cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25422640
title: <b>Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures</b>

description: <b>Background</b><b>：</b>T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current prediction algorithms for tumor neoantigens are not reliable and many tumor neoantigens are derive from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently need.<b>Methods</b><b>：</b>In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulating of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot (ELISPOT) assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxic of TCRs were confirmed by transferring to primary peripheral blood T cells.<b>Results: </b>The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumors, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner.<b>Conclusions: </b>The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes (TILs) of patients with colorectal cancer (CRC), and tumor-specific TCRs can potentially be used for personalized TCR-Ts therapy.
DOI: 10.6084/m9.figshare.25422640.v1
title: <b>Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures</b>

description: <b>Background</b><b>：</b>T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current prediction algorithms for tumor neoantigens are not reliable and many tumor neoantigens are derive from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently need.<b>Methods</b><b>：</b>In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulating of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot (ELISPOT) assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxic of TCRs were confirmed by transferring to primary peripheral blood T cells.<b>Results: </b>The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumors, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner.<b>Conclusions: </b>The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes (TILs) of patients with colorectal cancer (CRC), and tumor-specific TCRs can potentially be used for personalized TCR-Ts therapy.
DOI: 10.34740/kaggle/dsv/7857677
title: Egypt Gold Prices | Daily Updated
DOI: 10.5281/zenodo.6905331
title: N20EM dataset for multimodal lyric transcription

description: N20EM dataset for multimodal lyric transcription, proposed in our ACM MM 2022 paper, MM-ALT: A Multimodal Automatic Lyric Transcription System. This dataset contains recordings of three modalities: audio, video, and IMU motion signal. 

Our paper's camera ready version: https://arxiv.org/abs/2207.06127

Project website: https://n20em.github.io/

Note: 



Once you download the dataset, we assume you have read and agreed with the Terms and Conditions.

Commercial usage is strictly prohibited.


Please cite our work as:

@inproceedings{gu2022mm,  title={MM-ALT: A multimodal automatic lyric transcription system},  author={Gu, Xiangming and Ou, Longshen and Ong, Danielle and Wang, Ye},  booktitle={Proceedings of the 30th ACM International Conference on Multimedia},  pages={3328--3337},  year={2022} }

 
description: Add data for VAD training and accompaniment of each utterance.
DOI: 10.5281/zenodo.7545968
title: N20EM dataset for multimodal lyric transcription

description: N20EM dataset for multimodal lyric transcription, proposed in our ACM MM 2022 paper, MM-ALT: A Multimodal Automatic Lyric Transcription System. This dataset contains recordings of three modalities: audio, video, and IMU motion signal. 

Our paper's camera ready version: https://arxiv.org/abs/2207.06127

Project website: https://n20em.github.io/

Note: 



Once you download the dataset, we assume you have read and agreed with the Terms and Conditions.

Commercial usage is strictly prohibited.


Please cite our work as:

@inproceedings{gu2022mm,  title={MM-ALT: A multimodal automatic lyric transcription system},  author={Gu, Xiangming and Ou, Longshen and Ong, Danielle and Wang, Ye},  booktitle={Proceedings of the 30th ACM International Conference on Multimedia},  pages={3328--3337},  year={2022} }

 
description: Add data for VAD training and accompaniment of each utterance.
DOI: 10.5281/zenodo.10824455
title: Optimised geometries of a number of protonation models.

description: Optimised geometries in pdb format presented in Fig.S12 of "A novel subgroup of light-driven sodium pumps with an additional Schiff base counterion" paper (https://doi.org/10.1101/2023.10.11.561842).
DOI: 10.5281/zenodo.10824456
title: Optimised geometries of a number of protonation models.

description: Optimised geometries in pdb format presented in Fig.S12 of "A novel subgroup of light-driven sodium pumps with an additional Schiff base counterion" paper (https://doi.org/10.1101/2023.10.11.561842).
DOI: 10.34740/kaggle/dsv/7857868
title: AutoXGB
DOI: 10.34740/kaggle/dsv/7857869
title: OnlineFree
DOI: 10.6084/m9.figshare.25415851.v1
title: Helmet and Reflective Clothing Dataset

description: The dataset comprises 6680 images and 35166 labels across four categories: 'head', 'helmet', 'other_clothes', and 'reflective_clothes'. The 'head' category has 4899 tags, 'helmet' has 15022 tags, 'other_clothes' has 9903 tags, and 'reflective_clothes' has 5352 tags.
DOI: 10.34740/kaggle/dsv/7857859
title: LUFlow Network Intrusion Detection Data Set
DOI: 10.5281/zenodo.10511307
title: Raw data and statistical analysis

description: Supplementary data for https://doi.org/10.1084/jem.20221190
DOI: 10.5281/zenodo.10511308
title: Raw data and statistical analysis
DOI: 10.6084/m9.figshare.25422700
title: Supplementary Material for: De novo Inflammatory Bowel Disease in Kidney Transplant Recipients: A Single-center case series study

description: Introduction 
Gastrointestinal complications are common after solid organ transplantation. New-onset inflammatory bowel disease (IBD) after transplantation (de novo) is a major differential diagnosis of diarrhea after liver transplantation (LT) because of its high incidence in the field. However, the incidence of IBD after kidney transplantation (KT) remains unknown.
Methods
This case series comprised six de novo IBD patients who had undergone KT at our hospital from April 1998 to December 2020. In this period, 232 KT recipients were identified. Participants were analyzed based on their colonoscopy diagnoses. Detailed clinical information regarding both KT- and IBD-related symptoms or outcomes was obtained, and we calculated the incidence of de novo IBD from the date of KT. 
Results
Of the 232 recipients in the median observation period of 6.1 (interquartile range: 2.6, 10.8) years, six recipients (one with Crohn’s disease and five with ulcerative colitis) were diagnosed with de novo IBD. The incidence of de novo IBD after KT was 355.8/100,000 person-years (95% confidence interval [CI], 159.8–791.9 per 100,000 person-years). Bloody stools and diarrhea did not always occur, with bloody stools occurring in three and diarrhea in two patients at the time of diagnosis. No recipient developed graft failure or extraintestinal complications (e.g., IBD-related nephritis or arthritis).
Conclusion
Despite a small sample size, this study’s results indicate that the incidence of de novo IBD after KT may be similar to that after LT and higher than that in the general population. Larger studies are required to validate these preliminary findings.
DOI: 10.6084/m9.figshare.25422700.v1
title: Supplementary Material for: De novo Inflammatory Bowel Disease in Kidney Transplant Recipients: A Single-center case series study

description: Introduction 
Gastrointestinal complications are common after solid organ transplantation. New-onset inflammatory bowel disease (IBD) after transplantation (de novo) is a major differential diagnosis of diarrhea after liver transplantation (LT) because of its high incidence in the field. However, the incidence of IBD after kidney transplantation (KT) remains unknown.
Methods
This case series comprised six de novo IBD patients who had undergone KT at our hospital from April 1998 to December 2020. In this period, 232 KT recipients were identified. Participants were analyzed based on their colonoscopy diagnoses. Detailed clinical information regarding both KT- and IBD-related symptoms or outcomes was obtained, and we calculated the incidence of de novo IBD from the date of KT. 
Results
Of the 232 recipients in the median observation period of 6.1 (interquartile range: 2.6, 10.8) years, six recipients (one with Crohn’s disease and five with ulcerative colitis) were diagnosed with de novo IBD. The incidence of de novo IBD after KT was 355.8/100,000 person-years (95% confidence interval [CI], 159.8–791.9 per 100,000 person-years). Bloody stools and diarrhea did not always occur, with bloody stools occurring in three and diarrhea in two patients at the time of diagnosis. No recipient developed graft failure or extraintestinal complications (e.g., IBD-related nephritis or arthritis).
Conclusion
Despite a small sample size, this study’s results indicate that the incidence of de novo IBD after KT may be similar to that after LT and higher than that in the general population. Larger studies are required to validate these preliminary findings.
DOI: 10.6084/m9.figshare.25422701
title: Raw_data_for_figures from Individualistic attitudes in iterative Prisoner’s Dilemma undermine evolutionary fitness and may drive cooperative human players to extinction

description: Contains all the raw numerical estimates to generate the figures.
DOI: 10.6084/m9.figshare.25422701.v1
title: Raw_data_for_figures from Individualistic attitudes in iterative Prisoner’s Dilemma undermine evolutionary fitness and may drive cooperative human players to extinction

description: Contains all the raw numerical estimates to generate the figures.
DOI: 10.6084/m9.figshare.25422721
title: 2016-2020-Dajiuhu peatland-CO2 flux.xlsx

description: The contents of the dataset are the CO2 flux data and environmental factor data of the Dajiu Lake peatland in Shennongjia from 2016 to 2020. The raw data was collected through the LI-7500 Open circuit infrared CO2/H2O gas analyzer ( Licor,USA). The dataset uploaded this time is data that has been processed by the software EddyPro and Tovi (Licor,USA). NEE, Reco, and GEP are the three forms of CO2 fluxes, which are software-process data. The purpose of collecting these data was to explore the carbon source and sink function and carbon flux drivers of the Dajiuhu peatland.<br>
DOI: 10.1285/i20398573v8n1p15
title: Powered by caring: daily struggles to keep the WPS Agenda alive. Interview with Sanam Naraghi-Anderlini

description: The interview originated from the encounter between the Guest Editors and Sanam Naraghi-Anderlini during the activities of the project "Enhancing Women's Participation in Peace and Security (WEPPS)". The interview was held via Zoom on the afternoon of October 1, 2021. At the time, the international community was dealing with the consequences of the sudden US withdrawal from Afghanistan that occurred on August 31.
DOI: 10.17632/2vrnwk3p4r.1
title: Medjool dates images with two synchronized cameras

description: Medjool dates are primum dates which require thinning. Two synchronized sets of 87 of Medjool date fruit-bunch images were taken as part of a large-scale project for developing a robotic Medjool thinning system. The images were taken in May (during the thinning period) 2021 in the Southern Arava R&D date farm (Israel). The images were acquired with two digital single-lens reflex (DSLR) cameras (NIKON D5600, USA) (camera 1 and 2) with a resolution of 4000×6000 pixels. Each pair of images from each camera with the same serial number, were taken simultaneously. Camera 1 was located 15 cm to the left and 15 cm above Camera 2. The resolution of the original images was reduced to 1024X1024. The Medjool bunches and the bunch sub parts (rachis and spikelets) were manually annotated. In the annotated image mask files, each mask is a 1024×1024×N matrix (where N is the number of ground truth instances of bunches or twice this number for the spikelets and rachises, in the image) so that each instance is documented in a separate 1024×1024×1 binary mask. In the sub-bunch annotation, the masks are sequentially ordered such that a mask of the rachis follows the mask of the spikelets. The database includes six files: cam1Img.zip and cam2Img.zip – The image files with 4000×6000 resolution. cam1MasksBunch.zip and cam2MasksBunch.zip - Ground truth masks for the fruit bunch manually annotated for all the fruit-bunches in each image in npy format. cam1Masks.zip and cam2Masks.zip - Ground truth masks for two sub-bunch part classes (spikelets and rachis) manually annotated for all the fruit-bunches in each image in npy format.
DOI: 10.17632/k7xk2nwgrh.1
title: Medjoul-date images - annotated

description: images.zip - 146 images of fruit-bunches from 13 Medjoul date palms. The images were taken in 2019 from two Medjoul farms in the Southern Arava region of Israel during the beginning and middle of the thinning period. The images were acquired with a digital single-lens reflex (DSLR) camera (NIKON D5600, USA) with a resolution of 4000×6000 pixels. masks_npz_2cl.zip - Ground truth masks for two classes (spikelets and rachis) manually annotated for all the fruit-bunches in each image in npz format. Each mask is a 4000×6000×N matrix (where N is the number of ground truth instances of spikelets and rachises, in the image) so that each instance is documented in a separate 4000×6000×1 binary mask. The masks are sequentially ordered such that a mask of the rachis follows the mask of the spikelets. An empty mask is defined in case the rachis was not visible (spikelets were always visible). When using this data please cite: Tal Shoshan, Avital Bechar, Yuval Cohen, Avraham Sadowsky, Sigal Berman, Segmentation and motion parameter estimation for robotic Medjoul-date thinning
DOI: 10.3886/e199007
title: The shifting landscape of private healthcare providers before and during the COVID-19 pandemic and the potential impacts on tuberculosis care in Bandung, Indonesia

description: COVID-19
pandemic changed many aspects of healthcare services and deliveries, including among
private healthcare providers (i.e., private healthcare facilities [HCFs] and
private practitioners [PPs]). We aimed to compare the spatial distribution of private
providers and describe changes in characteristics and services offered during and
before the COVID-19 pandemic, and explore its potential impact on tuberculosis
care. We conducted a cross-sectional survey in 36 randomly
selected community health centers areas (locally referred to as Puskesmas) in Bandung, Indonesia, during the
COVID-19 pandemic from April – December 2021. Data pertaining to before the COVID-19
pandemic was abstracted from a similar survey conducted in 2017 (i.e., INSTEP
study). We obtained latitude and longitude coordinates
of private healthcare providers and then compared the geographical spread with
data collected for INSTEP study. We also compared characteristics of, and
services provided by private healthcare providers interviewed during the COVID-19
pandemic with those previously interviewed for INSTEP study. Differences were summarized
using descriptive
and bivariate analyses.
During the study period,
we surveyed 367 private HCFs and interviewed 637 PPs. Compared to INSTEP study data,
the number of operating HCFs was reduced by 3% during the COVID-19 pandemic (401
vs. 412 before COVID-19), although we
observed increases in laboratory service (37.8% increase), x-ray service (66.7%
increase), and pharmacy (18.1% increase). Among a subset of private HCFs
managing patients with respiratory tract infection symptoms, a quarter (60/235,
25.3%) indicated that they had to close their facilities in response to the emerging
situation during the COVID-19 pandemic. For PPs, the number of practicing PPs
was reduced by 7% during the COVID-19 pandemic (872 vs. 936 before COVID-19). Interestingly,
the number of practicing PPs encountering patients with TB disease increased during
the COVID-19 pandemic (42.9% vs. 35.7% before COVID-19, p=0.008). This study confirmed that
the COVID-19 pandemic adversely impacted health care service deliveries in private
sectors, largely marked by closures and shortened business hours. However, the
increased service capacities (laboratory and pharmacy), as well as significant
increase in the number of patients cared for TB disease by PPs during the COVID-19
pandemic, made a more compelling case to further the implementation of public-private
mix model for TB care in Indonesia.
description: We used convenience sampling method to select
individuals working in private healthcare facilities to be surveyed in the
present study. Clinic managers, clinic owners, doctor(s) in charge, general practitioners,
or other clinic staff were eligible to be interviewed for the mapping survey.
For the providers survey, eligible study participants included GPs and
specialists.
description: face-to-face interview; on-site questionnaire; paper and pencil interview (PAPI);
DOI: 10.6084/m9.figshare.25422769
title: Study on the impact of kinesiophobia after Total knee replacement on the rehabilitation of patients during hospitalization.xlsx

description: Kinesiophobia following knee replacement surgery significantly impacts patients' ability to engage in postoperative rehabilitation exercises. However, research on this topic is relatively new in China. Current efforts to identify and address kinesiophobia are not yet comprehensive. Our team focused on a subset of patients who had undergone unilateral knee replacement for our study. We first identified patients experiencing kinesiphobia and then compared the rehabilitation progress of patients with and without kinesiophobia during their hospital stay. This comparison included assessing pain levels, knee flexion at various postoperative time points, and milestones such as getting out of bed for the first time and completing the 2-minute walk test on the day of discharge. This pioneering research in China aims to bridge existing gaps in knowledge and may serve as a valuable foundation for future interventional studies.
DOI: 10.6084/m9.figshare.25422793
title: <b>Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures</b>

description: <b>Background</b><b>：</b>T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current prediction algorithms for tumor neoantigens are not reliable and many tumor neoantigens are derive from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently need.<b>Methods</b><b>：</b>In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulating of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot (ELISPOT) assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxic of TCRs were confirmed by transferring to primary peripheral blood T cells.<b>Results: </b>The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumors, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner.<b>Conclusions: </b>The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes (TILs) of patients with colorectal cancer (CRC), and tumor-specific TCRs can potentially be used for personalized TCR-Ts therapy.
DOI: 10.5281/zenodo.10824516
title: uiPSF datasets for Figure 5

description: Fig5_dataset

 Field-dependent aberrations imaging of NPC 



Bead data (Fig.5a-c): 



astigmatism_beads_2um_10nm_1608x1608_prime95B_1



Cell data (Fig.5a,Fig.5d-l):



NUP96_SNP647_astigmatism_3D_1608_15ms_hama_mm_1800mW_2
DOI: 10.5281/zenodo.10824517
title: uiPSF datasets for Figure 5

description: Fig5_dataset

 Field-dependent aberrations imaging of NPC 



Bead data (Fig.5a-c): 



astigmatism_beads_2um_10nm_1608x1608_prime95B_1



Cell data (Fig.5a,Fig.5d-l):



NUP96_SNP647_astigmatism_3D_1608_15ms_hama_mm_1800mW_2
DOI: 10.6084/m9.figshare.25406197
title: Elsafty_RBCs_Slide_15

description: Each one of (Elsafty_RBCs_Slide_1-25) contains the field images/patches of a specific slide/patient. The names of the patches start with the respective slide/patient number, followed by the unique patch/field number. There is a total of 47,363 patches with 1076x535 pixels size from the 25 slides/patients, the counts of patches per slide/patient are as follows: 1690, 1709, 2697, 2400, 1905, 1803, 2964, 3049, 2464, 2080, 1894, 1852, 2590, 2263, 3328, 983, 1066, 935, 1131, 1237, 1874, 1393, 1277, 1199, and 1580.