cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2bzdwm
title: CCDC 2174181: Experimental Crystal Structure Determination

description: Related Article: Fabio Marchetti, Alessia Tombesi, Corrado Di Nicola, Riccardo Pettinari, Federico Verdicchio, Alessandra Crispini, Francesca Scarpelli, Cecilia Baldassarri, Elisa Marangoni, Anders Hofer, Agustín Galindo, Riccardo Petrelli|2022|Inorg.Chem.|61|13561|doi:10.1021/acs.inorgchem.2c02201
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.cc2b0h62
title: CCDC 2145423: Experimental Crystal Structure Determination

description: Related Article: Rishi R. Sapkota, Raj Kumar Tak, Vivek Aryal, Doleshwar Niroula, Nicholas C. Secosky, Roshan K. Dhungana, Ramesh Giri|2022|Org.Lett.|24|6213|doi:10.1021/acs.orglett.2c02531
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.6341803
title: Dataset: 800 QM/MM minimum energy pathway conformations for the acylation reactions of Toho-1/ampicillin and Toho-1/cefalexin

description: This dataset consists of 800 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the acylation reactions between a Class A beta-lactamases (Toho-1) and two beta-lactam antibiotic molecules (ampicillin and cefalexin). These files are: toho_amp.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Ampicillin (200 pathways); toho_amp.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Ampicillin (200 pathways); toho_cex.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Cefalexin (200 pathways); toho_cex.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Cefalexin (200 pathways); energies.zip: the replica energies at B3LYP-D3/6-31+G**/C36 level; chelpgs.zip: the ChElPG charges of all reactant replicas at B3LYP-D3/6-31+G**/C36 level; farrys.zip: the featurzied NumPy arrays for model training; peephole.zip: an example file for how the optimized MEPs look like; dftb3_benchmark.zip: the reference calculations to justify the use of DFTB3/3OB-F/C36 in MEP optimizations, the reference level of theory is B3LYP-D3/6-31G**/C36. The R1-AE pathways are the acylation uses Glu166 as the general base; the R2-AE pathways uses Lys73 and Glu166 as the concerted base. All QM/MM pathways are optimized at the DFTB3/3OB-f/CHARMM36 level of theory. Z. Song et al Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. <em>ACS Phys. Chem Au</em> 2022, <strong>2</strong>, 4, 316–330. DOI: 10.1021/acsphyschemau.2c00005
DOI: 10.5281/zenodo.5701371
title: Dataset: 800 QM/MM minimum energy pathway conformations for the acylation reactions of Toho-1/ampicillin and Toho-1/cefalexin

description: This dataset consists of 800 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the acylation reactions between a Class A beta-lactamases (Toho-1) and two beta-lactam antibiotic molecules (ampicillin and cefalexin). These files are: toho_amp.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Ampicillin (200 pathways); toho_amp.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Ampicillin (200 pathways); toho_cex.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Cefalexin (200 pathways); toho_cex.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Cefalexin (200 pathways); energies.zip: the replica energies at B3LYP-D3/6-31+G**/C36 level; chelpgs.zip: the ChElPG charges of all reactant replicas at B3LYP-D3/6-31+G**/C36 level; farrys.zip: the featurzied NumPy arrays for model training; peephole.zip: an example file for how the optimized MEPs look like; dftb3_benchmark.zip: the reference calculations to justify the use of DFTB3/3OB-F/C36 in MEP optimizations, the reference level of theory is B3LYP-D3/6-31G**/C36. The R1-AE pathways are the acylation uses Glu166 as the general base; the R2-AE pathways uses Lys73 and Glu166 as the concerted base. All QM/MM pathways are optimized at the DFTB3/3OB-f/CHARMM36 level of theory. Z. Song et al Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. <em>ACS Phys. Chem Au</em> 2022, <strong>2</strong>, 4, 316–330. DOI: 10.1021/acsphyschemau.2c00005
DOI: 10.5281/zenodo.6617839
title: Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem

description: This dataset consists of 1,000 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the deacylation reactions between a Class A beta-lactamases (GES-5) and the imipenem antibiotic molecules. All pathway conformations were optimized at DFTB3/3OB-f/CHARMM36 level with 36 replicas. All single point calculations and charge population analysis were done at B3LYP-D3/6-31+G(d,p)/CHARMM36 level. 0.paths_ges_imi_d1.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions. 0.paths_ges_imi_d2.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions. 1.eners.zip: The single point replica energies along all GES-5/IPM pathways. 1.chrgs.zip: The NBO charges of the QM region of all replica conformations along all GES-5/IPM pathways. 2.datasets.zip: The Python codes to postprocess the molecular data and the featurized the NumPy arrays. 3.gnn.zip: The Python codes that implements the edge-conditioned graph convolutional NN to predict the deacylation barriers. 5.representative_conf.zip: The pathway conformations of all cluster centroids and an energetic representative (pathway id 22) pathway. Note: This file also serves as a peephole of how the pathway conformations from Reaction Path with Holonomic Constrains calculations looks like. 6.benchmark.zip: The benchmark calculations that validates the DFTB3/3OB-f/CHARMM36 against DFTB3/3OB/CHARMM36 and B3LYP/6-31G(d,p)/CHARMM36 level of theory on the energetic representative (pathway id 22) pathway conformations. p.figures.zip: A series of Jupyter Notebooks that produces the visualizations in the work. README.md: A markdown file that contains additional descriptions. environment.yml: The Conda environment used for the graph-learning. Z. Song and P. Tao, Graph-Learning Guided Mechanistic Insights into Imipenem Hydrolysis in GES Carbapenemases. <strong><em>Electron. Struct.</em></strong> 2022, <strong>4</strong>, 034001. DOI: 10.1088/2516-1075/ac7993
DOI: 10.5281/zenodo.6473976
title: Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem

description: This dataset consists of 1,000 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the deacylation reactions between a Class A beta-lactamases (GES-5) and the imipenem antibiotic molecules. All pathway conformations were optimized at DFTB3/3OB-f/CHARMM36 level with 36 replicas. All single point calculations and charge population analysis were done at B3LYP-D3/6-31+G(d,p)/CHARMM36 level. 0.paths_ges_imi_d1.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions. 0.paths_ges_imi_d2.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions. 1.eners.zip: The single point replica energies along all GES-5/IPM pathways. 1.chrgs.zip: The NBO charges of the QM region of all replica conformations along all GES-5/IPM pathways. 2.datasets.zip: The Python codes to postprocess the molecular data and the featurized the NumPy arrays. 3.gnn.zip: The Python codes that implements the edge-conditioned graph convolutional NN to predict the deacylation barriers. 5.representative_conf.zip: The pathway conformations of all cluster centroids and an energetic representative (pathway id 22) pathway. Note: This file also serves as a peephole of how the pathway conformations from Reaction Path with Holonomic Constrains calculations looks like. 6.benchmark.zip: The benchmark calculations that validates the DFTB3/3OB-f/CHARMM36 against DFTB3/3OB/CHARMM36 and B3LYP/6-31G(d,p)/CHARMM36 level of theory on the energetic representative (pathway id 22) pathway conformations. p.figures.zip: A series of Jupyter Notebooks that produces the visualizations in the work. README.md: A markdown file that contains additional descriptions. environment.yml: The Conda environment used for the graph-learning. Z. Song and P. Tao, Graph-Learning Guided Mechanistic Insights into Imipenem Hydrolysis in GES Carbapenemases. <strong><em>Electron. Struct.</em></strong> 2022, <strong>4</strong>, 034001. DOI: 10.1088/2516-1075/ac7993
DOI: 10.26180/5d09946e4e64d
title: Handover Orientation and Motion Capture Dataset

description: This dataset contains the motion capture data recorded, the giver and receiver upper body joint angles and positions, and handover configurations (object pose) extracted from a user study involving twenty participants handing over twenty objects in three conditions.<br>The three test conditions are: Condition A - natural handover, Condition B - giver centered handover, Condition C - receiver centered handover.<br>For details regarding the user study design and data collection procedure, refer to:<br>- Wesley P. Chan, Matthew K.X.J. Pan, Elizabeth A. Croft, and Masayuki Inaba. An affordance and distance minimization based method for computing object orientations for robot human handovers. International Journal of Social Robotics. doi:10.1007/s12369-019-00546-7.<br><br>If you use this dataset please cite the reference above.<br>Description of the dataset file structure can be found in the file "Handover Orientation and Motion Capture Dataset description.txt"
DOI: 10.12755/nrct.res.1981.1
title: นโยบายและแผนงานวิจัยของสภาวิจัยแห่งชาติ พ.ศ. 2520-2524
DOI: 10.25505/fiz.icsd.cc2czycp
title: CSD 2204483: Experimental Crystal Structure Determination

description: Related Article: Maung Thway, Wenhao Zhai, Fengxia Wei, Jose Recatala-Gomez, Yang Bai, Haiwen Dai, Andy Paul Chen, Siyu Isaac Paarker Tian, D. V. Maheshwar Repaka, Tonio Buonassisi, Pieremanuele Canepa, Kedar Hippalgaonkar|2022|ICSD Communication|||
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25909/630ef15a13de5
title: Statistical overview of data of corrosion investigations of fibre-reinforced concrete

description: An understanding of the potential for fibres to corrode in aggressive environments is essential to the long-term design of fibre reinforced concretes. Given a significant number of individual tests that have been conducted using a range of different specimen types (variations in specimen dimension and material properties) and accelerating conditions (variation in corrosion technique and exposure time), existing tests are summarized to provide an overview of the field and to help inform future experimental design. This dataset consists of 342 individual tests from 20 existing research studies. The parameters in the database include concrete strength, fiber geometry, fiber pre-damage (with/without pre-corrosion), the technique used to accelerate corrosion, corrosion measurement techniques, and number of specimens for any specific scenario.
DOI: 10.6084/m9.figshare.13284883.v2
title: Non-prescribed drug use and predictors among pregnant women in Ethiopia: systematic review and meta-analysis

description: The use of non-prescribed drugs are common to pregnant women. It may lead to undesirable effects, such as birth defects. Study results on the occurrence and predictor of non-prescribed drug use among pregnant women throughout Ethiopia are highly variable and inconsistent. Therefore, the objective of this systematic review and meta-analysis was to estimate the pooled prevalence of non-prescribed drug use and predictors among pregnant women in Ethiopia. We systematically searched studies from the international databases, including PubMed, EMBASE, Web of Science, Science Direct, Google Scholar, the Cochrane Library and others. The meta-analysis was conducted using Stata15. I<sup>2</sup> test and Egger’s test were used to assess the heterogeneity and publication bias respectively. The random-effect model was used to estimate the pooled prevalence of non-prescribed drug use at a 95% CI. Eleven studies with a total of 4492 pregnant women fulfilled the inclusion criteria and were included. The pooled national level non-prescribed drug use among pregnant women was 30.38% (95% CI: 20.28, 40.48). The highest use of non-prescribed drug among pregnant women was observed in Amhara region 36.71%, while the lowest was in Tigray region 9.67%, respectively. The most frequently consumed non prescribed drugs by pregnant mothers were paracetamol 34.38%, amoxicillin 14.73%, aspirin 4.25%, metronidazole 2.81% and ciprofloxacin 2.80%. Maternal previous history of self-medication, maternal illness during pregnancy and maternal marital status were significantly associated with women non-prescribed drug use during pregnancy. The overall prevalence of non- prescribed drug use among pregnant women in Ethiopia is relatively high, and varies across different regions. The most frequently consumed non- prescribed drug by pregnant mothers was paracetamol. Maternal; previous history of self-medication, illness during pregnancy and marital status were significantly associated with pregnant women non-prescribed drug use. Awareness of the possible side effects of taking non-prescribed drugs for all pregnant women is very relevant in the media and in the maternity ward. In particular, it is important to make clear to mothers who have a history of self-medication, to those who have a history of illness during pregnancy and to those who are pregnant, unmarried or divorced.
DOI: 10.6084/m9.figshare.13284883
title: Non-prescribed drug use and predictors among pregnant women in Ethiopia: systematic review and meta-analysis

description: The use of non-prescribed drugs are common to pregnant women. It may lead to undesirable effects, such as birth defects. Study results on the occurrence and predictor of non-prescribed drug use among pregnant women throughout Ethiopia are highly variable and inconsistent. Therefore, the objective of this systematic review and meta-analysis was to estimate the pooled prevalence of non-prescribed drug use and predictors among pregnant women in Ethiopia. We systematically searched studies from the international databases, including PubMed, EMBASE, Web of Science, Science Direct, Google Scholar, the Cochrane Library and others. The meta-analysis was conducted using Stata15. I<sup>2</sup> test and Egger’s test were used to assess the heterogeneity and publication bias respectively. The random-effect model was used to estimate the pooled prevalence of non-prescribed drug use at a 95% CI. Eleven studies with a total of 4492 pregnant women fulfilled the inclusion criteria and were included. The pooled national level non-prescribed drug use among pregnant women was 30.38% (95% CI: 20.28, 40.48). The highest use of non-prescribed drug among pregnant women was observed in Amhara region 36.71%, while the lowest was in Tigray region 9.67%, respectively. The most frequently consumed non prescribed drugs by pregnant mothers were paracetamol 34.38%, amoxicillin 14.73%, aspirin 4.25%, metronidazole 2.81% and ciprofloxacin 2.80%. Maternal previous history of self-medication, maternal illness during pregnancy and maternal marital status were significantly associated with women non-prescribed drug use during pregnancy. The overall prevalence of non- prescribed drug use among pregnant women in Ethiopia is relatively high, and varies across different regions. The most frequently consumed non- prescribed drug by pregnant mothers was paracetamol. Maternal; previous history of self-medication, illness during pregnancy and marital status were significantly associated with pregnant women non-prescribed drug use. Awareness of the possible side effects of taking non-prescribed drugs for all pregnant women is very relevant in the media and in the maternity ward. In particular, it is important to make clear to mothers who have a history of self-medication, to those who have a history of illness during pregnancy and to those who are pregnant, unmarried or divorced.
DOI: 10.6084/m9.figshare.13258070.v2
title: Prevalence of methicillin-sensitive, methicillin-resistant <i>Staphylococcus aureus</i>, and extended-spectrum beta-lactamase-producing <i>Escherichia coli</i> in newborns: a cross-sectional study

description: The prevalence of antimicrobial-resistant bacteria and methicillin-sensitive <i>Staphylococcus aureus</i> (MSSA) in healthy newborns and the role of maternal transmission are scarcely discussed. The objective of this study was to evaluate the prevalence of MSSA, MRSA, and ESBL among healthy newborns. Additionally, mother-to-newborn transmission rates were investigated as well as antibiotic susceptibility of MSSA, MRSA, and ESBL isolates. Swabs of 658 newborns and their mothers were collected to investigate the presence of MSSA, MRSA, and ESBL. Swabs were taken from the nose and umbilicus immediately after birth. Additional swabs were taken from the nose, perianal area, and umbilicus 3 days after birth. Samples were screened and further characterized using culture and molecular methods. Prevalence of MSSA, MRSA, and ESBL colonization was 10.9, 0.5, and 2.6%, respectively. There was no association between the colonization status of the newborn and infections at any time point. Mother-to-newborn transmission rates (confirmed by PFGE) were 53.6% for MSSA/MRSA and 100% for ESBL. Maternal carriage of MSSA, MRSA, or ESBL was a risk factor for colonization of the newborn. Some isolates were resistant to the antibiotics recommended for therapy, including clindamycin and daptomycin for MSSA/MRSA isolates and ertapenem, fosfomycin, and tigecyclin for ESBL isolates. No association between infections and the newborns’ colonization status could be detected. Maternal colonization played an important role in newborn colonization, but not every case of colonization could be explained by mother-to-newborn transmission. General screening of pregnant women and healthy newborns in the absence of other risk factors is not necessary. To prevent the possibility of transmission in the healthcare setting, professionals, pregnant women, parents, hospital visitors, and obstetricians should receive regular training on appropriate hygiene measures. With regard to the emergence of resistance to recommended antibiotics, an antibiogram should be conducted before treating MSSA/MRSA/ESBL infections to ensure the efficacy of the antibiotics.
DOI: 10.6084/m9.figshare.13258070
title: Prevalence of methicillin-sensitive, methicillin-resistant <i>Staphylococcus aureus</i>, and extended-spectrum beta-lactamase-producing <i>Escherichia coli</i> in newborns: a cross-sectional study

description: The prevalence of antimicrobial-resistant bacteria and methicillin-sensitive <i>Staphylococcus aureus</i> (MSSA) in healthy newborns and the role of maternal transmission are scarcely discussed. The objective of this study was to evaluate the prevalence of MSSA, MRSA, and ESBL among healthy newborns. Additionally, mother-to-newborn transmission rates were investigated as well as antibiotic susceptibility of MSSA, MRSA, and ESBL isolates. Swabs of 658 newborns and their mothers were collected to investigate the presence of MSSA, MRSA, and ESBL. Swabs were taken from the nose and umbilicus immediately after birth. Additional swabs were taken from the nose, perianal area, and umbilicus 3 days after birth. Samples were screened and further characterized using culture and molecular methods. Prevalence of MSSA, MRSA, and ESBL colonization was 10.9, 0.5, and 2.6%, respectively. There was no association between the colonization status of the newborn and infections at any time point. Mother-to-newborn transmission rates (confirmed by PFGE) were 53.6% for MSSA/MRSA and 100% for ESBL. Maternal carriage of MSSA, MRSA, or ESBL was a risk factor for colonization of the newborn. Some isolates were resistant to the antibiotics recommended for therapy, including clindamycin and daptomycin for MSSA/MRSA isolates and ertapenem, fosfomycin, and tigecyclin for ESBL isolates. No association between infections and the newborns’ colonization status could be detected. Maternal colonization played an important role in newborn colonization, but not every case of colonization could be explained by mother-to-newborn transmission. General screening of pregnant women and healthy newborns in the absence of other risk factors is not necessary. To prevent the possibility of transmission in the healthcare setting, professionals, pregnant women, parents, hospital visitors, and obstetricians should receive regular training on appropriate hygiene measures. With regard to the emergence of resistance to recommended antibiotics, an antibiogram should be conducted before treating MSSA/MRSA/ESBL infections to ensure the efficacy of the antibiotics.
DOI: 10.6084/m9.figshare.13257935
title: Intrahepatic bile ductal ectasia in autosomal recessive polycystic kidney disease evaluated by fetal magnetic resonance imaging: a more frequent complication

description: This study aimed to evaluate liver malformations and intrahepatic bile ductal ectasia and dilatation (IBDED) in cases of prenatal diagnosis of autosomal recessive polycystic kidney disease (ARPKD) using magnetic resonance imaging (MRI). This retrospective study involved 209 cases referred for fetal MRI studies (f-MRI) from March 2004 and December 2019, suspicious of congenital renal disease. Fetuses that met the criteria for ARPKD were selected. Six cases were diagnosed as ARPKD (2.8%). The median gestational age at MRI examination was 28 weeks (24–36 weeks). IBDED was observed in 84% of cases. Moreover, 66% presented multilobar liver lesions, and 33% exhibited monolobar lesions. The “central dot sign” (CDS) was found in half of the cases. In this case series of prenatal diagnosis of ARPKD using f-MRI, IBDED was present in the majority of the cases, and the CDS was noted in half of the cases.
DOI: 10.6084/m9.figshare.13257935.v2
title: Intrahepatic bile ductal ectasia in autosomal recessive polycystic kidney disease evaluated by fetal magnetic resonance imaging: a more frequent complication

description: This study aimed to evaluate liver malformations and intrahepatic bile ductal ectasia and dilatation (IBDED) in cases of prenatal diagnosis of autosomal recessive polycystic kidney disease (ARPKD) using magnetic resonance imaging (MRI). This retrospective study involved 209 cases referred for fetal MRI studies (f-MRI) from March 2004 and December 2019, suspicious of congenital renal disease. Fetuses that met the criteria for ARPKD were selected. Six cases were diagnosed as ARPKD (2.8%). The median gestational age at MRI examination was 28 weeks (24–36 weeks). IBDED was observed in 84% of cases. Moreover, 66% presented multilobar liver lesions, and 33% exhibited monolobar lesions. The “central dot sign” (CDS) was found in half of the cases. In this case series of prenatal diagnosis of ARPKD using f-MRI, IBDED was present in the majority of the cases, and the CDS was noted in half of the cases.