cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28936904.v1
title: Catechins anti-diabetic actions are mediated via multiple receptors, a mechanism deduced via molecular docking and dynamic simulations

description: Diabetes mellitus is a growing burden that affects a large proportion of the population worldwide, with long-term complications that cause a devastating effect on the function of various organs. The currently available treatments lack optimum therapeutic goals, increasing the need for new drug discovery. Catechins are natural flavonoids that demonstrate anti-diabetic effects; however, catechin’s mechanism of action remains unclear. This study was aimed to unleash the molecular mechanism behind the catechin’s effect on blood glucose levels. For that, we explored the capability of some catechins to bind and interact with glucagon-like peptide-1 receptor-1, pancreatic ATP-sensitive potassium channel, dipeptidyl peptidase-4, and sodium-glucose transporter-2, which is essential for euglycemia, using molecular docking screening and dynamic simulations. The results showed that all the tested catechins are potential sodium-glucose transporter-2 inhibitors, a mechanism revealed for the first time, and glucagon-like peptide-1 receptor-1 agonists with various affinities to these receptors. Moreover, among these compounds, (−)-Epigallocatechin 3-O-gallate, (−)-Gallocatechin 3-O-gallate demonstrated the ability to act as an ATP-sensitive potassium channel inhibitor, and dipeptidyl peptidase-4 inhibitor in addition to the previously mentioned mechanisms. The discovery introduces (−)-gallocatechin 3-O-gallate and (−)-Epigallocatechin 3-O-gallate as a hot subject for research, as the compounds require further optimization to initiate further pre-clinical and clinical studies.
DOI: 10.25549/garland-ouc11399mx1u
title: Lee W. Haggin, letter, 1916-05-19, to Hamlin Garland

description: Lee W. Haggin, Lärad, Onteora Park, Tannersville, New York, USA, letter, [1916] May 19, to Hamlin Garland. "I am going to town on the 22nd and shall be stopping..." -- first line.
DOI: 10.25549/garland-ouc11399mx1w
title: Lee W. Haggin, letter, 1916-02-03, to Hamlin Garland

description: Lee W. Haggin, 121 Madison Avenue, New York, New York, USA, letter, 1916 February 3, to Hamlin Garland. "I am pretty well thank you. How are you?" -- first line.
DOI: 10.6084/m9.figshare.27316624
title: Structural insights into the toxicity of type II ribosome inactivating proteins (RIPs): a molecular dynamics study

description: Ribosome Inactivating Proteins (RIPs) act by irreversibly depurinating the 28S rRNA ricin-sarcin loop (SRL) of the eukaryotic ribosome resulting in protein synthesis inhibition. In general, they consist of two variants: Type I which is single chained (∼30 kDa), and Type II, a more toxic variant which is a Type I N-glycosidase chain covalently linked to a lectin chain. These proteins are believed to play a pivotal role in defence mechanisms. Intriguingly, non-toxic variants of such toxic proteins do exist in nature. To explore their mode of action, in the present study we have selected three toxic (Ricin, Ebulin and HmRIP) as well as two non-toxic (BGSL and SGSL) RIPs and performed molecular docking and molecular dynamic simulations with the SRL loop. This study throws light on the structural stability and plasticity of the toxic and non-toxic RIP complexes. Furthermore, analysis of the active site cavity volume and binding free energy calculations reveal that the SRL, particularly the specific adenine (A4605), is relatively unstable in the case of non-toxic RIPs which is also supported by the free binding energy calculations, and the pocket size analysis indicates the abnormal increase in active site cavity volume of non-toxic RIPs with time. This first-of-its-kind comprehensive study of toxic and non-toxic RIPs gives insights about the mode of action and the dynamic nature of their interaction with the SRL loop. These observations will be helpful in the development of toxoids against RIPs and also in designing novel therapeutic approaches against human diseases.
DOI: 10.6084/m9.figshare.27316624.v1
title: Structural insights into the toxicity of type II ribosome inactivating proteins (RIPs): a molecular dynamics study

description: Ribosome Inactivating Proteins (RIPs) act by irreversibly depurinating the 28S rRNA ricin-sarcin loop (SRL) of the eukaryotic ribosome resulting in protein synthesis inhibition. In general, they consist of two variants: Type I which is single chained (∼30 kDa), and Type II, a more toxic variant which is a Type I N-glycosidase chain covalently linked to a lectin chain. These proteins are believed to play a pivotal role in defence mechanisms. Intriguingly, non-toxic variants of such toxic proteins do exist in nature. To explore their mode of action, in the present study we have selected three toxic (Ricin, Ebulin and HmRIP) as well as two non-toxic (BGSL and SGSL) RIPs and performed molecular docking and molecular dynamic simulations with the SRL loop. This study throws light on the structural stability and plasticity of the toxic and non-toxic RIP complexes. Furthermore, analysis of the active site cavity volume and binding free energy calculations reveal that the SRL, particularly the specific adenine (A4605), is relatively unstable in the case of non-toxic RIPs which is also supported by the free binding energy calculations, and the pocket size analysis indicates the abnormal increase in active site cavity volume of non-toxic RIPs with time. This first-of-its-kind comprehensive study of toxic and non-toxic RIPs gives insights about the mode of action and the dynamic nature of their interaction with the SRL loop. These observations will be helpful in the development of toxoids against RIPs and also in designing novel therapeutic approaches against human diseases.
DOI: 10.25549/garland-ouc11399mwma
title: George Bird Grinnell, letter, 1902-04-23, to Hamlin Garland

description: George Bird Grinnell (Forest and Stream Publishing Company), 346 Broadway, New York, New York, USA, letter, 1902 April 23, to Hamlin Garland, 474 Elm Street, Chicago, USA. "Your letter of the 15th reached here two or three days since, and I am glad to hear from you." -- first line.
DOI: 10.6084/m9.figshare.27643940
title: Structural and functional consequences of non-synonymous SNPs within the LAMA2 protein: a molecular dynamics perspective

description: Clinical phenotypic presentations associated with LAMA2 deficiency have shown a variety of manifestations. LAMA2 mutations are mainly linked to congenital muscular dystrophy, but there is also mounting evidence suggesting their presence in inflammatory breast cancer, laryngopharyngeal squamous cell carcinoma, and ventricular tachycardia related to coronary artery disease and cardiomyopathy. This study examined the structural and functional impacts of 144 non-synonymous single nucleotide polymorphisms (nsSNPs) within the LAMA2 gene. Through multi-tiered sequence and structure-based methods, 11 deleterious and destabilizing mutations were identified (A1362T, E1308Q, E1360G, I1276S, L1195P, M1359T, P1232H, P1238A, P1272L, Y1234H, Y1338C). Further, four mutations (L1195P, Y1234H, P1238A, A1362T), which aligned with conserved positions, were subjected to 500 ns molecular dynamics (MD) simulations. RMSD calculated from MD trajectories highlighted structural disparities between wild-type and mutant forms, with the latter showing greater flexibility. Radius of gyration analysis indicated reduced compactness, solvent accessibility changes suggested unfolding, and hydrogen bond (HB) analysis demonstrated disrupted integrity. The HB analysis revealed disruptions in structural integrity due to diminished hydrogen bonds in mutants. Secondary structure analysis revealed significant alterations in secondary structural content. Principal Component Analysis unveiled increased dynamic behavior in mutants. Gibbs free energy landscape analysis reflected distinct energy minima regions in mutants, indicating structural destabilization. Overall, this study revealed the functional and structural ramifications of nsSNPs in the LAMA2 gene, providing valuable insights into potential disease-causing mutations and warranting future research on understanding LAMA2 associated diseases and disorders.
DOI: 10.6084/m9.figshare.27643940.v1
title: Structural and functional consequences of non-synonymous SNPs within the LAMA2 protein: a molecular dynamics perspective

description: Clinical phenotypic presentations associated with LAMA2 deficiency have shown a variety of manifestations. LAMA2 mutations are mainly linked to congenital muscular dystrophy, but there is also mounting evidence suggesting their presence in inflammatory breast cancer, laryngopharyngeal squamous cell carcinoma, and ventricular tachycardia related to coronary artery disease and cardiomyopathy. This study examined the structural and functional impacts of 144 non-synonymous single nucleotide polymorphisms (nsSNPs) within the LAMA2 gene. Through multi-tiered sequence and structure-based methods, 11 deleterious and destabilizing mutations were identified (A1362T, E1308Q, E1360G, I1276S, L1195P, M1359T, P1232H, P1238A, P1272L, Y1234H, Y1338C). Further, four mutations (L1195P, Y1234H, P1238A, A1362T), which aligned with conserved positions, were subjected to 500 ns molecular dynamics (MD) simulations. RMSD calculated from MD trajectories highlighted structural disparities between wild-type and mutant forms, with the latter showing greater flexibility. Radius of gyration analysis indicated reduced compactness, solvent accessibility changes suggested unfolding, and hydrogen bond (HB) analysis demonstrated disrupted integrity. The HB analysis revealed disruptions in structural integrity due to diminished hydrogen bonds in mutants. Secondary structure analysis revealed significant alterations in secondary structural content. Principal Component Analysis unveiled increased dynamic behavior in mutants. Gibbs free energy landscape analysis reflected distinct energy minima regions in mutants, indicating structural destabilization. Overall, this study revealed the functional and structural ramifications of nsSNPs in the LAMA2 gene, providing valuable insights into potential disease-causing mutations and warranting future research on understanding LAMA2 associated diseases and disorders.
DOI: 10.6084/m9.figshare.28943658
title: Computational study of diol camptothecin drug delivery process using MPEG-1-based nanosome structure: molecular dynamics approach

description: In recent years, the drug delivery process has become important for effective treatments of various diseases. However, drug carrier design is a complex procedure and many of designed structures do not perform well. Nanostructures are promising systems for effective drug delivery process. Between nanostructures, nanosomes are effective vesicles of spherical shape that can be created from different self-assembled nanosize components. It is expected the appropriate design of nanosome-based samples, introduced a suitable drug carrier for clinical applications. In current research, we introduced macrophage-expressed gene (MPEG-1) protein-based nanosome performance in diol camptothecin (CPT(OH)<sub>2</sub>) drug delivery process in aqueous environment for the first time. The molecular dynamics (MD) method implemented for this purpose by using dreiding force field. Our MD simulations were performed two main phases. In the first phase, defined samples equilibrated at initial condition (<i>T</i><sub>0</sub> = 300 K and <i>P</i><sub>0</sub> = 1 bar). Then, drug delivery performance of equilibrated samples was reported. Computational outputs predicted atomic stability of samples in standard condition. This performance is conducted from kinetic and potential energies convergence in equilibrium phase. Also, drug delivery process was detected after 0.12 ns in aqueous environment. Numerically, drug delivery ratio reached to 66%. Furthermore, zeta potential converged to −2.20 mV after 100 ns. From these outputs, we concluded MPEG-1-based nanosome can be used in actual cases for drug delivery in clinical applications.
DOI: 10.6084/m9.figshare.28943658.v1
title: Computational study of diol camptothecin drug delivery process using MPEG-1-based nanosome structure: molecular dynamics approach

description: In recent years, the drug delivery process has become important for effective treatments of various diseases. However, drug carrier design is a complex procedure and many of designed structures do not perform well. Nanostructures are promising systems for effective drug delivery process. Between nanostructures, nanosomes are effective vesicles of spherical shape that can be created from different self-assembled nanosize components. It is expected the appropriate design of nanosome-based samples, introduced a suitable drug carrier for clinical applications. In current research, we introduced macrophage-expressed gene (MPEG-1) protein-based nanosome performance in diol camptothecin (CPT(OH)<sub>2</sub>) drug delivery process in aqueous environment for the first time. The molecular dynamics (MD) method implemented for this purpose by using dreiding force field. Our MD simulations were performed two main phases. In the first phase, defined samples equilibrated at initial condition (<i>T</i><sub>0</sub> = 300 K and <i>P</i><sub>0</sub> = 1 bar). Then, drug delivery performance of equilibrated samples was reported. Computational outputs predicted atomic stability of samples in standard condition. This performance is conducted from kinetic and potential energies convergence in equilibrium phase. Also, drug delivery process was detected after 0.12 ns in aqueous environment. Numerically, drug delivery ratio reached to 66%. Furthermore, zeta potential converged to −2.20 mV after 100 ns. From these outputs, we concluded MPEG-1-based nanosome can be used in actual cases for drug delivery in clinical applications.
DOI: 10.25549/garland-ouc11399mwn2
title: Hamlin Garland, letter, 1916-05-10, to Alexander Grosset

description: Hamlin Garland, letter, [1916] May 10, to Alexander Grosset. "There is some talk of putting Hesper out in June." -- first line.
DOI: 10.6084/m9.figshare.28333495
title: Unraveling the gender-specific molecular landscape of lung squamous cell carcinoma progression

description: Lung squamous cell carcinoma (LUSC) is a type of non-small cell lung cancer that is the most common and deadly type of lung cancer, originating from the cells lining the bronchi. The progression of LUSC is influenced by various factors, such as genetic, viral, environmental and hormonal factors, immune system response, and smoking history. Despite extensive studies aimed at improving patient survival, the role of gender-specific molecular variants in LUSC progression remains unclear. Using a systems biology approach, combining differential gene expression, network analysis, and machine learning, aberrant mRNA and ncRNAs implicated in LUSC have been identified to improve patient survival, stratify patients and develop novel prognostic strategies. Furthermore, a systematic analysis of the prognostic implications and functional annotations of the molecular variants results in the filtering of key protein-coding genes and non-coding RNAs that are involved in tumor progression. We found several common molecular variants in both genders, including 4 mRNA, 4 miRNAs, and 27 lncRNAs. Among the shared lncRNAs, 5 were novel for both genders. These were found to have a poor prognostic performance in patients with lung cancer. The key players are involved in DNA replication, nucleotide excision repair, complement and coagulation cascades, and estrogen signaling pathways. In this study, we report lncRNAs (PVT1, FAM13A-AS1, LINC00461, NAV2-AS5, PRICKLE2-AS1, and VCAN-AS1) that may function as oncogenes or tumor suppressors by regulating the expression of coding genes, such as RAB24, HECW2, LGR4, and FKBP5. These lncRNAs and coding genes may play important roles in LUSC development and progression.
DOI: 10.6084/m9.figshare.28333495.v1
title: Unraveling the gender-specific molecular landscape of lung squamous cell carcinoma progression

description: Lung squamous cell carcinoma (LUSC) is a type of non-small cell lung cancer that is the most common and deadly type of lung cancer, originating from the cells lining the bronchi. The progression of LUSC is influenced by various factors, such as genetic, viral, environmental and hormonal factors, immune system response, and smoking history. Despite extensive studies aimed at improving patient survival, the role of gender-specific molecular variants in LUSC progression remains unclear. Using a systems biology approach, combining differential gene expression, network analysis, and machine learning, aberrant mRNA and ncRNAs implicated in LUSC have been identified to improve patient survival, stratify patients and develop novel prognostic strategies. Furthermore, a systematic analysis of the prognostic implications and functional annotations of the molecular variants results in the filtering of key protein-coding genes and non-coding RNAs that are involved in tumor progression. We found several common molecular variants in both genders, including 4 mRNA, 4 miRNAs, and 27 lncRNAs. Among the shared lncRNAs, 5 were novel for both genders. These were found to have a poor prognostic performance in patients with lung cancer. The key players are involved in DNA replication, nucleotide excision repair, complement and coagulation cascades, and estrogen signaling pathways. In this study, we report lncRNAs (PVT1, FAM13A-AS1, LINC00461, NAV2-AS5, PRICKLE2-AS1, and VCAN-AS1) that may function as oncogenes or tumor suppressors by regulating the expression of coding genes, such as RAB24, HECW2, LGR4, and FKBP5. These lncRNAs and coding genes may play important roles in LUSC development and progression.
DOI: 10.15468/dl.trrru9
title: Occurrence Download

description: A dataset containing 793347 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hypochaeris radicata"
 ]
}

 The dataset includes 793347 records from 2921 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002102-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/4n4-e9p-86n
title: †Prolagus Pomel, 1853

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a14-pxj-26d
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c5q-d1m-x2p
title: †Prolagus Pomel, 1853

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0tw-a25-qrh
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a46-03x-2fc
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h7r-hyk-rpf
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3zj-jec-f5f
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/n3d-9a4-npm
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kks-jhj-1s8
title: Balclutha Kirkaldy, 1900

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w0d-3hb-ph3
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/91s-79j-vy6
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pax-h40-6qe
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z8z-1qp-ysf
title: Megalomys Trouessart, 1881

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dgt-j89-5f8
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rvd-k7z-pby
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c6c-zmq-s37
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vcs-4wz-g1k
title: Oryzomys Baird, 1857

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/21v-am4-dgc
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b89-sca-0g0
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hg5-bln-btl
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pv4-v50-hqv
title: Testudines

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9j8-e6j-glq
title: †Prolagus Pomel, 1853

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yeg-0h8-mml
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pvz-r8g-z1j
title: Pseudopus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qn6-l7e-7kl
title: Bos taurus primigenius Bojanus, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cxs-924-9xc
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y2l-3p3-hl2
title: Megalomys Trouessart, 1881

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nmj-m8f-j6g
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/21k-pp1-hyy
title: Elephas Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/azw-gzt-jkf
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3cq-hxq-89j
title: Megalomys Trouessart, 1881

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/504-yzt-ss4
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7zr-hzs-mt0
title: Pseudopus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.