Weber Jeffrey S. , Woods David
Published: October 2023

Teee vs Treg Clusters DEGs
Supplementary Table S1 from Memory-like Differentiation, Tumor-Targeting mAbs, and Chimeric Antigen Receptors Enhance Natural Killer Cell Responses to Head and Neck Cancer
Authors: Jacobs Miriam T. , Wong Pamela , Zhou Alice Y. , Becker-Hapak Michelle , Marin Nancy D. , Marsala Lynne , Foster Mark , Foltz Jennifer A. , Cubitt Celia C. , Tran Jennifer , Russler-Germain David A. , Neal Carly , Kersting-Schadek Samantha , Chang Lily , Schappe Timothy , Pence Patrick , McClain Ethan , Zevallos Jose P. , Rich Jason T. , Paniello Randal C. , Jackson Ryan S. , Pipkorn Patrik , Adkins Douglas R. , DeSelm Carl J. , Berrien-Elliott Melissa M. , Puram Sidharth V. , Fehniger Todd A.
Published: October 2023

Supplementary Table S1. Demographic and clinical data of advanced head and neck squamous cell carcinoma patients. 
Supplementary Figure S5 from Memory-like Differentiation, Tumor-Targeting mAbs, and Chimeric Antigen Receptors Enhance Natural Killer Cell Responses to Head and Neck Cancer
Authors: Jacobs Miriam T. , Wong Pamela , Zhou Alice Y. , Becker-Hapak Michelle , Marin Nancy D. , Marsala Lynne , Foster Mark , Foltz Jennifer A. , Cubitt Celia C. , Tran Jennifer , Russler-Germain David A. , Neal Carly , Kersting-Schadek Samantha , Chang Lily , Schappe Timothy , Pence Patrick , McClain Ethan , Zevallos Jose P. , Rich Jason T. , Paniello Randal C. , Jackson Ryan S. , Pipkorn Patrik , Adkins Douglas R. , DeSelm Carl J. , Berrien-Elliott Melissa M. , Puram Sidharth V. , Fehniger Todd A.
Published: October 2023

Supplementary Figure 5. Expression of EphA2 on target cells and gating strategy for CAR-expressing NK cells
Supplementary Figure S3 from Memory-like Differentiation, Tumor-Targeting mAbs, and Chimeric Antigen Receptors Enhance Natural Killer Cell Responses to Head and Neck Cancer
Authors: Jacobs Miriam T. , Wong Pamela , Zhou Alice Y. , Becker-Hapak Michelle , Marin Nancy D. , Marsala Lynne , Foster Mark , Foltz Jennifer A. , Cubitt Celia C. , Tran Jennifer , Russler-Germain David A. , Neal Carly , Kersting-Schadek Samantha , Chang Lily , Schappe Timothy , Pence Patrick , McClain Ethan , Zevallos Jose P. , Rich Jason T. , Paniello Randal C. , Jackson Ryan S. , Pipkorn Patrik , Adkins Douglas R. , DeSelm Carl J. , Berrien-Elliott Melissa M. , Puram Sidharth V. , Fehniger Todd A.
Published: October 2023

Supplementary Figure 3. Individual blockade of DNAM-1, NKG2D and CD2 modestly impairs NK cell activity against HNSCC.
Supplementary Table S7 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients
Authors: Sarén Tina , Ramachandran Mohanraj , Gammelgård Gustav , Lövgren Tanja , Mirabello Claudio , Björklund Åsa K. , Wikström Kristina , Hashemi Jamileh , Freyhult Eva , Ahlström Håkan , Amini Rose-Marie , Hagberg Hans , Loskog Angelica , Enblad Gunilla , Essand Magnus
Published: October 2023

DEGs R vs NR CD8 CAR-T
Supplementary Table S6 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients
Authors: Sarén Tina , Ramachandran Mohanraj , Gammelgård Gustav , Lövgren Tanja , Mirabello Claudio , Björklund Åsa K. , Wikström Kristina , Hashemi Jamileh , Freyhult Eva , Ahlström Håkan , Amini Rose-Marie , Hagberg Hans , Loskog Angelica , Enblad Gunilla , Essand Magnus
Published: October 2023

Gene list used for computing AUCell signatures
Supplementary Table S16 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients
Authors: Sarén Tina , Ramachandran Mohanraj , Gammelgård Gustav , Lövgren Tanja , Mirabello Claudio , Björklund Åsa K. , Wikström Kristina , Hashemi Jamileh , Freyhult Eva , Ahlström Håkan , Amini Rose-Marie , Hagberg Hans , Loskog Angelica , Enblad Gunilla , Essand Magnus
Published: October 2023

DEGs R vs NR CD4 CAR T-cells
Supplementary Table S15 from Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients
Authors: Sarén Tina , Ramachandran Mohanraj , Gammelgård Gustav , Lövgren Tanja , Mirabello Claudio , Björklund Åsa K. , Wikström Kristina , Hashemi Jamileh , Freyhult Eva , Ahlström Håkan , Amini Rose-Marie , Hagberg Hans , Loskog Angelica , Enblad Gunilla , Essand Magnus
Published: October 2023

Univariate and multivariate analysis of OS and PFS of lymphoma patients including patient characteristics and clinical procedures