cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8215106
title: A machine learning-based high-precision density functional method for drug-like molecules

description: Models
The repo contains the models and test datasets for our aticles. The energy unit is in Hartree, The coordinate unit is in Bohr.
## DeePHF
you need first prepare the `dm_eig.npy` in data_test and do predict `l_e_delta.npy`, you can use
```
deepks test -m model.pth -o test/test -d data_test/* -D dm_eig -G
```
## DeePKS
first you should prepare the `atom.npy`, and `energy.npy` in data_test. you can test the datasets by command. 
```
deepks scf scf_input.yaml -m model.pth -s data_test -d test_out
```
# Datasets
All datasets only have `atom.npy` and `energy.npy`. The coordinate unit is `bohr`, and energy unit is `Hartree`.
## small molecules torsion
Contains 62 small molecules with 36 conformation for each under CCSD(T)/def2-TZVP.
 
[1] B. D. Sellers, N. C. James, A. Gobbi, A comparison of quantum and molecular mechanical methods to estimate strain energy in druglike fragments, Journal of chemical information and modeling 57 (6) (2017) 1265–127
 
## MPCONF91
Contains 6 molecules with 91 conformations under LNO-CCSD(T)/def2-TZVP.
 
[1] J. Rezac, D. Bím, O. Gutten, L. Rulisek, Toward accurate conformational energies of smaller peptides and medium-sized macrocycles: Mpconf196 benchmark energy data set, Journal of chemical theory and computation 14 (3) (2018) 1254–1
 
## torsionNet206
Contains 206 molecules with 4494 conformations under CCSD(T)/def2-TZVP.
 
[1] B. K. Rai, V. Sresht, Q. Yang, R. Unwalla, M. Tu, A. M. Mathiowetz,G. A. Bakken, Torsionnet: A deep neural network to rapidly predict small-molecule torsional energy profiles with the accuracy of quantum mechanics, Journal of Chemical Information and Modeling 62 (4) (2022) 785–80
 
## Out-of-plane bending
Contains 242 molecules with 3315 conformations under CCSD(T)/def2-TZVP.
 
[1] X. Yang, C. Liu, P. Ren, High order ab initio valence force field with chemical pattern based parameter assignment., Journal of Computational Biophysics and Chemistry 21 (4) (2021) 43
 
## DrugBank-T
Contains 165 molecules with 1155 conformations under CCSD(T)/def2-TZVP.
 
[1] V. Law, C. Knox, Y. Djoumbou, T. Jewison, A. C. Guo, Y. Liu, A. Maciejewski, D. Arndt, M. Wilson, V. Neveu, et al., Drugbank
4.0: shedding new light on drug metabolism, Nucleic acids research 42 (D1) (2014) D1091–D1097  
[2] Z. Qiao, M. Welborn, A. Anandkumar, F. R. Manby, T. F. Miller III, Orbnet: Deep learning for quantum chemistry using symmetry adapted atomic-orbital features, The Journal of chemical physics 153 (12) (2020) 124111
## Notice
if you use above datasets, please cite the original articals too
DOI: 10.6084/m9.figshare.24965211
title: Divergent responses between lineages of arbuscular mycorrhizal fungi to soil phosphorus and nitrogen availability

description: Here, we analysed data from a DNA-based survey of fungal communities in soils collected throughout Australia to observe relationships among soil fertility and the abundance of two arbuscular mycorrhizal fungal taxa that reportedly vary in function – the Gigasporaceae (putatively more important for nutrient uptake) and Glomeraceae (putatively more important for biotic stress). Relationships were assessed in three vegetation types – grasslands, forests and woodlands – to assess whether associations with soil fertility varied depending on carbon availability for arbuscular mycorrhizal fungi.
DOI: 10.6084/m9.figshare.13580290
title: Diagnosis of Dry Eye Disease Using Principal Component Analysis: A Study in Animal Models of the Disease

description: To evaluate whether principal component analysis (PCA) can assess various diagnostic tests of dry eye disease (DED), providing a simplified, more informative measure of disease status than individual clinical test parameters (ICTP). ICTP were analyzed using PCA in two groups of normal rabbits (Groups 1 and 2). Group 3, not truly normal, was also assessed. DED was induced in Group 1 by complete dacryoadenectomy; in Groups 2 and 3 by injection of concanavalin A. Tear break up time, tear osmolarity, Schirmer’s tear test and rose bengal staining were the ICTP measured in all groups. Statistical analysis including descriptive statistics, t test, correlation coefficients and PCA was done. PCA using ICTP data from Group 1 generated axes; Group 2 and 3 were plotted over these axes. All groups had induction of DED. Correlations for all ICTP were in the correct direction and were strongest for Group 1 and weakest in Group 3. PCA clearly separated DED and normal eyes. Principal component (PC) 1, made up of nearly equal contributions from the four clinical tests, explained 73% of the variation and provided a means to separate normal from DED. PC 1 values under 0.52 can be mathematically defined as DED. Of all pairwise comparisons, PC 1 vs PC 2 and PC 1 vs PC 3 were the most informative providing excellent spatial separation and additional information regarding DED status. PCA proved useful for evaluating DED providing a simpler, more comprehensive assessment than ICTP. PC 1 is a valuable, clinically relevant, and informative metric for DED status and severity having superior diagnostic value and statistical strength compared to ICTP. Spatial information on biplots of PC 1 vs PC 3 is also informative. PCA, and specifically PC 1, has the potential to serve as a biomarker for DED.
DOI: 10.6084/m9.figshare.13580290.v1
title: Diagnosis of Dry Eye Disease Using Principal Component Analysis: A Study in Animal Models of the Disease

description: To evaluate whether principal component analysis (PCA) can assess various diagnostic tests of dry eye disease (DED), providing a simplified, more informative measure of disease status than individual clinical test parameters (ICTP). ICTP were analyzed using PCA in two groups of normal rabbits (Groups 1 and 2). Group 3, not truly normal, was also assessed. DED was induced in Group 1 by complete dacryoadenectomy; in Groups 2 and 3 by injection of concanavalin A. Tear break up time, tear osmolarity, Schirmer’s tear test and rose bengal staining were the ICTP measured in all groups. Statistical analysis including descriptive statistics, t test, correlation coefficients and PCA was done. PCA using ICTP data from Group 1 generated axes; Group 2 and 3 were plotted over these axes. All groups had induction of DED. Correlations for all ICTP were in the correct direction and were strongest for Group 1 and weakest in Group 3. PCA clearly separated DED and normal eyes. Principal component (PC) 1, made up of nearly equal contributions from the four clinical tests, explained 73% of the variation and provided a means to separate normal from DED. PC 1 values under 0.52 can be mathematically defined as DED. Of all pairwise comparisons, PC 1 vs PC 2 and PC 1 vs PC 3 were the most informative providing excellent spatial separation and additional information regarding DED status. PCA proved useful for evaluating DED providing a simpler, more comprehensive assessment than ICTP. PC 1 is a valuable, clinically relevant, and informative metric for DED status and severity having superior diagnostic value and statistical strength compared to ICTP. Spatial information on biplots of PC 1 vs PC 3 is also informative. PCA, and specifically PC 1, has the potential to serve as a biomarker for DED.
DOI: 10.6084/m9.figshare.13013086
title: High Correlation between Glaucoma Treatment with Topical Prostaglandin Analogs and BDNF Immunoreactivity in Human Retina

description: To examine the expression of brain-derived neurotrophic factor (BDNF) and its high-affinity receptor, tropomyosin-related kinase receptor-B (TrkB), in normal and glaucomatous human retinas. Human retinas were collected from 8 donors who had been clinically diagnosed and treated for glaucoma, and from 9 control donors. Immunohistochemical analysis for BDNF and TrkB was performed. The percent of each retina expressing BDNF and TrkB was quantified for the total retinal thickness, and separately for the retinal ganglion cell (RGC) complex + retinal nerve fiber layer (RNFL). The expression of each protein was correlated with clinical outcomes obtained from the subject’s ocular histories. There was no significant difference in BDNF or TrkB expression when comparing glaucomatous and control retinas. Correlation analysis revealed a significant relationship between BDNF expression and the use of prostaglandin analogs. TrkB expression was highly correlated with the last-measured intraocular pressure (IOP), the use of carbonic anhydrase inhibitors, the use of beta blockers, and the total number of drugs used for the treatment of glaucoma. Topical drugs used to treat glaucoma were associated with an increase in retinal BDNF and TrkB expression in human retina, independent of IOP, which may represent molecular evidence of neuroprotective pathway activation.
DOI: 10.6084/m9.figshare.13013086.v1
title: High Correlation between Glaucoma Treatment with Topical Prostaglandin Analogs and BDNF Immunoreactivity in Human Retina

description: To examine the expression of brain-derived neurotrophic factor (BDNF) and its high-affinity receptor, tropomyosin-related kinase receptor-B (TrkB), in normal and glaucomatous human retinas. Human retinas were collected from 8 donors who had been clinically diagnosed and treated for glaucoma, and from 9 control donors. Immunohistochemical analysis for BDNF and TrkB was performed. The percent of each retina expressing BDNF and TrkB was quantified for the total retinal thickness, and separately for the retinal ganglion cell (RGC) complex + retinal nerve fiber layer (RNFL). The expression of each protein was correlated with clinical outcomes obtained from the subject’s ocular histories. There was no significant difference in BDNF or TrkB expression when comparing glaucomatous and control retinas. Correlation analysis revealed a significant relationship between BDNF expression and the use of prostaglandin analogs. TrkB expression was highly correlated with the last-measured intraocular pressure (IOP), the use of carbonic anhydrase inhibitors, the use of beta blockers, and the total number of drugs used for the treatment of glaucoma. Topical drugs used to treat glaucoma were associated with an increase in retinal BDNF and TrkB expression in human retina, independent of IOP, which may represent molecular evidence of neuroprotective pathway activation.
DOI: 10.13026/n8k7-bh29
title: Neurocritical care waveform recordings in pediatric patients

description: This database contains de-identified, time-locked waveform recordings from
pediatric patients in neurocritical care. Typical waveforms collected at the
bedside include arterial blood pressure, intracranial pressure, and cerebral
blood flow velocity. Additionally, information include the hematocrit and the
vertical location (i.e. height) of the blood pressure transducer and
intracranial pressure transducer to account for potential hydrostatic pressure
differences between the two pressure measurements. In total, the initial
release contains data from 12 patients with a variety of pathologies
necessitating invasive intracranial pressure monitoring. The total recording
duration is about 10 hours across all patients and studies.
DOI: 10.13026/5kvn-pp29
title: Neurocritical care waveform recordings in pediatric patients

description: This database contains de-identified, time-locked waveform recordings from
pediatric patients in neurocritical care. Typical waveforms collected at the
bedside include arterial blood pressure, intracranial pressure, and cerebral
blood flow velocity. Additionally, information include the hematocrit and the
vertical location (i.e. height) of the blood pressure transducer and
intracranial pressure transducer to account for potential hydrostatic pressure
differences between the two pressure measurements. In total, the initial
release contains data from 12 patients with a variety of pathologies
necessitating invasive intracranial pressure monitoring. The total recording
duration is about 10 hours across all patients and studies.
DOI: 10.17909/ms3f-q239
title: TESS light curves of OO Leo

description: OO Leo DOI
DOI: 10.6084/m9.figshare.13146166
title: Variants in <i>RCBTB1</i> are Associated with Autosomal Recessive Retinitis Pigmentosa but Not Autosomal Dominant FEVR

description: Variants in <i>RCBTB1</i> have been reported in autosomal recessive inherited retinal dystrophies and autosomal dominant familial exudative vitreoretinopathy (FEVR). This study aims to verify the correlation between <i>RCBTB1</i> variations and phenotypes. Variants in <i>RCBTB1</i> were selected from 6303 unrelated families with different forms of eye conditions based on whole exome sequencing and targeted exome sequencing. Potential pathogenic truncation variants were filtered by multistep bioinformatics analysis and identified by Sanger sequencing. Segregation and enrichment analysis were used to evaluate the association of truncation variants in <i>RCBTB1</i> with phenotypes. Biallelic damaging variants in <i>RCBTB1</i> were found in one family while heterozygous truncation variants were detected in 28 unrelated families based on our in-house data from 6303 unrelated families. Totally, 11 variants were present in the 29 families, including seven frameshift variants, three splicing variants, and one nonsense variant. The biallelic variants, c.170delG and c.905_906insTT, were identified in an isolated case with retinitis pigmentosa (RP). Heterozygous truncation variants were distributed in different forms of eye conditions (including normal) without significant enrichment in FEVR, suggesting unrelatedness to specific eye diseases. The frequency and location of truncation variants in the 6303 samples are comparable with the East Asian data from gnomAD. Segregation analysis of available family members further demonstrated the nonpathogenic nature of heterozygous truncation variants. Contrary to the previous report, heterozygous truncation variants in <i>RCBTB1</i> are not associated with FEVR based on our data. The extreme rareness of biallelic truncation variants present in a singleton case with RP further suggests that variants in <i>RCBTB1</i> are responsible for autosomal recessive RP. This result reminds us that variants of a gene with certain diseases should be thoroughly verified before the use of such information in clinical practice.
DOI: 10.6084/m9.figshare.13146166.v1
title: Variants in <i>RCBTB1</i> are associated with autosomal recessive retinitis pigmentosa but not autosomal dominant FEVR

description: Purpose: Variants in <i>RCBTB1</i> have been reported in autosomal recessive inherited retinal dystrophies and autosomal dominant familial exudative vitreoretinopathy (FEVR). This study aims to verify the correlation between <i>RCBTB1</i> variations and phenotypes. Methods: Variants in <i>RCBTB1</i> were selected from 6303 unrelated families with different forms of eye conditions based on whole exome sequencing and targeted exome sequencing. Potential pathogenic truncation variants were filtered by multistep bioinformatics analysis and identified by Sanger sequencing. Segregation and enrichment analysis were used to evaluate the association of truncation variants in <i>RCBTB1</i> with phenotypes. Results: Biallelic damaging variants in <i>RCBTB1</i> were found in one family while heterozygous truncation variants were detected in 28 unrelated families based on our in-house data from 6303 unrelated families. Totally, 11 variants were present in the 29 families, including seven frameshift variants, three splicing variants, and one nonsense variant. The biallelic variants, c.170delG and c.905_906insTT, were identified in an isolated case with retinitis pigmentosa (RP). Heterozygous truncation variants were distributed in different forms of eye conditions (including normal) without significant enrichment in FEVR, suggesting unrelatedness to specific eye diseases. The frequency and location of truncation variants in the 6303 samples are comparable with the East Asian data from gnomAD. Segregation analysis of available family members further demonstrated the nonpathogenic nature of heterozygous truncation variants. Conclusions: Contrary to the previous report, heterozygous truncation variants in <i>RCBTB1</i> are not associated with FEVR based on our data. The extreme rareness of biallelic truncation variants present in a singleton case with RP further suggests that variants in <i>RCBTB1</i> are responsible for autosomal recessive RP. This result reminds us that variants of a gene with certain diseases should be thoroughly verified before the use of such information in clinical practice.
DOI: 10.6084/m9.figshare.13146166.v2
title: Variants in <i>RCBTB1</i> are Associated with Autosomal Recessive Retinitis Pigmentosa but Not Autosomal Dominant FEVR

description: Variants in <i>RCBTB1</i> have been reported in autosomal recessive inherited retinal dystrophies and autosomal dominant familial exudative vitreoretinopathy (FEVR). This study aims to verify the correlation between <i>RCBTB1</i> variations and phenotypes. Variants in <i>RCBTB1</i> were selected from 6303 unrelated families with different forms of eye conditions based on whole exome sequencing and targeted exome sequencing. Potential pathogenic truncation variants were filtered by multistep bioinformatics analysis and identified by Sanger sequencing. Segregation and enrichment analysis were used to evaluate the association of truncation variants in <i>RCBTB1</i> with phenotypes. Biallelic damaging variants in <i>RCBTB1</i> were found in one family while heterozygous truncation variants were detected in 28 unrelated families based on our in-house data from 6303 unrelated families. Totally, 11 variants were present in the 29 families, including seven frameshift variants, three splicing variants, and one nonsense variant. The biallelic variants, c.170delG and c.905_906insTT, were identified in an isolated case with retinitis pigmentosa (RP). Heterozygous truncation variants were distributed in different forms of eye conditions (including normal) without significant enrichment in FEVR, suggesting unrelatedness to specific eye diseases. The frequency and location of truncation variants in the 6303 samples are comparable with the East Asian data from gnomAD. Segregation analysis of available family members further demonstrated the nonpathogenic nature of heterozygous truncation variants. Contrary to the previous report, heterozygous truncation variants in <i>RCBTB1</i> are not associated with FEVR based on our data. The extreme rareness of biallelic truncation variants present in a singleton case with RP further suggests that variants in <i>RCBTB1</i> are responsible for autosomal recessive RP. This result reminds us that variants of a gene with certain diseases should be thoroughly verified before the use of such information in clinical practice.
DOI: 10.6084/m9.figshare.22579600
title: Raw data: Behavioural sleep in salmonid fish with flexible diel activity

description: This is the raw data for Behavioural sleep in salmonid fish with flexible diel activity, which was used in the study on Furusawa and Koizumi (unpublished data)
DOI: 10.6084/m9.figshare.22579600.v1
title: Raw data: Behavioural sleep in salmonid fish with flexible diel activity

description: This is the raw data for Behavioural sleep in salmonid fish with flexible diel activity, which was used in the study on Furusawa and Koizumi (unpublished data)
DOI: 10.25914/tt34-0b43
title: AURA - Historical Ground Reflectivity
DOI: 10.5281/zenodo.10046414
title: Increase in the Indian Southwest monsoon strength since the seventeenth century

description: The following data constitute grain size distribution, stable isotope data of oxygen, carbon, and nitrogen isotopes, and XRF data.
DOI: 10.5281/zenodo.10046415
title: Increase in the Indian Southwest monsoon strength since the seventeenth century

description: The following data constitute grain size distribution, stable isotope data of oxygen, carbon, and nitrogen isotopes, and XRF data.
DOI: 10.5281/zenodo.10472691
title: Increase in the Indian Southwest monsoon strength since the seventeenth century

description: The following data constitute grain size distribution, stable isotope data of oxygen, carbon, and nitrogen isotopes, and XRF data.
DOI: 10.5281/zenodo.10467482
title: Data for: Carbapenemase-producing Enterobacterales colonisation status does not lead to more frequent admissions: a linked patient study

description: Data required to reproduce results for the paper titled Carbapenemase-producing Enterobacterales colonisation status does not lead to more frequent admissions: a linked patient study. Dataset was provided by the Centre for Victorian Data Linkage, Government of Victoria, Australia.
DOI: 10.5281/zenodo.10467483
title: Data for: Carbapenemase-producing Enterobacterales colonisation status does not lead to more frequent admissions: a linked patient study

description: Data required to reproduce results for the paper titled Carbapenemase-producing Enterobacterales colonisation status does not lead to more frequent admissions: a linked patient study. Dataset was provided by the Centre for Victorian Data Linkage, Government of Victoria, Australia.
DOI: 10.6084/m9.figshare.24966156
title: Supplementary Material for: Systemic glucose regulation by a hindbrain inhibitory circuit in a mouse model of type 1 diabetes

description: Introduction. Previous work showed that increasing the electrical activity of inhibitory neurons in the dorsal vagal complex (DVC) is sufficient to increase whole-body glucose concentration in normoglycemic mice. Here we tested the hypothesis that deactivating GABAergic neurons in the dorsal hindbrain of hyperglycemic mice decreases synaptic inhibition of parasympathetic motor neurons in the dorsal motor nucleus of the vagus (DMV) and reduces systemic glucose levels. 
Methods. Chemogenetic activation or inactivation of GABAergic neurons in the nucleus tractus solitarius (NTS) was used to assess effects of modulating parasympathetic output on blood glucose concentration in normoglycemic and hyperglycemic mice. Patch-clamp electrophysiology in vitro was used to assess cellular effects of chemogenetic manipulation of NTS GABA neurons.
Results. Chemogenetic activation of GABAergic NTS neurons in from normoglycemic mice increased their action potential firing, resulting in increased inhibitory synaptic input to DMV motor neurons and elevated blood glucose concentration. Deactivation of GABAergic DVC neurons in normoglycemic mice altered their electrical activity but did not alter systemic glucose levels. Conversely, stimulation of GABAergic DVC neurons in mice that were hyperglycemic subsequent to treatment with streptozotocin changed their electrical activity but did not alter whole-body glucose concentration, while deactivation of this inhibitory circuit significantly decreased circulating glucose concentration. Peripheral administration of a brain impermeant muscarinic acetylcholine receptor antagonist abolished these effects. 
Conclusion. Disinhibiting vagal motor neurons decreases hyperglycemia in a mouse model of type 1 diabetes. This inhibitory brainstem circuit emerges as a key parasympathetic regulator of whole-body glucose homeostasis that undergoes functional plasticity in hyperglycemic conditions.