cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10642388
title: Supporting data for: Crystal Structure Generation with Autoregressive Large Language Modeling

description: The generation of plausible crystal structures is often an important step in the computational prediction of crystal structures from composition. Here, we introduce a methodology for crystal structure generation involving autoregressive large language modeling of the Crystallographic Information File (CIF) format. Our model, CrystaLLM, is trained on a comprehensive dataset of millions of CIF files, and is capable of reliably generating correct CIF syntax and plausible crystal structures for many classes of inorganic compounds. Moreover, we provide general and open access to the model by deploying it as a web application, available to anyone over the internet. Our results indicate that the model promises to be a reliable and efficient tool for both crystallography and materials informatics.
DOI: 10.5281/zenodo.10124588
title: AutoWCEBleedGen-Test Dataset (Improved)

description: AutoWCEBleedGen-Test dataset (Improved)  is a part of the AutoWCEBleedGen Challenge version v2 organized by MISAHUB in collaboration with ICIP 2024.  This improved version includes medically annotated bounding boxes in three different formats (txt, XML and YOLO txt). Sample excel sheet and pdf file for result submission has also been included. Participants are strictly adviced to follow the submission guidelines.

For more details : https://misahub.in/ICIP/index.html
DOI: 10.5281/zenodo.10124589
title: AutoWCEBleedGen-Test Dataset

description: AutoWCEBleedGen-Test dataset is an independently collected WCE data containing bleeding and non-bleeding frames of more than 30 patients suffering from acute, chronic and occult GI bleeding referred at Department of Gastroenterology and HNU, All India Institute of Medical Sciences, New Delhi, India. This dataset was a part of the AutoWCEBleedGen Challenge organized by MISAHUB in collaboration with CVIP 2023. An Improved version of this dataset has also been included. 
For more details : https://misahub.in/CVIP/challenge.html
DOI: 10.5281/zenodo.10642779
title: AutoWCEBleedGen-Test Dataset (Improved)

description: AutoWCEBleedGen-Test dataset (Improved)  is a part of the AutoWCEBleedGen Challenge version v2 organized by MISAHUB in collaboration with ICIP 2024.  This improved version includes medically annotated bounding boxes in three different formats (txt, XML and YOLO txt). Sample excel sheet and pdf file for result submission has also been included. Participants are strictly adviced to follow the submission guidelines.

For more details : https://misahub.in/ICIP/index.html
DOI: 10.6084/m9.figshare.25200818
title: Supplementary Material for: Durable Response to PD-1 Directed Antibodies in Hypermutated Triple Negative Breast Cancer, A Case Report

description: Recent clinical trials have demonstrated the success of Pembrolizumab (Keytruda ™) in combination with chemotherapy against triple-negative breast cancer. Here, we report the case of a 65-year-old Native American and African American woman with incomplete lines of pretreatment diagnosed with recurrent triple-negative breast cancer (TNBC) and pulmonary metastases. Next-generation sequencing of the metastatic nodules demonstrated a significantly hypermutated tumor with rare polyploidy. The patient had a durable (14 months) and ongoing remission of the metastatic lesions after administering Programmed cell death1 (PD-1) inhibitor Pembrolizumab. No serious immune checkpoint inhibitor-related toxicities or worsening of the infection were observed during the treatment. Our report describes recurrent TNBC with a rare amount of hypermutation and the successful use of an immune-oncologic agent as a treatment.
DOI: 10.6084/m9.figshare.25200818.v1
title: Supplementary Material for: Durable Response to PD-1 Directed Antibodies in Hypermutated Triple Negative Breast Cancer, A Case Report

description: Recent clinical trials have demonstrated the success of Pembrolizumab (Keytruda ™) in combination with chemotherapy against triple-negative breast cancer. Here, we report the case of a 65-year-old Native American and African American woman with incomplete lines of pretreatment diagnosed with recurrent triple-negative breast cancer (TNBC) and pulmonary metastases. Next-generation sequencing of the metastatic nodules demonstrated a significantly hypermutated tumor with rare polyploidy. The patient had a durable (14 months) and ongoing remission of the metastatic lesions after administering Programmed cell death1 (PD-1) inhibitor Pembrolizumab. No serious immune checkpoint inhibitor-related toxicities or worsening of the infection were observed during the treatment. Our report describes recurrent TNBC with a rare amount of hypermutation and the successful use of an immune-oncologic agent as a treatment.
DOI: 10.5517/ccdc.csd.cc2j56zx
title: CCDC 2328719: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold and James A.Golen|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j570z
title: CCDC 2328720: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold and James A.Golen|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j6lhv
title: CCDC 2330037: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, J.D. Kennedy, D. Cundy, R.D. Kennedy, N.J. Bullen|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2j6lkx
title: CCDC 2330039: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, J.D. Kennedy, D. Cundy, R.D. Kennedy, N.J. Bullen|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.25200845.v1
title: Supplementary Material for: A case of long-term survival with recurrent liver metastases from gastric cancer treated with nivolumab

description: Introduction: Improvements in overall survival from advanced gastric cancer have recently been reported with nivolumab. However, few reports have described long-term survival after discontinuing treatment. Case presentation: A 67-year-old man diagnosed with advanced gastric cancer and abdominal aortic aneurysm initially underwent distal gastrectomy with D2 dissection. Histological examination revealed tub2 and T2N1M0 stage IIA. One month later, endovascular aneurysm repair was performed. Six weeks after gastrectomy, adjuvant chemotherapy with S-1 was started. Six months later, liver metastases were identified and liver segments S1 and S7 were resected. S-1 and oxaliplatin were added postoperatively, but multiple liver metastases recurred. Paclitaxel and ramucirumab, irinotecan, and docetaxel were administered. Liver metastases showed a temporary reduction in size then enlarged again. Nivolumab was therefore administered and the liver metastases showed a significant reduction in size. The interval between doses gradually increased due to persistent general fatigue. At 28 months after starting nivolumab therapy, bronchitis and adrenal insufficiency appeared, so treatment was discontinued. As of 3.5 years after cessation of nivolumab immunotherapy, tumor regression continued to be maintained. The patient remains alive as of 8 years after recurrence of liver metastases. Conclusion: We encountered a case in which the patient received nivolumab therapy for recurrent liver metastases from gastric cancer and survived long-term after discontinuing treatment.
DOI: 10.6084/m9.figshare.25200845
title: Supplementary Material for: A case of long-term survival with recurrent liver metastases from gastric cancer treated with nivolumab

description: Introduction: Improvements in overall survival from advanced gastric cancer have recently been reported with nivolumab. However, few reports have described long-term survival after discontinuing treatment. Case presentation: A 67-year-old man diagnosed with advanced gastric cancer and abdominal aortic aneurysm initially underwent distal gastrectomy with D2 dissection. Histological examination revealed tub2 and T2N1M0 stage IIA. One month later, endovascular aneurysm repair was performed. Six weeks after gastrectomy, adjuvant chemotherapy with S-1 was started. Six months later, liver metastases were identified and liver segments S1 and S7 were resected. S-1 and oxaliplatin were added postoperatively, but multiple liver metastases recurred. Paclitaxel and ramucirumab, irinotecan, and docetaxel were administered. Liver metastases showed a temporary reduction in size then enlarged again. Nivolumab was therefore administered and the liver metastases showed a significant reduction in size. The interval between doses gradually increased due to persistent general fatigue. At 28 months after starting nivolumab therapy, bronchitis and adrenal insufficiency appeared, so treatment was discontinued. As of 3.5 years after cessation of nivolumab immunotherapy, tumor regression continued to be maintained. The patient remains alive as of 8 years after recurrence of liver metastases. Conclusion: We encountered a case in which the patient received nivolumab therapy for recurrent liver metastases from gastric cancer and survived long-term after discontinuing treatment.
DOI: 10.6084/m9.figshare.25200848
title: Supplementary Material for: Eicosanoids and oxylipin signature in HH patients are similar to DIOS patients but are impacted by dietary iron absorption.

description: Introduction: Oxylipins are mediators of oxidative stress. To characterize the underlying inflammatory processes and phenotype the effect of iron metabolism disorders, we investigated the oxylipin profile in hereditary hemochromatosis (HH) and dysmetabolic iron overload syndrome (DIOS) patients. 
Methods: LC-MS/MS based method to quantify plasma oxylipins in 20 HH and 20 DIOS patients in fasting conditions and 3 hours after an iron-rich meal in HH patients. 
Results: Principal component analysis showed no separation between HH and DIOS, suggesting that the clinical phenotype has no direct impact on oxylipin metabolism. 20-HETE was higher in DIOS and correlated with hypertension (p = 0.03). Different oxylipin signatures were observed in HH before and after the iron-rich meal. Discriminant oxylipins include epoxy fatty acids derived from docosahexaenoic acid and arachidonic acid as well as 13-HODE and 9-HODE. Mediation analysis found no major contribution of dietary iron absorption for 16/22 oxylipins significantly affected by the meal. 
Discussion: The oxylipin profiles of HH and DIOS seemed similar except for 20-HETE, possibly reflecting different hypertension prevalence between the two groups. Oxylipins were significantly affected by the iron-rich meal but the specific contribution of iron was not clear. Although iron may contribute to oxidative stress and inflammation in HH and DIOS, this does not seem to directly affect oxylipin metabolism.
DOI: 10.6084/m9.figshare.25200848.v1
title: Supplementary Material for: Eicosanoids and oxylipin signature in HH patients are similar to DIOS patients but are impacted by dietary iron absorption.

description: Introduction: Oxylipins are mediators of oxidative stress. To characterize the underlying inflammatory processes and phenotype the effect of iron metabolism disorders, we investigated the oxylipin profile in hereditary hemochromatosis (HH) and dysmetabolic iron overload syndrome (DIOS) patients. 
Methods: LC-MS/MS based method to quantify plasma oxylipins in 20 HH and 20 DIOS patients in fasting conditions and 3 hours after an iron-rich meal in HH patients. 
Results: Principal component analysis showed no separation between HH and DIOS, suggesting that the clinical phenotype has no direct impact on oxylipin metabolism. 20-HETE was higher in DIOS and correlated with hypertension (p = 0.03). Different oxylipin signatures were observed in HH before and after the iron-rich meal. Discriminant oxylipins include epoxy fatty acids derived from docosahexaenoic acid and arachidonic acid as well as 13-HODE and 9-HODE. Mediation analysis found no major contribution of dietary iron absorption for 16/22 oxylipins significantly affected by the meal. 
Discussion: The oxylipin profiles of HH and DIOS seemed similar except for 20-HETE, possibly reflecting different hypertension prevalence between the two groups. Oxylipins were significantly affected by the iron-rich meal but the specific contribution of iron was not clear. Although iron may contribute to oxidative stress and inflammation in HH and DIOS, this does not seem to directly affect oxylipin metabolism.
DOI: 10.15151/esrf-es-1304133457
title: NORWAY BAG

description: The fourteen PIs associated to this proposal represent the entire crystallography community in Norway and are affiliated to the major Norwegian universities. The research interests of the PIs and their collaborators revolves around topics linked to structural biology and material sciences.

We apply for beam time for single- and multi-wavelength MX, Bio-SAXS and Cryo-EM, in support of our research projects funded e.g. by the Research Council of Norway and the ERC. Examples of research projects or topics are carbohydrate-active proteins of medical or bioeconomic relevance, inhibition of DNA repair enzymes, metalloprotein function and catalysis, regulation of cell-cycle processes, enzyme discovery, antibiotic resistance/drug-discovery and neurological diseases.

Our overarching aim is to use bright synchrotron sources to produce high quality science.
DOI: 10.15151/esrf-es-1409466538
title: Munich Crystallography BAG

description: The diverse groups of the Munich Crystallography BAG study a far range of subjects, reaching from structural aspects of fundamental cellular processes - such as RNA processing, protein folding and degradation, DNA repair, chromatin remodelling, enzymes - to the design of foldamers. The research groups are located at the LMU and TUM universities in Munich, at the Max-Planck-Institute of Biochemistry, Martinsried, and the Helmholtz Center, Neuherberg. Out-groups are located at the universities in Darmstadt and Ulm, Germany. The research groups use X-ray crystallography, single-particle cryo-EM, SAXS, NMR and HDX and XL-MS mass-spectrometry for structural studies.
DOI: 10.15151/esrf-es-1413550764
title: IBS BAG

description: The IBS BAG includes in this proposal IBS teams and external groups from CEA-Cadarache (St Paul lez Durance) and IRBA (Brétigny-sur-Orge). We study structure-function relationships of proteins emphasizing in human health, biotechnology and methodology. Most of the projects are a continuation of the MX-2398 proposal and can be grouped into different topics as follows: host-pathogen interaction, new drug targets, fundamental cellular mechanisms, membrane proteins, biotechnological applications and methodology. Some of these projects use integrative approaches (X-ray crystallography, SAXS, NMR (and cryo-EM), together with other biophysical studies) with the aim to fully understand the complexity of the biological macromolecular systems on study.
DOI: 10.21227/h9vq-t415
title: Image data for MF-SFF 3D reconstruction

description: Structural analysis of minuscule height objects holds paramount significance in fields such as industrial manufacturing and medical testing. Currently, 3D reconstruction method based on shape from focus (SFF) has emerged as an efficacious approach for acquiring submicron-level height change information. A novel multi-field SFF(MF-SFF) framework incorporates pulse-controlled continuous acquisition methods and parallel chain processing (PCP) strategy, effectively addressing challenges associated with minuscule height objects. The MF-SFF framework not only accomplishes high-precision and rapid 3D reconstruction but also demonstrates robust adaptability. It overcomes issues related to the rapid collection and processing of massive image data during the 3D reconstruction of objects. This is a image dataset for 3D reconstruction based on MF-SFF.
DOI: 10.5517/ccdc.csd.cc23hb87
title: CCDC 1951148: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23hbcb
title: CCDC 1951151: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23hbdc
title: CCDC 1951152: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23hbfd
title: CCDC 1951153: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23hbgf
title: CCDC 1951154: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23hbhg
title: CCDC 1951155: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23hbjh
title: CCDC 1951156: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23hbkj
title: CCDC 1951157: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23hblk
title: CCDC 1951158: Experimental Crystal Structure Determination

description: Related Article: Nóra V. May, G. Tamás Gál, Tamás Holczbauer, Laura Bereczki, Valerio B. Di Marco, Petra Bombicz|2024|Cryst.Growth Des.|24|1096|doi:10.1021/acs.cgd.3c01118
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc24nlzd
title: CCDC 1986014: Experimental Crystal Structure Determination

description: Related Article: Le Guo, Wanrong Zhao, Yanpeng Gao, Meimei Wu, Shufeng Chen|2024|J.Org.Chem.|89|1956|doi:10.1021/acs.joc.3c02686
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.