cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0ks6rx4
title: CIL:57241. In Cell Image Library

description: Ebola virus Huh7 infected cells 18 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6084/m9.figshare.30499847
title: Supplementary Material for: CYTOLOGICAL ASSESSMENT OF PAEDIATRIC BREAST LESIONS: A SYSTEMATIC REVIEW

description: INTRODUCTION
Paediatric breast lesions are rare and mostly benign. Despite their benign nature, the presence of these lesions in this population often raises concerns. Fine-needle aspiration biopsy (FNAB) offers a minimally invasive, though its application in paediatric populations remains debated due to interpretative challenges. This systematic review aims to assess the utility, limitations, and diagnostic performance of FNAB in the evaluation of paediatric breast lesions.

METHODS
A systematic search was performed in Pubmed for articles published from January 2014 to February 2025. Non-humans and non-English language reports were excluded. Based on title and abstract screening, 25 articles were selected, and 13 additional articles were retrieved through reference list, yielding a total of 38 studies for qualitative analysis. Data were manually extracted and synthesized. 

RESULTS
Benign lesions represented the majority of cases, with fibroadenomas being the most frequent (65%–95%), followed by benign phyllodes tumours, hamartomas, tubular adenomas, pseudoangiomatous stromal hyperplasia (PASH), and cystic lesions. Malignant lesions were rare and included metastatic tumours, malignant phyllodes tumours, secretory carcinoma, and primary breast sarcomas. FNAB demonstrated high diagnostic accuracy for benign lesions but showed limitations in distinguishing benign from malignant tumours. ROSE was identified as a valuable adjunct, improving sample adequacy, reducing the rate of inconclusive results and enhancing diagnostic reliability.

CONCLUSION
FNAB is an effective first-line diagnostic modality for paediatric breast lesions, offering high accuracy for benign conditions. However, limitations exist in discriminating borderline and malignant lesions, warranting correlation with clinical, radiological findings, and, in some cases, core biopsy confirmation. The integration of ROSE enhances FNAB diagnostic yield and may further refine management strategies. A multidisciplinary approach remains essential to ensure optimal, minimally invasive care for paediatric patients.
DOI: 10.6084/m9.figshare.30499847.v1
title: Supplementary Material for: CYTOLOGICAL ASSESSMENT OF PAEDIATRIC BREAST LESIONS: A SYSTEMATIC REVIEW

description: INTRODUCTION
Paediatric breast lesions are rare and mostly benign. Despite their benign nature, the presence of these lesions in this population often raises concerns. Fine-needle aspiration biopsy (FNAB) offers a minimally invasive, though its application in paediatric populations remains debated due to interpretative challenges. This systematic review aims to assess the utility, limitations, and diagnostic performance of FNAB in the evaluation of paediatric breast lesions.

METHODS
A systematic search was performed in Pubmed for articles published from January 2014 to February 2025. Non-humans and non-English language reports were excluded. Based on title and abstract screening, 25 articles were selected, and 13 additional articles were retrieved through reference list, yielding a total of 38 studies for qualitative analysis. Data were manually extracted and synthesized. 

RESULTS
Benign lesions represented the majority of cases, with fibroadenomas being the most frequent (65%–95%), followed by benign phyllodes tumours, hamartomas, tubular adenomas, pseudoangiomatous stromal hyperplasia (PASH), and cystic lesions. Malignant lesions were rare and included metastatic tumours, malignant phyllodes tumours, secretory carcinoma, and primary breast sarcomas. FNAB demonstrated high diagnostic accuracy for benign lesions but showed limitations in distinguishing benign from malignant tumours. ROSE was identified as a valuable adjunct, improving sample adequacy, reducing the rate of inconclusive results and enhancing diagnostic reliability.

CONCLUSION
FNAB is an effective first-line diagnostic modality for paediatric breast lesions, offering high accuracy for benign conditions. However, limitations exist in discriminating borderline and malignant lesions, warranting correlation with clinical, radiological findings, and, in some cases, core biopsy confirmation. The integration of ROSE enhances FNAB diagnostic yield and may further refine management strategies. A multidisciplinary approach remains essential to ensure optimal, minimally invasive care for paediatric patients.
DOI: 10.6075/j06h4gs3
title: CIL:45876, Homo sapiens. In Cell Image Library

description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
description: Plate 25585 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
DOI: 10.6075/j0p55m6d
title: CIL:13708, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: EYFP; probe for mitochondria; tetramethylrhodamine, ethyl ester (TMRE)
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: YFP-Parkin (green) does not translocate to mitochondria (red) when HeLa cells are transfected with control siRNA (siCtrl). HeLa cells stably expressing YFP-Parkin were transfected with control siRNA for 192 hours, treated with DMSO for 1 hour and then stained with TMRE, a cationic fluorescent dye that is readily sequestered by active mitochondria. Cells were imaged using an inverted microscope (LSM510 Meta; Carl Zeiss, Inc.) with a 63× 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the accompanying image browser (LSM; Carl Zeiss, Inc.). Image corresponds to Fig1f, top panels and is a control for other images in Fig1f in J Cell Biol. 191: 933-942, 2010. Images in Fig1f include CIL#s 13707, 13708, 13709.
DOI: 10.6084/m9.figshare.30499850
title: Supplementary Material for: Immunohistochemical staining for disseminated carcinomatosis of the bone marrow in a patient with post-colonoscopy colorectal cancer: a case report

description: Introduction: The incidence of disseminated carcinomatosis of the bone marrow (DCBM) associated with colorectal cancer is low, but it can rapidly progress and cause even death. A previous study has suggested a relationship between mucin profiles and prognosis of colorectal cancer. However, there are no reports of mucin staining in cases of DCBM with post-colonoscopy colorectal cancer (PCCRC). Case Presentation: A 58-year-old man who had undergone colonoscopy (CS) 1 year ago complained of fatigue and fever. The man was diagnosed with virus-associated hemophagocytic syndrome and received steroid pulse therapy. Despite treatment, his condition deteriorated. 18F-fluorodeoxyglucose positron emission tomography–computed tomography revealed diffuse uptake in the bone marrow. A bone marrow biopsy revealed atypical CK20-positive and CK7-negative cellular nests, suggesting a primary gastrointestinal tumor. Subsequent CS at our hospital revealed a 30-mm type 4 transverse colorectal cancer lesion. Thus, the patient was diagnosed with DCBM associated with PCCRC. The patient died 18 days after his last CS. Mucin staining revealed that the cancer cells were MUC2-positive and MUC5AC-negative. MUC5AC negativity has been associated with poor prognosis in colorectal cancer and may have suggested rapid disease progression. Conclusion: The mucin staining result of MUC5AC negativity suggested rapid disease progression and poor prognosis in this case.
DOI: 10.6084/m9.figshare.30499850.v1
title: Supplementary Material for: Immunohistochemical staining for disseminated carcinomatosis of the bone marrow in a patient with post-colonoscopy colorectal cancer: a case report

description: Introduction: The incidence of disseminated carcinomatosis of the bone marrow (DCBM) associated with colorectal cancer is low, but it can rapidly progress and cause even death. A previous study has suggested a relationship between mucin profiles and prognosis of colorectal cancer. However, there are no reports of mucin staining in cases of DCBM with post-colonoscopy colorectal cancer (PCCRC). Case Presentation: A 58-year-old man who had undergone colonoscopy (CS) 1 year ago complained of fatigue and fever. The man was diagnosed with virus-associated hemophagocytic syndrome and received steroid pulse therapy. Despite treatment, his condition deteriorated. 18F-fluorodeoxyglucose positron emission tomography–computed tomography revealed diffuse uptake in the bone marrow. A bone marrow biopsy revealed atypical CK20-positive and CK7-negative cellular nests, suggesting a primary gastrointestinal tumor. Subsequent CS at our hospital revealed a 30-mm type 4 transverse colorectal cancer lesion. Thus, the patient was diagnosed with DCBM associated with PCCRC. The patient died 18 days after his last CS. Mucin staining revealed that the cancer cells were MUC2-positive and MUC5AC-negative. MUC5AC negativity has been associated with poor prognosis in colorectal cancer and may have suggested rapid disease progression. Conclusion: The mucin staining result of MUC5AC negativity suggested rapid disease progression and poor prognosis in this case.
DOI: 10.6084/m9.figshare.30499853
title: Supplementary Material for: Continuous regression of metastatic pancreatic adenocarcinoma after suspending chemotherapy: a case report.

description: Background:
Regression of malignancy in the absence of cancer-directed therapy is an uncommon and poorly understood phenomenon. Its occurrence is particularly rare for pancreatic ductal adenocarcinoma (PDAC). The interaction between tumor and microenvironment may induce an immune response in which both innate and acquired immunity have been found to be implicated. An immunogenic tumor may promote antigen presentation and effector T cell activity, leading to cancer cell death and tumor inhibition.

Case:
We present the case of a 57-year-old man diagnosed three years ago with a borderline-resectable PDAC confirmed by biopsy. The patient received first-line 5-fluorouracil-based chemotherapy with progression of disease including new hepatic metastases. He then received twelve cycles of gemcitabine and nab-paclitaxel with successful reduction in the number and size of liver metastases. Upon patient request, a treatment holiday was initiated, during which his abdominal imaging showed continued tumor regression. After eleven months without any systemic therapy, there are no remaining metastases in the liver, and the primary pancreatic mass continues to recede. He currently remains on surveillance.

Conclusion:
Our patient’s rare clinical course raises questions including the optimal next steps in treatment, such as continued observation or local treatment such as surgical resection. The decision to continue observation results from our belief that minimal disruption of the tumor microenvironment (TME) may allow for continued control and cancer regression. More laboratory and clinical studies are imperative to understanding the physiological basis of sustained tumor regression after chemotherapy discontinuation and may impact real-world clinical decision-making. Additionally, the definition of spontaneous tumor regression may need revision to distinguish between prolonged therapeutic response and regression due to immunogenic features in the absence of prior therapy.
DOI: 10.6084/m9.figshare.30499853.v1
title: Supplementary Material for: Continuous regression of metastatic pancreatic adenocarcinoma after suspending chemotherapy: a case report.

description: Background:
Regression of malignancy in the absence of cancer-directed therapy is an uncommon and poorly understood phenomenon. Its occurrence is particularly rare for pancreatic ductal adenocarcinoma (PDAC). The interaction between tumor and microenvironment may induce an immune response in which both innate and acquired immunity have been found to be implicated. An immunogenic tumor may promote antigen presentation and effector T cell activity, leading to cancer cell death and tumor inhibition.

Case:
We present the case of a 57-year-old man diagnosed three years ago with a borderline-resectable PDAC confirmed by biopsy. The patient received first-line 5-fluorouracil-based chemotherapy with progression of disease including new hepatic metastases. He then received twelve cycles of gemcitabine and nab-paclitaxel with successful reduction in the number and size of liver metastases. Upon patient request, a treatment holiday was initiated, during which his abdominal imaging showed continued tumor regression. After eleven months without any systemic therapy, there are no remaining metastases in the liver, and the primary pancreatic mass continues to recede. He currently remains on surveillance.

Conclusion:
Our patient’s rare clinical course raises questions including the optimal next steps in treatment, such as continued observation or local treatment such as surgical resection. The decision to continue observation results from our belief that minimal disruption of the tumor microenvironment (TME) may allow for continued control and cancer regression. More laboratory and clinical studies are imperative to understanding the physiological basis of sustained tumor regression after chemotherapy discontinuation and may impact real-world clinical decision-making. Additionally, the definition of spontaneous tumor regression may need revision to distinguish between prolonged therapeutic response and regression due to immunogenic features in the absence of prior therapy.
DOI: 10.6075/j05m657p
title: CIL: 51959, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6084/m9.figshare.30499856
title: Supplementary Material for: Combined Extracorporeal Therapy with Pathogen Hemoadsorption and Cell-Directed Immunomodulation Strategies: A Two-Case Series

description: BACKGROUND: Sepsis remains a critical global health issue, causing multiple organ failure and high mortality rates, despite advances in antimicrobial therapies and supportive care. Extracorporeal blood purification (EBP) techniques have emerged as promising adjunctive strategies for the management of severe infections. The Seraph® 100 Microbind® Affinity Blood Filter (Seraph 100, ExThera Medical, Martinez, CA) targets pathogens, while the Selective Cytopheretic Device (SCD, SeaStar Medical, Denver, CO) neutralizes activated leukocytes. Although individually validated, evidence of the combined use of Seraph 100 and SCD remains scarce. 
CASE SUMMARY: We present two cases that illustrate the combined use of Seraph 100 and SCD. The first case involves a 43-year-old woman with bacterial pneumonia, septic shock, and acute kidney injury (AKI). She underwent Seraph 100 hemoperfusion followed by SCD therapy, which improved her hemodynamics, oxygenation, and renal function, ultimately leading to full recovery. The second case involved a 31-year-old man with Influenza, severe hypoxemia, and multiorgan failure. Despite advanced therapies, including veno-arterial venous ECMO (VAV-ECMO), Seraph 100, and SCD, his condition deteriorated, resulting in multiorgan failure and eventual death. 
CONCLUSION: These cases highlight the potential benefits and challenges of combining EBP, such as Seraph 100 and SCD. While successful in one case, the fatal outcome in the second underscores the importance of optimal patient selection, timing, and therapeutic strategies. Further research is needed to evaluate the efficacy of combined EBP and to identify approaches for improving outcomes in critically ill patients.
DOI: 10.6084/m9.figshare.30499856.v1
title: Supplementary Material for: Combined Extracorporeal Therapy with Pathogen Hemoadsorption and Cell-Directed Immunomodulation Strategies: A Two-Case Series

description: BACKGROUND: Sepsis remains a critical global health issue, causing multiple organ failure and high mortality rates, despite advances in antimicrobial therapies and supportive care. Extracorporeal blood purification (EBP) techniques have emerged as promising adjunctive strategies for the management of severe infections. The Seraph® 100 Microbind® Affinity Blood Filter (Seraph 100, ExThera Medical, Martinez, CA) targets pathogens, while the Selective Cytopheretic Device (SCD, SeaStar Medical, Denver, CO) neutralizes activated leukocytes. Although individually validated, evidence of the combined use of Seraph 100 and SCD remains scarce. 
CASE SUMMARY: We present two cases that illustrate the combined use of Seraph 100 and SCD. The first case involves a 43-year-old woman with bacterial pneumonia, septic shock, and acute kidney injury (AKI). She underwent Seraph 100 hemoperfusion followed by SCD therapy, which improved her hemodynamics, oxygenation, and renal function, ultimately leading to full recovery. The second case involved a 31-year-old man with Influenza, severe hypoxemia, and multiorgan failure. Despite advanced therapies, including veno-arterial venous ECMO (VAV-ECMO), Seraph 100, and SCD, his condition deteriorated, resulting in multiorgan failure and eventual death. 
CONCLUSION: These cases highlight the potential benefits and challenges of combining EBP, such as Seraph 100 and SCD. While successful in one case, the fatal outcome in the second underscores the importance of optimal patient selection, timing, and therapeutic strategies. Further research is needed to evaluate the efficacy of combined EBP and to identify approaches for improving outcomes in critically ill patients.