cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19431364.v1
title: The role of FYCO1-dependent autophagy in lens fiber cell differentiation

description: FYCO1 (FYVE and coiled-coil domain containing 1) is an adaptor protein, expressed ubiquitously and required for microtubule-dependent, plus-end-directed transport of macroautophagic/autophagic vesicles. We have previously shown that loss-of-function mutations in <i>FYCO1</i> cause cataracts with no other ocular and/or extra-ocular phenotype. Here, we show <i>fyco1</i> homozygous knockout (<i>fyco1<sup>−/−</sup></i>) mice recapitulate the cataract phenotype consistent with a critical role of FYCO1 and autophagy in lens morphogenesis. Transcriptome coupled with proteome and metabolome profiling identified many autophagy-associated genes, proteins, and lipids respectively perturbed in <i>fyco1<sup>−/−</sup></i> mice lenses. Flow cytometry of <i>FYCO1</i> (c.2206C&gt;T) knock-in (KI) human lens epithelial cells revealed a decrease in autophagic flux and autophagic vesicles resulting from the loss of FYCO1. Transmission electron microscopy showed cellular organelles accumulated in <i>FYCO1</i> (c.2206C&gt;T) KI lens-like organoid structures and in <i>fyco1<sup>−/−</sup></i> mice lenses. In summary, our data confirm the loss of FYCO1 function results in a diminished autophagic flux, impaired organelle removal, and cataractogenesis. <b>Abbreviations:</b> CC: congenital cataracts; DE: differentially expressed; ER: endoplasmic reticulum; FYCO1: FYVE and coiled-coil domain containing 1; hESC: human embryonic stem cell; KI: knock-in; OFZ: organelle-free zone; qRT-PCR: quantitative real-time PCR; PE: phosphatidylethanolamine; RNA-Seq: RNA sequencing; SD: standard deviation; sgRNA: single guide RNA; shRNA: shorthairpin RNA; TEM: transmission electron microscopy; WT: wild type
DOI: 10.6084/m9.figshare.6848030
title: Additional file 3: of Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae)

description: Primers designed for fluorescence quantitative real-time PCR. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6847739
title: Additional file 2: of Molecular mechanism of estrogen-mediated neuroprotection in the relief of brain ischemic injury

description: The interaction pairs of nodes in protein-protein interaction network. This excel presents 243 nodes and 590 interaction pairs (combined scoreâ &gt;â 0.4) in Fig. 1. In addition, it contains the combined score values of these 590 interaction pairs. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.6849656
title: Risk factors for abnormally invasive placenta: a systematic review and meta-analysis

description: <b>Purpose of the article.</b> To explore the strength of association between different maternal and pregnancy characteristics and the occurrence of abnormally invasive placenta (AIP). <b>Materials and methods:</b> Pubmed, Embase, CINAHL databases were searched. The risk factors for AIP explored were: obesity, age &gt;35 years, smoking before or during pregnancy, placenta previa, prior cesarean section (CS), placenta previa and prior CS, prior uterine surgery, abortion and uterine curettage, <i>in vitro</i> fertilization (IVF) pregnancy and interval between a previous CS, and a subsequent pregnancy. Random-effect head-to-head meta-analyses were used to analyze the data. <b>Results:</b> Forty-six were included in the systematic review. Maternal obesity (Odd ratio, OR: 1.4, 95% CI 1.0–1.8), advanced maternal age (OR: 3.1, 95% CI 1.4–7.0) and parity (OR: 2.5, 95% CI 1.7–3.6), but not smoking were associated with a higher risk of AIP. The presence of placenta previa in women with at least a prior CS was associated with a higher risk of AIP compared to controls, with an OR of 12.0, 95% CI 1.6–88.0. Furthermore, the risk of AIP increased with the number of prior CS (OR of 2.6, 95% CI 1.6–4.4 and 5.4, 95% CI 1.7–17.4 for two and three prior CS respectively). Finally, IVF pregnancies were associated with a high risk of AIP, with an OR of 2.8 (95% CI 1.2–6.8). <b>Conclusion:</b> A prior CS and placenta previa are among the strongest risk factors for the occurrence of AIP.
DOI: 10.6084/m9.figshare.6848063
title: Additional file 5: of Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae)

description: BLASTx annotation against the NCBI non-redundant protein database for putative olfactory genes. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.6849656.v2
title: Risk factors for abnormally invasive placenta: a systematic review and meta-analysis

description: <b>Purpose of the article.</b> To explore the strength of association between different maternal and pregnancy characteristics and the occurrence of abnormally invasive placenta (AIP). <b>Materials and methods:</b> Pubmed, Embase, CINAHL databases were searched. The risk factors for AIP explored were: obesity, age &gt;35 years, smoking before or during pregnancy, placenta previa, prior cesarean section (CS), placenta previa and prior CS, prior uterine surgery, abortion and uterine curettage, <i>in vitro</i> fertilization (IVF) pregnancy and interval between a previous CS, and a subsequent pregnancy. Random-effect head-to-head meta-analyses were used to analyze the data. <b>Results:</b> Forty-six were included in the systematic review. Maternal obesity (Odd ratio, OR: 1.4, 95% CI 1.0–1.8), advanced maternal age (OR: 3.1, 95% CI 1.4–7.0) and parity (OR: 2.5, 95% CI 1.7–3.6), but not smoking were associated with a higher risk of AIP. The presence of placenta previa in women with at least a prior CS was associated with a higher risk of AIP compared to controls, with an OR of 12.0, 95% CI 1.6–88.0. Furthermore, the risk of AIP increased with the number of prior CS (OR of 2.6, 95% CI 1.6–4.4 and 5.4, 95% CI 1.7–17.4 for two and three prior CS respectively). Finally, IVF pregnancies were associated with a high risk of AIP, with an OR of 2.8 (95% CI 1.2–6.8). <b>Conclusion:</b> A prior CS and placenta previa are among the strongest risk factors for the occurrence of AIP.
DOI: 10.6084/m9.figshare.6848075
title: Additional file 6: of Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae)

description: Expression levels of candidate olfactory receptors measured in the RNA-Seq analysis. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.6847772
title: Additional file 4: of Molecular mechanism of estrogen-mediated neuroprotection in the relief of brain ischemic injury

description: The degrees of nodes in Modules. The excel describes the up/down-regulated status and degrees of nodes in modules a, b c and d. Module a consists of 7 up-regulated and 5 down-regulated genes, and the degrees of those nodes were ranged from 16 to 7. There were 3 up-regulated and 2 down-regulated genes in module b, and the degrees of nodes were ranged from 18 (Lep) to 4 (Fabp4). Additionally, two upregulated and two downregulated comprised of module c, in which the degrees of nodes were ranged from 15 to 8. In module d, the degrees of nodes were ranged from 19 (Th) to 3(Grik4). (XLSX 222 kb)
DOI: 10.6084/m9.figshare.6847754.v1
title: Additional file 3: of Molecular mechanism of estrogen-mediated neuroprotection in the relief of brain ischemic injury

description: The degrees of nodes in protein-protein interaction network. The excel describes the up/down-regulated status and degrees of 243 nodes in the PPI network. A total of 119 nodes were up-regulated genes and 124 nodes were down-regulated genes. The nodes degrees were ranged from 37 to 1. (XLSX 227 kb)
DOI: 10.6084/m9.figshare.13663851
title: Comparative Transcriptome Analysis Providing Resistance Mechanism of <i>Aspergillus oryzae</i> Under Arsenate Stress

description: The molecular resistance mechanism of <i>Aspergillus oryzae</i> (<i>A. oryzae</i>) under arsenate (As(V)) stress was investigated by comparative transcriptome analysis. In total, 4911 differentially expressed genes (DEGs) of <i>A. oryzae</i> were detected under As(V) stress, including 2103 up-regulated genes and 2808 down-regulated genes. Genes induced by As(V) were involved in metal ion binding and transportation, redox homeostasis, efflux carrier, DNA repair, volatilization, etc. Moreover, eight genes were selected for qRT-PCR verification, and their trends were consistent with RNA-Seq analysis, which proved that RNA-Seq analysis was efficient and reliable. The results indicated that the extracellular and intracellular synergistic resistance mechanisms contributed to the improvement of <i>A. oryzae</i> resistance to As (V).
DOI: 10.6084/m9.figshare.24151215
title: Additional file 1 of A nomogram for predicting sepsis-associated delirium: a retrospective study in MIMIC III

description: Additional file 1: ICD-9 codes for excluding diagnosis
DOI: 10.6084/m9.figshare.16807787.v1
title: Additional file 5 of Glutamine involvement in nitrogen regulation of cellulase production in fungi

description: Additional file 5: Table S5. DEGs involved in amino acids in T. reesei RUT-C30 cultured in TMM with the addition of glutamine.
DOI: 10.5281/zenodo.10360951
title: EPFL EPFL_ROOF_2011 10 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_ROOF_2011 10 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_ROOF_2011/metadata/10.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.57906/8w8q-0f86
title: UK Research and Innovation Workforce Survey
DOI: 10.5281/zenodo.10360952
title: EPFL EPFL_ROOF_2011 11 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_ROOF_2011 11 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_ROOF_2011/metadata/11.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360953
title: EPFL EPFL_ROOF_2011 11 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_ROOF_2011 11 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_ROOF_2011/metadata/11.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360954
title: EPFL HYMEX_LTE_SOP3 32 disdrometer station data

description: Disdrometer measurements of the EPFL HYMEX_LTE_SOP3 32 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/HYMEX_LTE_SOP3/metadata/32.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360955
title: EPFL HYMEX_LTE_SOP3 32 disdrometer station data

description: Disdrometer measurements of the EPFL HYMEX_LTE_SOP3 32 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/HYMEX_LTE_SOP3/metadata/32.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360956
title: EPFL HYMEX_LTE_SOP3 10 disdrometer station data

description: Disdrometer measurements of the EPFL HYMEX_LTE_SOP3 10 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/HYMEX_LTE_SOP3/metadata/10.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360957
title: EPFL HYMEX_LTE_SOP3 10 disdrometer station data

description: Disdrometer measurements of the EPFL HYMEX_LTE_SOP3 10 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/HYMEX_LTE_SOP3/metadata/10.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.6084/m9.figshare.21976468
title: Commercial impact of adding real-world evidence to clinical trials at regulatory approval: a Markovian-like transition model

description: Regulatory use of real-world evidence (RWE) has been recognized as a useful supplement to clinical trial evidence and could benefit patients by reducing time to treatment. However, commercial benefits have not been documented. The aim was to determine commercial impact of regulatory RWE, using ambrisentan as an illustrative example. A Markovian-like transition model was constructed to simulate the drug development workflow across a simulation time of <i>t</i> = 20 years. RWE was assumed to be incorporated at pII–pIII and pII–pIII–pIV, and its multiplicative median transition rate was determined by biopharma expert opinion. Each model was subjected to “with” and “without” RWE rates. Commercial impact was estimated using potential decrease in time to launch. Time to first medicine adoption and potential lives saved were also estimated. Based on cumulative first prescriptions for ambrisentan among pulmonary arterial hypertension patients (<i>N</i> = 487), in comparison to standard drug development, RWE incorporation has the potential to expedite first medicine adoption by 10.4 weeks. The duration of market launch was estimated at 2.5–3.0 years earlier than standard, and approximately 9% of patients would benefit in survival. Potential earnings for an earlier launch would be GBP £43,597.86 per patient, with launch being brought forward from 2009 to 2007. Regulatory RWE has the potential to increase overall survival rates and potential earnings by reducing time to launch. This study provides further support for industry efforts to generate RWE in time for regulatory approval.
DOI: 10.6084/m9.figshare.22058784
title: Development, validation and implementation of the medical affairs pharmaceutical physician work-related quality of life instrument

description: Medical affairs pharmaceutical physicians (MAPPs) are at risk for low work-related quality of life (WRQoL). The aim of this study was to develop, validate and implement the first WRQoL instrument for this population. A prospective observational cohort clinical study, the Medical Affairs Pharmaceutical Physician Work-related Quality of Life (MAPPWrQoL) Instrument Development and Patient Registry (MAPPWrQoLReg), was registered in November 2021 (NCT05123846). Thirteen MAPPs and 12 non-MAPPs participated in development and validation between December 2021 and January 2022. Development used the Jandhyala method for observing proportional group awareness and consensus. Discriminant validity analysis used the WRQoL Scale as a reference standard and assessed whether the instrument could differentiate between the groups. Twelve MAPPs and 12 non-MAPPs self-reported their WRQoL in the registry each month from February 2022. Recruitment and data collection are ongoing; 6-month data between February 2022 and August 2022 are reported here. Two participants were excluded from the registry. Chi-squared analysis showed a significant difference between the MAPPWRQoL instrument and WRQoL Scale (<i>p</i> = 1.029e-08) with acceptable sensitivity (89.19%) and specificity (75.00%). There were significant between-group differences for total scores at each follow-up (<i>p</i> = .003; <i>n</i> = 6 questions). Chi-squared analysis showed a significant difference between MAPPs’ and non-MAPPs’ ability to answer MAPPWRQoL instrument items (<i>p</i> = .002629), with acceptable sensitivity (91.9%) and near-acceptable specificity (66.7%). MAPPs’ WRQoL did not change significantly over 6 months. Discriminant validity of the 39-item MAPPWRQoL instrument was confirmed. The Jandhyala method successfully developed and validated a specific WRQoL instrument and may be applied to similar populations, such as junior doctors and UK general practitioners.
DOI: 10.6084/m9.figshare.21976468.v2
title: Commercial impact of adding real-world evidence to clinical trials at regulatory approval: a Markovian-like transition model

description: Regulatory use of real-world evidence (RWE) has been recognized as a useful supplement to clinical trial evidence and could benefit patients by reducing time to treatment. However, commercial benefits have not been documented. The aim was to determine commercial impact of regulatory RWE, using ambrisentan as an illustrative example. A Markovian-like transition model was constructed to simulate the drug development workflow across a simulation time of <i>t</i> = 20 years. RWE was assumed to be incorporated at pII–pIII and pII–pIII–pIV, and its multiplicative median transition rate was determined by biopharma expert opinion. Each model was subjected to “with” and “without” RWE rates. Commercial impact was estimated using potential decrease in time to launch. Time to first medicine adoption and potential lives saved were also estimated. Based on cumulative first prescriptions for ambrisentan among pulmonary arterial hypertension patients (<i>N</i> = 487), in comparison to standard drug development, RWE incorporation has the potential to expedite first medicine adoption by 10.4 weeks. The duration of market launch was estimated at 2.5–3.0 years earlier than standard, and approximately 9% of patients would benefit in survival. Potential earnings for an earlier launch would be GBP £43,597.86 per patient, with launch being brought forward from 2009 to 2007. Regulatory RWE has the potential to increase overall survival rates and potential earnings by reducing time to launch. This study provides further support for industry efforts to generate RWE in time for regulatory approval.
DOI: 10.6084/m9.figshare.21976468.v1
title: Commercial impact of adding real-world evidence to clinical trials at regulatory approval: A Markovian-like transition model

description: Regulatory use of real-world evidence (RWE) has been recognised as a useful supplement to clinical trial evidence and could benefit patients by reducing time to treatment. However, commercial benefits have not been documented. The aim was to determine commercial impact of regulatory RWE, using ambrisentan as an illustrative example. A Markovian-like transition model was constructed to simulate the drug development workflow across a simulation time of t = 20 years. RWE was assumed to be incorporated at pII - pIII and pII - pIII - pIV, and its multiplicative median transition rate was determined by biopharma expert opinion. Each model was subjected to ‘with’ and ‘without’ RWE rates. Commercial impact was estimated using potential decrease in time to launch. Time to first medicine adoption and potential lives saved were also estimated. Based on cumulative first prescriptions for ambrisentan among pulmonary arterial hypertension patients (N = 487), in comparison to standard drug development, RWE incorporation has the potential to expedite first medicine adoption by 10.4 weeks. The duration of market launch was estimated at 2.5–3.0 years earlier than standard, and approximately 9% of patients would benefit in survival. Potential earnings for an earlier launch would be GBP £43,597.86 per patient, with launch being brought forward from 2009 to 2007. Regulatory RWE has the potential to increase overall survival rates and potential earnings by reducing time to launch. This study provides further support for industry efforts to generate RWE in time for regulatory approval.
DOI: 10.6084/m9.figshare.22058784.v1
title: Development, validation and implementation of the medical affairs pharmaceutical physician work-related quality of life instrument

description: Medical affairs pharmaceutical physicians (MAPPs) are at risk for low work-related quality of life (WRQoL). The aim of this study was to develop, validate and implement the first WRQoL instrument for this population. A prospective observational cohort clinical study, the Medical Affairs Pharmaceutical Physician Work-related Quality of Life (MAPPWrQoL) Instrument Development and Patient Registry (MAPPWrQoLReg), was registered in November 2021 (NCT05123846). Thirteen MAPPs and 12 non-MAPPs participated in development and validation between December 2021 and January 2022. Development used the Jandhyala method for observing proportional group awareness and consensus. Discriminant validity analysis used the WRQoL Scale as a reference standard and assessed whether the instrument could differentiate between the groups. Twelve MAPPs and 12 non-MAPPs self-reported their WRQoL in the registry each month from February 2022. Recruitment and data collection are ongoing; 6-month data between February 2022 and August 2022 are reported here. Two participants were excluded from the registry. Chi-squared analysis showed a significant difference between the MAPPWRQoL instrument and WRQoL Scale (<i>p</i> = 1.029e-08) with acceptable sensitivity (89.19%) and specificity (75.00%). There were significant between-group differences for total scores at each follow-up (<i>p</i> = .003; <i>n</i> = 6 questions). Chi-squared analysis showed a significant difference between MAPPs’ and non-MAPPs’ ability to answer MAPPWRQoL instrument items (<i>p</i> = .002629), with acceptable sensitivity (91.9%) and near-acceptable specificity (66.7%). MAPPs’ WRQoL did not change significantly over 6 months. Discriminant validity of the 39-item MAPPWRQoL instrument was confirmed. The Jandhyala method successfully developed and validated a specific WRQoL instrument and may be applied to similar populations, such as junior doctors and UK general practitioners.
DOI: 10.5281/zenodo.10360958
title: EPFL HYMEX_LTE_SOP3 22 disdrometer station data

description: Disdrometer measurements of the EPFL HYMEX_LTE_SOP3 22 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/HYMEX_LTE_SOP3/metadata/22.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360959
title: EPFL HYMEX_LTE_SOP3 22 disdrometer station data

description: Disdrometer measurements of the EPFL HYMEX_LTE_SOP3 22 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/HYMEX_LTE_SOP3/metadata/22.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360961
title: EPFL HYMEX_LTE_SOP3 12 disdrometer station data

description: Disdrometer measurements of the EPFL HYMEX_LTE_SOP3 12 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/HYMEX_LTE_SOP3/metadata/12.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360960
title: EPFL HYMEX_LTE_SOP3 12 disdrometer station data

description: Disdrometer measurements of the EPFL HYMEX_LTE_SOP3 12 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/HYMEX_LTE_SOP3/metadata/12.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .