cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10572486
title: Dataset for "Integrated PIN modulator and photodetector operating in the mid-infrared range from 5.5 𝛍m to 10 𝛍m", Nanophotonics, 2023

description: This dataset contains the paper of the figures of the paper "Integrated PIN modulator and photodetector operating in the mid-infrared range from 5.5 𝛍m to 10 𝛍m", Nanophotonics, 2023, authors : Thi Hao Nhi Nguyen et al. ,  https://doi.org/10.1515/nanoph-2023-0692

 
description: Acknowledgments: The fabrication of the device was partially performed at the Platform de Micro-NanoTechnologie/C2N, which is partially funded by the “Conseil Général de l’Essonne”. This work was partly supported by the French RENATECH network. Co-funded by the European Union (ERC-Electrophot, 101097569). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. 

Research funding: ANR Light-up Project (ANR-19-CE24-0002-01). Fondazione Cariplo, Grant No. 2020–4427 (project MILESTONE), ERC-Electrophot (101097569).
DOI: 10.5281/zenodo.10572487
title: Dataset for "Integrated PIN modulator and photodetector operating in the mid-infrared range from 5.5 𝛍m to 10 𝛍m", Nanophotonics, 2023

description: This dataset contains the paper of the figures of the paper "Integrated PIN modulator and photodetector operating in the mid-infrared range from 5.5 𝛍m to 10 𝛍m", Nanophotonics, 2023, authors : Thi Hao Nhi Nguyen et al. ,  https://doi.org/10.1515/nanoph-2023-0692

 
description: Acknowledgments: The fabrication of the device was partially performed at the Platform de Micro-NanoTechnologie/C2N, which is partially funded by the “Conseil Général de l’Essonne”. This work was partly supported by the French RENATECH network. Co-funded by the European Union (ERC-Electrophot, 101097569). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. 

Research funding: ANR Light-up Project (ANR-19-CE24-0002-01). Fondazione Cariplo, Grant No. 2020–4427 (project MILESTONE), ERC-Electrophot (101097569).
DOI: 10.6084/m9.figshare.24973002
title: Supplementary Material for: Association of serum activin levels with allograft outcomes in patients with kidney transplant: Results from the KNOW-KT

description: Introduction: Serum activin A has been reported to contribute to vascular calcification and kidney fibrosis in chronic kidney disease. We aimed to investigate whether higher serum activin levels were associated with poor allograft outcomes in patients with kidney transplants (KT).
Methods: A total of 860 KT patients from KNOW-KT (KoreaN cohort study for Outcome in patients With Kidney Transplantation) were analyzed. We measured serum activin levels at pre-KT and 1 year after KT. The primary outcome was the composite of a ≥ 50% decline in eGFR and graft failure. Multivariable cause-specific hazard model was used to analyze association of 1-year activin levels with the primary outcome. The secondary outcome was coronary artery calcification score (CACS) at 5 years after KT.
Results: During the median follow-up of 6.7 years, the primary outcome occurred in 109 (12.7%) patients. The serum activin levels at 1 year were significantly lower than those at pre-KT (488.2 ± 247.3 vs. 704.0 ± 349.6). When patients were grouped based on the median activin level at 1 year, the high-activin group had a 1.91-fold higher risk (95% CI, 1.25-2.91) for the primary outcome compared to the low-activin group. A one standard deviation increase in activin levels as a continuous variable was associated with a 1.36-fold higher risk (95% CI, 1.16-1.60) for the primary outcome. Moreover, high activin levels were significantly associated with 1.56-fold higher CACS (95% CI, 1.12-2.18).
Conclusion: Post-transplant activin levels were independently associated with allograft functions as well as coronary artery calcification in kidney transplant patients.
DOI: 10.6084/m9.figshare.24973002.v1
title: Supplementary Material for: Association of serum activin levels with allograft outcomes in patients with kidney transplant: Results from the KNOW-KT

description: Introduction: Serum activin A has been reported to contribute to vascular calcification and kidney fibrosis in chronic kidney disease. We aimed to investigate whether higher serum activin levels were associated with poor allograft outcomes in patients with kidney transplants (KT).
Methods: A total of 860 KT patients from KNOW-KT (KoreaN cohort study for Outcome in patients With Kidney Transplantation) were analyzed. We measured serum activin levels at pre-KT and 1 year after KT. The primary outcome was the composite of a ≥ 50% decline in eGFR and graft failure. Multivariable cause-specific hazard model was used to analyze association of 1-year activin levels with the primary outcome. The secondary outcome was coronary artery calcification score (CACS) at 5 years after KT.
Results: During the median follow-up of 6.7 years, the primary outcome occurred in 109 (12.7%) patients. The serum activin levels at 1 year were significantly lower than those at pre-KT (488.2 ± 247.3 vs. 704.0 ± 349.6). When patients were grouped based on the median activin level at 1 year, the high-activin group had a 1.91-fold higher risk (95% CI, 1.25-2.91) for the primary outcome compared to the low-activin group. A one standard deviation increase in activin levels as a continuous variable was associated with a 1.36-fold higher risk (95% CI, 1.16-1.60) for the primary outcome. Moreover, high activin levels were significantly associated with 1.56-fold higher CACS (95% CI, 1.12-2.18).
Conclusion: Post-transplant activin levels were independently associated with allograft functions as well as coronary artery calcification in kidney transplant patients.
DOI: 10.6084/m9.figshare.24943155.v1
title: Supplementary Material for: Reference Ranges for Left Modified Myocardial Performance Index: Systematic Review and Meta-Analysis

description: Introduction: The modified myocardial performance index (mod-MPI) is a noninvasive Doppler-derived metric used to evaluate fetal cardiac function. However, the reference ranges for mod-MPI in normal fetuses are not clearly defined which limits the use of this technology in fetuses with potential cardiac compromise. Thus, we aimed to perform a systematic review and meta-analysis of published mod-MPI reference ranges across gestation.
Methods: The published literature was systematically searched, and all published articles in any language that provided values for the left ventricular mod-MPI obtained in low-risk, singleton fetuses were considered eligible for further review. All retrieved titles and abstracts were independently reviewed by two researchers. Mean and standard deviation by gestational week was extracted or calculated from published data. DerSimonian-Laird random effects models were used to estimate pooled means and 95% confidence intervals (CIs).
Results: The search resulted in 618 unique citations, of which 583 did not meet inclusion criteria, leaving 35 abstracts selected for full-text review. Review of the references of these 35 articles identified another 5 studies of interest. Of the 40 articles reviewed, six met inclusion criteria. There was significant heterogeneity seen in the mod-MPI results reported. Mod-MPI increased as pregnancy progressed in all studies. The pooled mean mod-MPI at 11 weeks’ gestation was 0.400 (95% CI 0.374- 0.426) and increased to 0.585 (95% CI 0.533-0.637) at 41 weeks’ gestation. The increase was linear in 5 of 6 studies, while in 1 study, the mod-MPI was stable until 27 weeks’ gestation, and then increased throughout the third trimester. Despite all having trends increasing over pregnancy, there was no study in which all the weekly means fell within the pooled 95% CI.
Conclusion: While mod-MPI does increase over gestation, the true “reference ranges” for fetuses remain elusive. Future efforts to further optimize calculation of time intervals possibly via automation are desperately needed to allow for reproducibility of this potentially very useful tool to assess fetal cardiac function.
DOI: 10.6084/m9.figshare.24943155
title: Supplementary Material for: Reference Ranges for Left Modified Myocardial Performance Index: Systematic Review and Meta-Analysis

description: Introduction: The modified myocardial performance index (mod-MPI) is a noninvasive Doppler-derived metric used to evaluate fetal cardiac function. However, the reference ranges for mod-MPI in normal fetuses are not clearly defined which limits the use of this technology in fetuses with potential cardiac compromise. Thus, we aimed to perform a systematic review and meta-analysis of published mod-MPI reference ranges across gestation.
Methods: The published literature was systematically searched, and all published articles in any language that provided values for the left ventricular mod-MPI obtained in low-risk, singleton fetuses were considered eligible for further review. All retrieved titles and abstracts were independently reviewed by two researchers. Mean and standard deviation by gestational week was extracted or calculated from published data. DerSimonian-Laird random effects models were used to estimate pooled means and 95% confidence intervals (CIs).
Results: The search resulted in 618 unique citations, of which 583 did not meet inclusion criteria, leaving 35 abstracts selected for full-text review. Review of the references of these 35 articles identified another 5 studies of interest. Of the 40 articles reviewed, six met inclusion criteria. There was significant heterogeneity seen in the mod-MPI results reported. Mod-MPI increased as pregnancy progressed in all studies. The pooled mean mod-MPI at 11 weeks’ gestation was 0.400 (95% CI 0.374- 0.426) and increased to 0.585 (95% CI 0.533-0.637) at 41 weeks’ gestation. The increase was linear in 5 of 6 studies, while in 1 study, the mod-MPI was stable until 27 weeks’ gestation, and then increased throughout the third trimester. Despite all having trends increasing over pregnancy, there was no study in which all the weekly means fell within the pooled 95% CI.
Conclusion: While mod-MPI does increase over gestation, the true “reference ranges” for fetuses remain elusive. Future efforts to further optimize calculation of time intervals possibly via automation are desperately needed to allow for reproducibility of this potentially very useful tool to assess fetal cardiac function.
DOI: 10.6084/m9.figshare.24943155.v3
title: Supplementary Material for: Reference Ranges for Left Modified Myocardial Performance Index: Systematic Review and Meta-Analysis

description: Introduction: The modified myocardial performance index (mod-MPI) is a noninvasive Doppler-derived metric used to evaluate fetal cardiac function. However, the reference ranges for mod-MPI in normal fetuses are not clearly defined which limits the use of this technology in fetuses with potential cardiac compromise. Thus, we aimed to perform a systematic review and meta-analysis of published mod-MPI reference ranges across gestation.
Methods: The published literature was systematically searched, and all published articles in any language that provided values for the left ventricular mod-MPI obtained in low-risk, singleton fetuses were considered eligible for further review. All retrieved titles and abstracts were independently reviewed by two researchers. Mean and standard deviation by gestational week was extracted or calculated from published data. DerSimonian-Laird random effects models were used to estimate pooled means and 95% confidence intervals (CIs).
Results: The search resulted in 618 unique citations, of which 583 did not meet inclusion criteria, leaving 35 abstracts selected for full-text review. Review of the references of these 35 articles identified another 5 studies of interest. Of the 40 articles reviewed, six met inclusion criteria. There was significant heterogeneity seen in the mod-MPI results reported. Mod-MPI increased as pregnancy progressed in all studies. The pooled mean mod-MPI at 11 weeks’ gestation was 0.400 (95% CI 0.374- 0.426) and increased to 0.585 (95% CI 0.533-0.637) at 41 weeks’ gestation. The increase was linear in 5 of 6 studies, while in 1 study, the mod-MPI was stable until 27 weeks’ gestation, and then increased throughout the third trimester. Despite all having trends increasing over pregnancy, there was no study in which all the weekly means fell within the pooled 95% CI.
Conclusion: While mod-MPI does increase over gestation, the true “reference ranges” for fetuses remain elusive. Future efforts to further optimize calculation of time intervals possibly via automation are desperately needed to allow for reproducibility of this potentially very useful tool to assess fetal cardiac function.
DOI: 10.6084/m9.figshare.24943155.v2
title: Supplementary Material for: Reference Ranges for Left Modified Myocardial Performance Index: Systematic Review and Meta-Analysis

description: Introduction: The modified myocardial performance index (mod-MPI) is a noninvasive Doppler-derived metric used to evaluate fetal cardiac function. However, the reference ranges for mod-MPI in normal fetuses are not clearly defined which limits the use of this technology in fetuses with potential cardiac compromise. Thus, we aimed to perform a systematic review and meta-analysis of published mod-MPI reference ranges across gestation.
Methods: The published literature was systematically searched, and all published articles in any language that provided values for the left ventricular mod-MPI obtained in low-risk, singleton fetuses were considered eligible for further review. All retrieved titles and abstracts were independently reviewed by two researchers. Mean and standard deviation by gestational week was extracted or calculated from published data. DerSimonian-Laird random effects models were used to estimate pooled means and 95% confidence intervals (CIs).
Results: The search resulted in 618 unique citations, of which 583 did not meet inclusion criteria, leaving 35 abstracts selected for full-text review. Review of the references of these 35 articles identified another 5 studies of interest. Of the 40 articles reviewed, six met inclusion criteria. There was significant heterogeneity seen in the mod-MPI results reported. Mod-MPI increased as pregnancy progressed in all studies. The pooled mean mod-MPI at 11 weeks’ gestation was 0.400 (95% CI 0.374- 0.426) and increased to 0.585 (95% CI 0.533-0.637) at 41 weeks’ gestation. The increase was linear in 5 of 6 studies, while in 1 study, the mod-MPI was stable until 27 weeks’ gestation, and then increased throughout the third trimester. Despite all having trends increasing over pregnancy, there was no study in which all the weekly means fell within the pooled 95% CI.
Conclusion: While mod-MPI does increase over gestation, the true “reference ranges” for fetuses remain elusive. Future efforts to further optimize calculation of time intervals possibly via automation are desperately needed to allow for reproducibility of this potentially very useful tool to assess fetal cardiac function.
DOI: 10.6084/m9.figshare.25075220
title: Supplementary_Table_5_Epigenetic_state_stool_DEmiRNA_loci.xlsx

description: Epigenetic states computed at miRNA loci considering the data from the Roadmap Epigenomics Project. AT, active TSS; E, Enhancer; Q, Quiescent region; R, Repressed region; ST, Strong transcription; WT, Weak transcription.
DOI: 10.6084/m9.figshare.25075220.v1
title: Supplementary_Table_5_Epigenetic_state_stool_DEmiRNA_loci.xlsx

description: Epigenetic states computed at miRNA loci considering the data from the Roadmap Epigenomics Project. AT, active TSS; E, Enhancer; Q, Quiescent region; R, Repressed region; ST, Strong transcription; WT, Weak transcription.
DOI: 10.6084/m9.figshare.25075217
title: Alignment data (Phylogenetic diversity and morphological characterization of cordycipitaceous species in Taiwan)

description: Species classified in <i>Cordycipitaceae</i> (<i>Hypocreales</i>) include multiple entomopathogenic fungi. Numerous changes have recently occurred in the nomenclature of cordycipitaceous fungi due to the single naming system proposed for pleomorphic fungi in 2011 based on multigene phylogenies. Species of <i>Cordycipitaceae</i> are also widely applied as herbal medicines, especially in Asian cultures. However, the diversity of <i>Cordycipitaceae</i> in Taiwan is based on relatively few records in the literature. Here we conducted a comprehensive survey of this family throughout the island of Taiwan and provided a glimpse of the diversity and distribution patterns. In addition, the present study reassesses the generic and species boundaries of <i>Cordycipitaceae</i> and finally provides an updated phylogenic overview of <i>Cordyceps</i> and allied genera. Phylogenetic reconstructions using combined ITS, nrLSU, <i>tef</i>1-α, <i>rpb</i>1, and <i>rpb</i>2 sequence data, along with morphological features, resulted in ten novel species:<b><i> </i></b><i>Akanthomyces taiwanicus </i><i>sp. nov.</i>,<b><i> </i></b><i>Blackwellomyces taiwanensis</i> <i>sp. nov.</i>, <i>Cordyceps hehuanensis sp. nov</i><i>.</i>, <i>C</i>.<i> locastrae</i><i> sp. nov.</i>, <i>C</i>.<i> malleiformis</i><i> sp. nov.</i>, <i>C</i>.<i> pseudorosea</i><i> sp. nov.</i>, <i>C</i>.<i> siangyangensis </i><i>sp. nov.</i>, <i>Samsoniella lasiocampidarum sp. nov.</i>, <i>S</i>.<i> yuanzuiensis sp. nov.</i>, and <i>Simplicillium salviniae </i><i>sp. nov.</i>; and nine new records for Taiwan: <i>A</i>.<i> kanyawimiae</i>, <i>A</i>.<i> muscarius</i>, <i>S</i>.<i> cardinalis</i>, <i>S</i>.<i> hepiali</i>, <i>B</i>.<i> lii</i>, <i>B</i>.<i> medogensis</i>, <i>C</i>.<i> lepidopterorum</i>, <i>C</i>.<i> neopruinosa</i>,<i> </i>and <i>Si</i>.<i> chinense</i>.<i> </i>Furthermore, we provided DNA sequence data of the ex-type strains of <i>C. ninchukispora </i>for the first time and determined the species limits of the taxon. In addition, the present study proposed to synonymize <i>B. staphylinidicola</i> and <i>C. jakajanicola</i> under <i>B. bassiana</i> and <i>C. lepidopterorum</i>, respectively. Moreover, three species, <i>C. roseostromata, C. kyushuensis</i>, and <i>C. shuifuensis</i>, that clustered within the species clade of <i>C. militaris</i> are proposed to be synonymized under the latter taxon. To maintain the monophyly of <i>Cordyceps</i>, we propose to classify <i>P</i><i>arahevansia koratensis</i> in <i>Cordyceps</i>, which makes the genus <i>P</i><i>arahevansia</i> obsolete.
DOI: 10.6084/m9.figshare.25075217.v1
title: Alignment data (Phylogenetic diversity and morphological characterization of cordycipitaceous species in Taiwan)

description: Species classified in <i>Cordycipitaceae</i> (<i>Hypocreales</i>) include multiple entomopathogenic fungi. Numerous changes have recently occurred in the nomenclature of cordycipitaceous fungi due to the single naming system proposed for pleomorphic fungi in 2011 based on multigene phylogenies. Species of <i>Cordycipitaceae</i> are also widely applied as herbal medicines, especially in Asian cultures. However, the diversity of <i>Cordycipitaceae</i> in Taiwan is based on relatively few records in the literature. Here we conducted a comprehensive survey of this family throughout the island of Taiwan and provided a glimpse of the diversity and distribution patterns. In addition, the present study reassesses the generic and species boundaries of <i>Cordycipitaceae</i> and finally provides an updated phylogenic overview of <i>Cordyceps</i> and allied genera. Phylogenetic reconstructions using combined ITS, nrLSU, <i>tef</i>1-α, <i>rpb</i>1, and <i>rpb</i>2 sequence data, along with morphological features, resulted in ten novel species:<b><i> </i></b><i>Akanthomyces taiwanicus </i><i>sp. nov.</i>,<b><i> </i></b><i>Blackwellomyces taiwanensis</i> <i>sp. nov.</i>, <i>Cordyceps hehuanensis sp. nov</i><i>.</i>, <i>C</i>.<i> locastrae</i><i> sp. nov.</i>, <i>C</i>.<i> malleiformis</i><i> sp. nov.</i>, <i>C</i>.<i> pseudorosea</i><i> sp. nov.</i>, <i>C</i>.<i> siangyangensis </i><i>sp. nov.</i>, <i>Samsoniella lasiocampidarum sp. nov.</i>, <i>S</i>.<i> yuanzuiensis sp. nov.</i>, and <i>Simplicillium salviniae </i><i>sp. nov.</i>; and nine new records for Taiwan: <i>A</i>.<i> kanyawimiae</i>, <i>A</i>.<i> muscarius</i>, <i>S</i>.<i> cardinalis</i>, <i>S</i>.<i> hepiali</i>, <i>B</i>.<i> lii</i>, <i>B</i>.<i> medogensis</i>, <i>C</i>.<i> lepidopterorum</i>, <i>C</i>.<i> neopruinosa</i>,<i> </i>and <i>Si</i>.<i> chinense</i>.<i> </i>Furthermore, we provided DNA sequence data of the ex-type strains of <i>C. ninchukispora </i>for the first time and determined the species limits of the taxon. In addition, the present study proposed to synonymize <i>B. staphylinidicola</i> and <i>C. jakajanicola</i> under <i>B. bassiana</i> and <i>C. lepidopterorum</i>, respectively. Moreover, three species, <i>C. roseostromata, C. kyushuensis</i>, and <i>C. shuifuensis</i>, that clustered within the species clade of <i>C. militaris</i> are proposed to be synonymized under the latter taxon. To maintain the monophyly of <i>Cordyceps</i>, we propose to classify <i>P</i><i>arahevansia koratensis</i> in <i>Cordyceps</i>, which makes the genus <i>P</i><i>arahevansia</i> obsolete.
DOI: 10.5281/zenodo.10561417
title: Supplementary data for: The mechanism of mammalian proton-coupled peptide transporters

description: This is the supplementary data for our paper "The mechanism of mammalian proton-coupled peptide transporters".

Abstract:

Proton-coupled oligopeptide transporters (POTs) are of great pharmaceutical interest owing to their promiscuoussubstrate binding site that has been linked to improved oral bioavailability of several classes of drugs. Members of thePOT family are conserved across all phylogenetic kingdoms and function by coupling peptide uptake to the protonelectrochemical gradient. Cryo-EM structures and alphafold models have recently provided new insights into differentconformational states of two mammalian POTs, SLC15A1 and SLC15A2. Nevertheless, these studies leave openimportant questions regarding the mechanism of proton and substrate coupling, while simultaneously providing aunique opportunity to investigate these processes using molecular dynamics (MD) simulations. Here, we employextensive unbiased and enhanced-sampling MD to map out the full SLC15A2 conformational cycle and itsthermodynamic driving forces. By computing conformational free energy landscapes in different protonation states andin the absence or presence of peptide substrate, we identify a likely sequence of intermediate protonation steps thatdrive inward-directed alternating access. These simulations identify key differences in the extracellular gate betweenmammalian and bacterial POTs, which we validate experimentally in cell-based transport assays. Our results fromconstant-PH MD and absolute binding free energy (ABFE) calculations also establish a mechanistic link between protonbinding and peptide recognition, revealing key details underpining secondary active transport in POTs. This studyprovides a vital step forward in understanding proton-coupled peptide and drug transport in mammals and pave theway to integrate knowledge of solute carrier structural biology with enhanced drug design to target tissue and organbioavailability.

 

This project was funded by the Wellcome Trust (Grant ID: 218514/Z/19/Z). Compute resources were also provided bythe EPSRC ARCHER2, Jade 2 and N8 CIR BEDE facilities, granted via the High-End Computing Consortium for BiomolecularSimulation (HECBioSim), supported by EPSRC (EP/X035603/1).