cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7049035
title: Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

description: In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.
description: RNA Seq data for no antibiotic samples: C. difficile in fresh media (CD_ABB), C. difficile in D. piger spent media (CD_DPSM), and C. difficile in coculture with D. piger (CD_DP).
DOI: 10.5281/zenodo.7049034
title: Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

description: In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.
description: RNA Seq data for no antibiotic samples: C. difficile in fresh media (CD_ABB), C. difficile in D. piger spent media (CD_DPSM), and C. difficile in coculture with D. piger (CD_DP).
DOI: 10.25582/data.2022-03.2453100/1936188
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453044/1936217
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453132/1936220
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452987/1936234
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453484/1936321
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453070/1936357
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453164/1936400
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453349/1936404
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453117/1936438
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453334/1937203
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453412/1937270
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453380/1937276
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452880/1937285
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453085/1937288
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453055/1937289
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453460/1937324
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452897/1937329
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452865/1937344
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453087/1937363
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453159/1937367
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453393/1937408
title: Data for EMSL Project 51132 from March 2022
DOI: 10.5281/zenodo.7049027
title: Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

description: In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.
description: RNA Seq data for metronidazole (MTZ) samples: C. difficile in fresh media (CD_ABB), C. difficile in D. piger spent media (CD_DPSM), and C. difficile in coculture with D. piger (CD_DP).
DOI: 10.5281/zenodo.7049026
title: Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

description: In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.
description: RNA Seq data for metronidazole (MTZ) samples: C. difficile in fresh media (CD_ABB), C. difficile in D. piger spent media (CD_DPSM), and C. difficile in coculture with D. piger (CD_DP).
DOI: 10.25582/data.2022-03.2453134/1937411
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453080/1937412
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453496/1937460
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453509/1937507
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453146/1937531
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453072/1937532
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453414/1937554
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453065/1937578
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453499/1937599
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453123/1937610
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453358/1937620
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453383/1938037
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453406/1938070
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453149/1938090
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452990/1938093
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453073/1938095
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453424/1938100
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453139/1938178
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453515/1938203
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453396/1938207
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453370/1938244
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453154/1938279
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453410/1938297
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453408/1938306
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453392/1938380
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453148/1939075
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453092/1939098
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453094/1939107
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453158/1939139
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453367/1939159
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452930/1939186
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452997/1939209
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453068/1939222
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453022/1939253
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453135/1939303
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453035/1939325
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453077/1939342
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453016/1939356
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453038/1939377
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453032/1939389
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453125/1939398
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452888/1939451
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453153/1940133
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453102/1940135
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453078/1940187
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453155/1940195
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453114/1940205
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453514/1940249
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453398/1940252
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453053/1940256
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453122/1940266
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452861/1941086
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453019/1941119
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453056/1941148
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2452968/1941157
title: Data for EMSL Project 51132 from March 2022
DOI: 10.25582/data.2022-03.2453395/1941175
title: Data for EMSL Project 51132 from March 2022
DOI: 10.6084/m9.figshare.22260061
title: Impact of NOTCH1 polymorphisms on liver cancer in a Chinese Han population

description: We enrolled 709 LC patients and 708 healthy controls. Genotyping of <em>NOTCH1</em> rs10521, rs2229971, and rs4489420 was determined through the Agena MassARRAY system.
DOI: 10.6084/m9.figshare.22260061.v2
title: Impact of NOTCH1 polymorphisms on liver cancer in a Chinese Han population

description: We enrolled 709 LC patients and 708 healthy controls. Genotyping of <em>NOTCH1</em> rs10521, rs2229971, and rs4489420 was determined through the Agena MassARRAY system.
DOI: 10.6084/m9.figshare.22260061.v1
title: Impact of NOTCH1 polymorphisms on liver cancer in a Chinese Han population

description: We enrolled 709 LC patients and 708 healthy controls. Genotyping of <em>NOTCH1</em> rs10521, rs2229971, and rs4489420 was determined through the Agena MassARRAY system.
DOI: 10.5281/zenodo.7726490
title: Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

description: In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.
description: Modelling computer scripts and required input data/parameters
DOI: 10.5281/zenodo.7726489
title: Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

description: In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.
description: Modelling computer scripts and required input data/parameters
DOI: 10.5281/zenodo.7726499
title: Spatiotemporal dissolution of calcite grain column packs

description: The binarized reference data from time-lapse high-resolution X-ray CT imaging of live flow experiments and effluent pH and TDS logs are stored here. Data post-processing and analysis were conducted using a commercial software Avizo - details if which are described in the methods and results sections of the companion manuscript.
DOI: 10.5517/ccdc.csd.cc2c2s7h
title: CCDC 2177416: Experimental Crystal Structure Determination

description: Related Article: Lifen Peng, Yanting Zhao, Yasuhiro Okuda, Liyuan Le, Zilong Tang, Shuang-Feng Yin, Renhua Qiu, Akihiro Orita|2023|J.Org.Chem.|88|3089|doi:10.1021/acs.joc.2c02876
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.cc2c2s8j
title: CCDC 2177417: Experimental Crystal Structure Determination

description: Related Article: Lifen Peng, Yanting Zhao, Yasuhiro Okuda, Liyuan Le, Zilong Tang, Shuang-Feng Yin, Renhua Qiu, Akihiro Orita|2023|J.Org.Chem.|88|3089|doi:10.1021/acs.joc.2c02876
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.cc2c2s9k
title: CCDC 2177418: Experimental Crystal Structure Determination

description: Related Article: Lifen Peng, Yanting Zhao, Yasuhiro Okuda, Liyuan Le, Zilong Tang, Shuang-Feng Yin, Renhua Qiu, Akihiro Orita|2023|J.Org.Chem.|88|3089|doi:10.1021/acs.joc.2c02876
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: 10.5281/zenodo.7726498
title: Spatiotemporal dissolution of calcite grain column packs

description: The binarized reference data from time-lapse high-resolution X-ray CT imaging of live flow experiments and effluent pH and TDS logs are stored here. Data post-processing and analysis were conducted using a commercial software Avizo - details if which are described in the methods and results sections of the companion manuscript.
DOI: 10.5517/ccdc.csd.cc2cz9m9
title: CCDC 2203871: Experimental Crystal Structure Determination

description: Related Article: Qiang Chen, Tingzhong Huang, Ying Shao, Shengbiao Tang, Jiangtao Sun|2023|J.Org.Chem.|88|3308|doi:10.1021/acs.joc.2c02730
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.cc2d7t3l
title: CCDC 2212039: Experimental Crystal Structure Determination

description: Related Article: Qiang Chen, Tingzhong Huang, Ying Shao, Shengbiao Tang, Jiangtao Sun|2023|J.Org.Chem.|88|3308|doi:10.1021/acs.joc.2c02730
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: 10.3886/e114798v1-133840
title: Replication data for: Discrimination in Grading

description: We report the results of an experiment that was designed to test for discrimination in grading in India. We recruited teachers to grade exams. We randomly assigned child "characteristics" (age, gender, and caste) to the cover sheets of the exams to ensure that there is no relationship between these observed characteristics and the exam quality. We find that teachers give exams that are assigned to be lower caste scores that are about 0.03 to 0.08 standard deviations lower than those that are assigned to be high caste. The teachers' behavior appears consistent with statistical discrimination. (JEL I21, J13, O15, O17, Z13)
DOI: 10.6084/m9.figshare.22259941
title: Characteristic remanent magnetization component

description: High-temperature characteristic remanent magnetization component and low-temperature characteristic remanent magnetization component obtained within the Simao basin <br>
DOI: 10.6084/m9.figshare.22259941.v2
title: Characteristic remanent magnetization component

description: High-temperature characteristic remanent magnetization component and low-temperature characteristic remanent magnetization component obtained within the Simao basin <br>
DOI: 10.6084/m9.figshare.22259941.v1
title: Characteristic remanent magnetization component

description: High-temperature characteristic remanent magnetization component and low-temperature characteristic remanent magnetization component obtained within the Simao basin <br>