cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14259914.v1
title: Molecular interaction study of novel indoline derivatives with EGFR-kinase domain using multiple computational analysis

description: Epidermal growth factor receptors are constitutively overexpressed in breast cancer cells, which in turn stimulate many downstream signaling pathways that are involved in many carcinogenic processes. This makes EGFR a striking target for cancer therapy. This study focuses on the EGFR kinase domain inactivation by novel synthesized indoline derivatives. The compounds used are N-(2-hydroxy-5-nitrophenyl (4’-methyl phenyl) methyl) indoline (HNPMI), alkylaminophenols − 2-((3,4-Dihydroquinolin-1(2H)-yl) (p-tolyl) methyl) phenol (THTMP) and 2-((1, 2, 3, 4-Tetrahydroquinolin-1-yl) (4 methoxyphenyl) methyl) phenol (THMPP). To get a clear insight into the molecular interaction of EGFR and the three compounds, we have used ADME/Tox prediction, Flexible docking analysis followed by MM/GB-SA, QM/MM analysis, E-pharmacophore mapping of the ligands and Molecular dynamic simulation of protein-ligand complexes. All three compounds showed good ADME/Tox properties obeying the rules of drug-likeliness and showed high human oral absorption. Molecular docking was performed with the compounds and EGFR using Glide Flexible docking mode. This showed that the HNPMI was best among the three compounds and had interactions with key residue Lys 721. The protein-ligand complexes were stable when simulated for 100 ns using Desmond software. The interactions were further substantiated using QM/MM analysis and MM-GB/SA analysis in which HNPMI was scored as the best molecule. All the analyses were carried out with a reference molecule—Gefitinib which is a known standard inhibitor of EGFR. Thus, the study elucidates the potential role of the indoline derivatives as an anti-cancer agent against breast cancer by effectively inhibiting EGFR. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14169219
title: Bioinformatics analysis of extracellular subtilisin E from <i>Bacillus subtilis</i>

description: <i>Bacillus</i> spp. are the main sources of subtilisin E, which has several applications in biotechnology. The 3D structure of subtilisin E has a significant impact on its efficacy. In this study, we evaluated subtilisin E from <i>Bacillus subtilis</i> subsp. <i>subtilis</i> str. 168 by bioinformatic methods. The results revealed that the subtilisin E sequence from <i>B. subtilis</i> contains highly conserved amino acids, including histidine (H), aspartic acid (D) and serine (S). Subtilisin E cleaves the bonds between hydrophobic and polar amino acids in keratin-associated proteins. The effects of point mutations on the crystal structure of subtilisin E (PDB ID: 1SCJ) showed that changes of asparagine 123 (N123) to valine (V) and serine 331 (S331) to leucine (L) respectively, were the most stabilizing. Genomic analysis of the subtilisin E-coding gene (<i>aprE</i>) indicated that this gene and the <i>yhfN</i> gene are expressed through a σA promoter. The analysis of TBFs revealed AbrB, ScoC, DegU, Hpr, σA, SinR, TenA, and DegU as relevant regulators of <i>aprE</i> expression. Phylogenetic analysis showed that subtilisin Es have highly conserved structures among <i>Bacillus</i> spp., sharing a common ancestor, where their coding genes were duplicated and evolved within the <i>Bacillus</i> spp. As the conclusion, our <i>in silico</i> study demonstrated that the overexpression of the <i>aprE</i> gene and stability of the produced subtilisin E can be improved though system biology methods such as point mutations and identifying the involved transcription factors (TFs) or/and TBFs. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14169219.v1
title: Bioinformatics analysis of extracellular subtilisin E from <i>Bacillus subtilis</i>

description: <i>Bacillus</i> spp. are the main sources of subtilisin E, which has several applications in biotechnology. The 3D structure of subtilisin E has a significant impact on its efficacy. In this study, we evaluated subtilisin E from <i>Bacillus subtilis</i> subsp. <i>subtilis</i> str. 168 by bioinformatic methods. The results revealed that the subtilisin E sequence from <i>B. subtilis</i> contains highly conserved amino acids, including histidine (H), aspartic acid (D) and serine (S). Subtilisin E cleaves the bonds between hydrophobic and polar amino acids in keratin-associated proteins. The effects of point mutations on the crystal structure of subtilisin E (PDB ID: 1SCJ) showed that changes of asparagine 123 (N123) to valine (V) and serine 331 (S331) to leucine (L) respectively, were the most stabilizing. Genomic analysis of the subtilisin E-coding gene (<i>aprE</i>) indicated that this gene and the <i>yhfN</i> gene are expressed through a σA promoter. The analysis of TBFs revealed AbrB, ScoC, DegU, Hpr, σA, SinR, TenA, and DegU as relevant regulators of <i>aprE</i> expression. Phylogenetic analysis showed that subtilisin Es have highly conserved structures among <i>Bacillus</i> spp., sharing a common ancestor, where their coding genes were duplicated and evolved within the <i>Bacillus</i> spp. As the conclusion, our <i>in silico</i> study demonstrated that the overexpression of the <i>aprE</i> gene and stability of the produced subtilisin E can be improved though system biology methods such as point mutations and identifying the involved transcription factors (TFs) or/and TBFs. Communicated by Ramaswamy H. Sarma
DOI: 10.5281/zenodo.7071035
title: TrypTag: plate L3530 (replicate dated 20170209)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L3530, replicate dated 20170209.
DOI: 10.5281/zenodo.6840751
title: TrypTag: plate L3530 (replicate dated 20170209)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L3530, replicate dated 20170209.
DOI: 10.21227/mfsb-ap42
title: Test Test

description: Bangla is one of the most spoken languages in the world but Bangla NLP research is in its early stage of development due to the lack of quality public corpus. In this article, we describe the detailed compilation methodology of a comprehensive monolingual Bangla corpus, KUMono. Thiscorpus consists of more than 353 million word tokens in total as well as more than one million unique tokens from 18 major text categories of online Bangla websites.
DOI: 10.5281/zenodo.7043268
title: Paleomagnetic directions, anisotropy of magnetic susceptibility (AMS), and anisotropy of anhysteretic remanent magnetization (AARM) from IODP Sites U1507 and U1511 (Exp. 371, Tasman Sea).

description: We present here paleomagnetic and magnetic anisotropy data from International Ocean Discovery Program (IODP) Sites U1507 and U1511 (Expedition 371, Tasman Sea). Data consist of three tables that contain: (1) the characteristic remanent magnetization (ChRM) directions, before and after correction for inclination flattening of magnetic remanence, for both sites (Table S2); (2) the anisotropy of magnetic susceptibility (AMS) data from Site U1507 (Table S3); (3) the anisotropy of anhysteretic remanence (AARM) from Site U1507 (Table S4).
description: {"references": ["Jel\u00ednek, V. (1981). Characterization of the magnetic fabric of rocks. Tectonophysics, 79(3\u20134), T63--T67."]}
DOI: 10.5281/zenodo.7043266
title: Paleomagnetic directions, anisotropy of magnetic susceptibility (AMS), and anisotropy of anhysteretic remanent magnetization (AARM) from IODP Sites U1507 and U1511 (Exp. 371, Tasman Sea).

description: We present here paleomagnetic and magnetic anisotropy data from International Ocean Discovery Program (IODP) Sites U1507 and U1511 (Expedition 371, Tasman Sea). Data consist of three tables that contain: (1) the characteristic remanent magnetization (ChRM) directions, before and after correction for inclination flattening of magnetic remanence, for both sites (Table S2); (2) the anisotropy of magnetic susceptibility (AMS) data from Site U1507 (Table S3); (3) the anisotropy of anhysteretic remanence (AARM) from Site U1507 (Table S4).
description: {"references": ["Jel\u00ednek, V. (1981). Characterization of the magnetic fabric of rocks. Tectonophysics, 79(3\u20134), T63--T67."]}
DOI: 10.24403/jp.1246448
title: Erster Nachtrag zur Flora von Thüringen (Zündorf et al. 2006) – Neu nachgewiesene oder wieder aufgefundene Arten / Heiko Korsch
DOI: 10.24403/jp.1246451
title: Beobachtungen zu verwilderten Frühblühern im Raum Jena von 2003 bis 2018 / Ilse Schönfelder
DOI: 10.6084/m9.figshare.16563885
title: Selecting Third-party Libraries: The Data Scientist’s Perspective

description: Artifacts for EMSE publication "Selecting Third-party Libraries: The Data Scientist’s Perspective" by Sarah Nadi and Nourhan Sakr.
DOI: 10.6084/m9.figshare.16563885.v1
title: Selecting Third-party Libraries: The Data Scientist’s Perspective

description: Artifacts for EMSE publication "Selecting Third-party Libraries: The Data Scientist’s Perspective" by Sarah Nadi and Nourhan Sakr.
DOI: 10.5281/zenodo.6909684
title: Public Debt and Government Finance Information - WB, IMF

description: Data are collected from the World Bank’s World Development Indicators and International Debt Statistics databases and IMF’s Fiscal Monitor and Government Finance Statistics databases
DOI: 10.5281/zenodo.6909685
title: Public Debt and Government Finance Information - WB, IMF

description: Data are collected from the World Bank’s World Development Indicators and International Debt Statistics databases and IMF’s Fiscal Monitor and Government Finance Statistics databases
DOI: 10.5281/zenodo.7071221
title: Public Debt and Government Finance Information - WB, IMF

description: Data are collected from the World Bank’s World Development Indicators and International Debt Statistics databases and IMF’s Fiscal Monitor and Government Finance Statistics databases
DOI: 10.5517/ccdc.csd.cc281n00
title: CCDC 2086951: Experimental Crystal Structure Determination

description: Related Article: Soumyadip Basu, Sauvik Chatterjee, Kajal De, Asim Bhaumik, Chhanda Mukhopadhyay|2022|J.Organomet.Chem.|979|122494|doi:10.1016/j.jorganchem.2022.122494
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc281n11
title: CCDC 2086952: Experimental Crystal Structure Determination

description: Related Article: Soumyadip Basu, Sauvik Chatterjee, Kajal De, Asim Bhaumik, Chhanda Mukhopadhyay|2022|J.Organomet.Chem.|979|122494|doi:10.1016/j.jorganchem.2022.122494
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc28c932
title: CCDC 2096223: Experimental Crystal Structure Determination

description: Related Article: Chang-Feng Wang, Chao Shi, Anyi Zheng, Yilei Wu, Le Ye, Na Wang, Heng-Yun Ye, Ming-Gang Ju, Pengfei Duan, Jinlan Wang, Yi Zhang|2022|Materials Horizons|9|2450|doi:10.1039/D2MH00698G
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2704dt
title: CCDC 2055715: Experimental Crystal Structure Determination

description: Related Article: Hong-Yan Wang, Yang Li, Jing Shi|2022|J.Indian Chem.Soc.|99|100691|doi:10.1016/j.jics.2022.100691
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2704fv
title: CCDC 2055716: Experimental Crystal Structure Determination

description: Related Article: Hong-Yan Wang, Yang Li, Jing Shi|2022|J.Indian Chem.Soc.|99|100691|doi:10.1016/j.jics.2022.100691
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.24403/jp.1246452
title: Orobanche beauverdii Uhlich & Rätzel, nom. nov. ‒ ein neuer Name für eine bisher übersehene Art aus der Alpenregion / Holger Uhlich & Stefan Rätzel
DOI: 10.24403/jp.1246453
title: Ehemaliges Truppenübungsgelände Jenaer Forst als Lebensraum – Untersuchung eines Himmelsteiches mit angrenzender Vegetationsfläche in Jena, Thüringen / Lisa Deak, Till Jonathan Deilmann, Alina Kessel, Maggie Preisser & Eileen Wiesenberger
DOI: 10.24403/jp.1246457
title: 4. Nachtrag zur „Flora des Kyffhäusergebirges und der näheren Umgebung“ (Barthel & Pusch 1999) mit wichtigen Bestätigungen / Jürgen Pusch
DOI: 10.24403/jp.1246460
title: Erste Checkliste der flechtenbewohnenden Pilze Thüringens mit neuen Funden für das Bundesland / Jan Eckstein, Wolfgang von Brackel, Jürgen Rettig, Rainer Cezanne & Marion Eichler
DOI: 10.6084/m9.figshare.19785925
title: Nature-based tourism in protected areas: a systematic review of socio-economic benefits and costs to local people

description: Nature-based tourism, which includes visits to protected areas, is a growing trend. This may include consumptive and non-consumptive activities, with nature-based tourists being motivated to experience local culture and nature. Thus, tourism can contribute economically and socially to communities associated with protected areas, with the outcomes being both benefits and costs to local people. We carried out a systematic literature review to document and characterise the outcomes of nature-based tourism for people living in and around protected areas (terrestrial and inland waters). We evaluated 89 papers published from 1996 to 2020, most of which were conducted in low- and middle-income countries. The main benefits were employment, business opportunities and income, and the main costs were acculturation and abandonment of traditional lifestyle/practices, price inflation and conflict/crime. While most benefits were economic, most costs were socio-cultural. We found that benefits were most frequently experienced individually and costs experienced mostly at the collective or community levels. Inconsistencies in reporting of impacts suggests that future research should take a more consistent and systematic approach to evaluating benefits and costs of nature-based tourism from both the demographic and geographic perspectives, be more inclusive, and pay equal attention to objective and subjective measures of costs and benefits.
DOI: 10.6084/m9.figshare.19785925.v1
title: Nature-based tourism in protected areas: a systematic review of socio-economic benefits and costs to local people

description: Nature-based tourism, which includes visits to protected areas, is a growing trend. This may include consumptive and non-consumptive activities, with nature-based tourists being motivated to experience local culture and nature. Thus, tourism can contribute economically and socially to communities associated with protected areas, with the outcomes being both benefits and costs to local people. We carried out a systematic literature review to document and characterise the outcomes of nature-based tourism for people living in and around protected areas (terrestrial and inland waters). We evaluated 89 papers published from 1996 to 2020, most of which were conducted in low- and middle-income countries. The main benefits were employment, business opportunities and income, and the main costs were acculturation and abandonment of traditional lifestyle/practices, price inflation and conflict/crime. While most benefits were economic, most costs were socio-cultural. We found that benefits were most frequently experienced individually and costs experienced mostly at the collective or community levels. Inconsistencies in reporting of impacts suggests that future research should take a more consistent and systematic approach to evaluating benefits and costs of nature-based tourism from both the demographic and geographic perspectives, be more inclusive, and pay equal attention to objective and subjective measures of costs and benefits.
DOI: 10.24403/jp.1246481
title: Vermittlung botanischer Artenkenntnis in der Schule als Teil Naturwissenschaftlicher Grundbildung / Tim Stammberger, Andreas Gerth & Uwe Hossfeld
DOI: 10.24403/jp.1246489
title: Bryophyta selecta ex Herbario Haussknecht, Nos. 251–300 : Duplicates of bryophytes from the historical collections of the Herbarium Haussknecht, University of Jena (JE) / Hans-Joachim Zündorf
DOI: 10.24403/jp.1246502
title: Bryophyta selecta ex Herbario Haussknecht, Nos. 301–350 : Duplicates of bryophytes from the historical collections of the Herbarium Haussknecht, University of Jena (JE) / Hans-Joachim Zündorf
DOI: 10.24403/jp.1246506
title: Neufund von Microcalicium ahlneri in Thüringen (Ascomycota, Microcaliciaceae) / Hagen Grünberg (Goßwitz)
DOI: 10.34740/kaggle/dsv/4193140
title: UNET Lung Segmentation Weights for Chest X Rays
DOI: 10.24403/jp.1246509
title: Ein gewichtiger Porling / Erika Ruske (Jena)
DOI: 10.24403/jp.1246520
title: Bericht über die Kartierungsexkursion der Thüringischen Botanischen Gesellschaft in das Gebiet westlich von Kölleda am 17. Mai 2014 : Führung: Heiko Korsch (Jena) / Peter Rode (Stadtroda)
DOI: 10.24403/jp.1246524
title: Kurzer Bericht über die Kartierungsexkursion der Thüringischen Botanischen Gesellschaft in das Gebiet nördlich von Meiningen am 30. Mai 2015 : Führung: Heiko Korsch (Jena) / Peter Rode (Jena)
DOI: 10.6084/m9.figshare.20240847
title: New l-fibroin sequences

description: New l-fibroins for Trichoptera <br> <br> <br> <br>
DOI: 10.6084/m9.figshare.20240847.v1
title: New l-fibroin sequences

description: New l-fibroins for Trichoptera <br> <br> <br> <br>
DOI: 10.6084/m9.figshare.21081385
title: Model connectome of multiple sclerosis

description: Nodes and connection of a multiple sclerosis model
DOI: 10.6084/m9.figshare.21081385.v1
title: Model connectome of multiple sclerosis

description: Nodes and connection of a multiple sclerosis model
DOI: 10.5281/zenodo.7030862
title: Data from: Crowdsourcing training material for automated bird sound classification – a pilot study

description: Data from the manuscript "Crowdsourcing training material for automated bird sound classification – a pilot study" by Petteri Lehikoinen, Meeri Rannisto, Ulisses Camargo, Aki Aintila, Patrik Lauha, Esko Piirainen, Panu Somervuo & Otso Ovaskainen
DOI: 10.6084/m9.figshare.21078607
title: buteogallus_gundlachii_decontaminated_FSCR.fasta.gz

description: .......
DOI: 10.6084/m9.figshare.21078607.v1
title: buteogallus_gundlachii_decontaminated_FSCR.fasta.gz

description: .......
DOI: 10.5281/zenodo.5992648
title: Convolutional Neural Networks for Classifying Combinatorial Metamaterials

description: This dataset contains the training and test data, as well as the trained neural networks as used for the paper 'Machine Learning of Combinatorial Rules in Mechanical Metamaterials', as published in XXX. In this paper, a neural network is used to classify each \(k \times k\) unit cell design into one of two classes (C or I). Additionally, the performance of the trained networks is analysed in detail. A more detailed description of the contents of the dataset follows below. <strong>NeuralNetwork_train_and_test_data.zip</strong> This file contains the train and test data used to train the Convolutional Neural Networks (CNNs) of the paper. Each unit cell size has its own file, and is saved in a zipped numpy file type (.npz). <strong>CNN_saves_kxk.zip</strong> This file contains the parameter configurations of the CNNs trained on \(k \times k\) unit cells. Every hyperparameter (number of filters<em> nf,</em> number of hidden neurons<em> nh</em>, learning rate<em> lr</em>) combination is saved separately. The neural networks can be loaded using Google's TensorFlow package in Python, specifically using the 'tf.keras.models.load_model' function.
DOI: 10.6084/m9.figshare.18281254
title: Metal accumulation by <i>Alyssum serpyllifolium</i> subsp. <i>malacitanum</i> Rivas Goday (Brassicaceae) across different petrographic entities in South-Iberian ultramafic massifs: plant-soil relationships and prospects for phytomining

description: In the ultramafic area of Spain, a high quantity of petrographic entities is present. Data on the variability among populations of hyperaccumulation are scarce. We investigated <i>Alyssum serpyllifolium</i> subsp. <i>malacitanum</i> for variations in eleven elements among populations growing in different ultramafic massifs in different petrographic entities (dunites, harzburgite-pyroxenic dunite, harzburgite-lherzolite, pyroxenite, and serpentinites). Samples of leaves and soils were collected from the ultramafic outcrops of Sierra Bermeja and Sierra de Mijas (Andalusia, Spain). The concentrations of Ni, Fe, Mg, Si, Cr, Co, Sr, Mn, Cu, Zn, and Ba and the bioaccumulation factors (BAF) were determined. Although analysis of variance of the data for each element revealed considerable variation in soil chemistry (for Fe, Mg, Sr, and Ba) among the different petrographic entities, population-level variation with regard to the hyperaccumulation in the leaves was not detected. BAF values &gt;1 were obtained for Sr and Ni depending on the petrographic entities. The correlation detected between the concentration of Ni in leaves and concentration in soil is relevant. The population-level variation obtained in the BAF values for Sr and Ni provides comprehensive information on the natural variation of hyperaccumulation. The BAF obtained for Ba is an important result for phytomining. To date, studies of hyperaccumulation in plant tissues on ultramafic rocks have not considered the great diversity of petrographic entities in the world's outcrops. One of them is the one that we studied in Spain with more than eight petrographic entities and different soils. Our hypothesis is that the different chemical compositions of the soils in ultramafic rocks significantly affect the hyperaccumulation of metals by specialized plants, which may have consequences for phytomining. For this purpose, individuals, populations, and different soils have been tested and the results have been subjected to the corresponding statistical tests. The obtained knowledge reflects the different behavior of the studied plant not only for the Ni: the obtained results for Sr and for Ba revealed interesting results for the hyperaccumulation in <i>Alyssum</i> of both metals.