cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4814632.v1
title: Effectiveness of fine root fingerprinting as a tool to identify plants of the Alps: Results of a preliminary study

description: To identify plants of the Alps through analysis of their roots is currently extremely difficult when using traditional identification methods such as dichotomous keys and/or illustrated atlases. Besides genetic analysis, other analytical methods, such as chromatographic analysis, could also be useful for root identification. Chromatographic fingerprints of root extracts of six species (<i>Betula pendula</i>, <i>Picea ab</i>ies, <i>Fagus sylvat</i>i<i>ca</i>, <i>Larix decidua</i>, <i>Fraxinus excelsior</i> and <i>Corylus avellana</i>) were analyzed in order to understand whether these species have a chromatographic fingerprint that identifies them, and hence to ascertain whether they can be identified by applying the method of analysis presented below. One hundred and sixty-two root samples were collected in various areas of the Alps and subjected to high-performance liquid chromatography (HPLC) analysis. Multivariate analysis techniques (e.g. cluster analysis) were employed for statistical analysis of chromatographic fingerprints. This study revealed that the chromatographic fingerprints of birch, spruce and larch samples were similar and that the method can therefore clearly identify the respective species. Instead, chromatographic fingerprint samples of beech, hazel and ash presented greater variability. Research proposals based on the results obtained in this study were also developed in order to implement and facilitate studies regarding plant roots.
DOI: 10.6084/m9.figshare.4814140
title: TAS Resolution Workshop

description: Data and Jupyter notebooks used in Tripple Axis Resolution Workshop 2017 @ MLZ, Garching
DOI: 10.6084/m9.figshare.4814140.v1
title: TAS Resolution Workshop

description: Data and Jupyter notebooks used in Tripple Axis Resolution Workshop 2017 @ MLZ, Garching
DOI: 10.6084/m9.figshare.4814131
title: Confined space facilitates G-quadruplex formation 1

description: These data are related to the article published in Nature Nanotechnology "Confined space facilitates G-quadruplex formation" (DOI: 10.1038/NNANO.2017.29), authored by Prakash Shrestha; Sagun Jonchhe; Tomoko Emura; Kumi Hidaka; Masayuki Endo; Hiroshi Sugiyama; and Hanbin Mao.These data were obtained from the experiments by using optical tweezers. The other items include the data set that are put in the order of figures reported in the article. The first column in each txt file is extension in nanometer while the second column in each txt file is force in piconewton.
DOI: 10.6084/m9.figshare.4814128
title: Confined space facilitates G-quadruplex formation 2

description: Figure S15-GQ wo Nanocage in 1M NaCl
DOI: 10.6084/m9.figshare.4814131.v1
title: Confined space facilitates G-quadruplex formation 1

description: These data are related to the article published in Nature Nanotechnology "Confined space facilitates G-quadruplex formation" (DOI: 10.1038/NNANO.2017.29), authored by Prakash Shrestha; Sagun Jonchhe; Tomoko Emura; Kumi Hidaka; Masayuki Endo; Hiroshi Sugiyama; and Hanbin Mao.These data were obtained from the experiments by using optical tweezers. The other items include the data set that are put in the order of figures reported in the article.
DOI: 10.6084/m9.figshare.4814131.v2
title: Confined space facilitates G-quadruplex formation 1

description: These data are related to the article published in Nature Nanotechnology "Confined space facilitates G-quadruplex formation" (DOI: 10.1038/NNANO.2017.29), authored by Prakash Shrestha; Sagun Jonchhe; Tomoko Emura; Kumi Hidaka; Masayuki Endo; Hiroshi Sugiyama; and Hanbin Mao.These data were obtained from the experiments by using optical tweezers. The other items include the data set that are put in the order of figures reported in the article. The first column in each txt file is extension in nanometer while the second column in each txt file is force in piconewton.
DOI: 10.6084/m9.figshare.4814128.v1
title: Confined space facilitates G-quadruplex formation 2

description: Figure S15-GQ wo Nanocage in 1M NaCl
DOI: 10.6084/m9.figshare.4814107
title: Netflix_4000.zip

description: Rating data for 4000 movies.
DOI: 10.6084/m9.figshare.4814113
title: Confined space facilitates G-quadruplex formation 4

description: Figure 5c-GQ wo NC in 40% BSA
DOI: 10.6084/m9.figshare.4814116
title: Confined space facilitates G-quadruplex formation 3

description: Figure S14-GQ in medium nanocage at 50mM KCl and 1M LiCl
DOI: 10.6084/m9.figshare.4814107.v1
title: Netflix_4000.zip

description: Rating data for 4000 movies.
DOI: 10.6084/m9.figshare.4814113.v1
title: Confined space facilitates G-quadruplex formation 4

description: Figure 5c-GQ wo NC in 40% BSA
DOI: 10.6084/m9.figshare.4814116.v1
title: Confined space facilitates G-quadruplex formation 3

description: Figure S14-GQ in medium nanocage at 50mM KCl and 1M LiCl
DOI: 10.6084/m9.figshare.4814101
title: Confined space facilitates G-quadruplex formation 5

description: Figure S11 and 4e-GQ in large nanocage
DOI: 10.6084/m9.figshare.4814086
title: Confined space facilitates G-quadruplex formation 6

description: Figure S10 and 4c-GQ in small nanocage
DOI: 10.6084/m9.figshare.4814101.v1
title: Confined space facilitates G-quadruplex formation 5

description: Figure S11 and 4e-GQ in large nanocage
DOI: 10.6084/m9.figshare.4814086.v1
title: Confined space facilitates G-quadruplex formation 6

description: Figure S10 and 4c-GQ in small nanocage
DOI: 10.6084/m9.figshare.4814056
title: Protista 18S ver. 4.5 database

description: Protist Ribosomal Reference database (PR2) reformatted for mg_classifier. <br>pr2_gb203_ver.4.5.fna.gz
DOI: 10.6084/m9.figshare.4814062
title: SILVA ver. 128 database

description: SILVA database reformatted for mg_classifier from the original files by P. Schloss for mothur.Version 132 is now available, consider using that instead.
DOI: 10.6084/m9.figshare.4814083
title: Confined space facilitates G-quadruplex formation 7

description: Figure 3c and 5b-GQ without nanocage
DOI: 10.6084/m9.figshare.4814056.v1
title: Protista 18S ver. 4.5 database

description: Protist Ribosomal Reference database (PR2) reformatted for mg_classifier. <br>pr2_gb203_ver.4.5.fna.gz
DOI: 10.6084/m9.figshare.4814062.v1
title: SILVA ver. 128 database

description: SILVA database reformatted for mg_classifier from the original files by P. Schloss for mothur.
DOI: 10.6084/m9.figshare.4814083.v1
title: Confined space facilitates G-quadruplex formation 7

description: Figure 3c and 5b-GQ without nanocage
DOI: 10.6084/m9.figshare.4814029
title: Confined space facilitates G-quadruplex formation 8

description: Figure 3b and 4d-GQ in medium nanocage<br>
DOI: 10.6084/m9.figshare.4814029.v1
title: Confined space facilitates G-quadruplex formation 8

description: Figure 3b and 4d-GQ in medium nanocage<br>
DOI: 10.6084/m9.figshare.4813882
title: Extensive impact of non-antibiotic drugs on human gut bacteria

description: Supplementary data files for a study to quantify the impact of drugs on human gut commensals.
DOI: 10.6084/m9.figshare.4813831
title: PINK1 and BECN1 relocalize at mitochondria-associated membranes during mitophagy and promote ER-mitochondria tethering and autophagosome formation

description: Mitophagy is a highly specialized process to remove dysfunctional or superfluous mitochondria through the macroautophagy/autophagy pathway, aimed at protecting cells from the damage of disordered mitochondrial metabolism and apoptosis induction. PINK1, a neuroprotective protein mutated in autosomal recessive Parkinson disease, has been implicated in the activation of mitophagy by selectively accumulating on depolarized mitochondria, and promoting PARK2/Parkin translocation to them. While these steps have been characterized in depth, less is known about the process and site of autophagosome formation upon mitophagic stimuli. A previous study reported that, in starvation-induced autophagy, the proautophagic protein BECN1/Beclin1 (which we previously showed to interact with PINK1) relocalizes at specific regions of contact between the endoplasmic reticulum (ER) and mitochondria called mitochondria-associated membranes (MAM), from which the autophagosome originates. Here we show that, following mitophagic stimuli, autophagosomes also form at MAM; moreover, endogenous PINK1 and BECN1 were both found to relocalize at MAM, where they promoted the enhancement of ER-mitochondria contact sites and the formation of omegasomes, that represent autophagosome precursors. PARK2 was also enhanced at MAM following mitophagy induction. However, <i>PINK1</i> silencing impaired BECN1 enrichment at MAM independently of PARK2, suggesting a novel role for PINK1 in regulating mitophagy. MAM have been recently implicated in many key cellular events. In this light, the observed prevalent localization of PINK1 at MAM may well explain other neuroprotective activities of this protein, such as modulation of mitochondrial calcium levels, mitochondrial dynamics, and apoptosis.
DOI: 10.6084/m9.figshare.4813831.v1
title: PINK1 and BECN1 relocalize at mitochondria-associated membranes during mitophagy and promote ER-mitochondria tethering and autophagosome formation

description: Mitophagy is a highly specialized process to remove dysfunctional or superfluous mitochondria through the macroautophagy/autophagy pathway, aimed at protecting cells from the damage of disordered mitochondrial metabolism and apoptosis induction. PINK1, a neuroprotective protein mutated in autosomal recessive Parkinson disease, has been implicated in the activation of mitophagy by selectively accumulating on depolarized mitochondria, and promoting PARK2/Parkin translocation to them. While these steps have been characterized in depth, less is known about the process and site of autophagosome formation upon mitophagic stimuli. A previous study reported that, in starvation-induced autophagy, the proautophagic protein BECN1/Beclin1 (which we previously showed to interact with PINK1) relocalizes at specific regions of contact between the endoplasmic reticulum (ER) and mitochondria called mitochondria-associated membranes (MAM), from which the autophagosome originates. Here we show that, following mitophagic stimuli, autophagosomes also form at MAM; moreover, endogenous PINK1 and BECN1 were both found to relocalize at MAM, where they promoted the enhancement of ER-mitochondria contact sites and the formation of omegasomes, that represent autophagosome precursors. PARK2 was also enhanced at MAM following mitophagy induction. However, <i>PINK1</i> silencing impaired BECN1 enrichment at MAM independently of PARK2, suggesting a novel role for PINK1 in regulating mitophagy. MAM have been recently implicated in many key cellular events. In this light, the observed prevalent localization of PINK1 at MAM may well explain other neuroprotective activities of this protein, such as modulation of mitochondrial calcium levels, mitochondrial dynamics, and apoptosis.
DOI: 10.6084/m9.figshare.4812469
title: Functional characterization of a novel 3D model of the epithelial-mesenchymal trophic unit

description: <b>Background/Aim</b>: Epithelial-mesenchymal communication plays a key role in tissue homeostasis and abnormal signaling contributes to chronic airways disease such as COPD. Most <i>in vitro</i> models are limited in complexity and poorly represent this epithelial-mesenchymal trophic unit. We postulated that cellular outgrowth from bronchial tissue would enable development of a mucosal structure that recapitulates better <i>in vivo</i> tissue architecture. <b>Materials and Methods</b>: Bronchial tissue was embedded in Matrigel and outgrowth cultures monitored using time-lapse microscopy, electrical resistance, light and electron microscopy. Cultures were challenged repetitively with cigarette smoke extract (CSE). <b>Results</b>: The outgrowths formed as a multicellular sheet with motile cilia becoming evident as the Matrigel was remodeled to provide an air interface; cultures were viable for more than one year. Immunofluorescence and electron microscopy (EM) identified an upper layer of mucociliary epithelium and a lower layer of highly organized extracellular matrix (ECM) interspersed with fibroblastic cells separated by a basement membrane. EM analysis of the mucosal construct after repetitive exposure to CSE revealed epithelial damage, loss of cilia, and ECM remodeling, as occurs <i>in vivo</i>. <b>Conclusions</b>: We have developed a robust bronchial mucosal model. The structural changes observed following CSE exposure suggest the model should have utility for drug discovery and preclinical testing, especially those targeting airway remodeling.
DOI: 10.6084/m9.figshare.4812469.v1
title: Functional characterization of a novel 3D model of the epithelial-mesenchymal trophic unit

description: <b>Background/Aim</b>: Epithelial-mesenchymal communication plays a key role in tissue homeostasis and abnormal signaling contributes to chronic airways disease such as COPD. Most <i>in vitro</i> models are limited in complexity and poorly represent this epithelial-mesenchymal trophic unit. We postulated that cellular outgrowth from bronchial tissue would enable development of a mucosal structure that recapitulates better <i>in vivo</i> tissue architecture. <b>Materials and Methods</b>: Bronchial tissue was embedded in Matrigel and outgrowth cultures monitored using time-lapse microscopy, electrical resistance, light and electron microscopy. Cultures were challenged repetitively with cigarette smoke extract (CSE). <b>Results</b>: The outgrowths formed as a multicellular sheet with motile cilia becoming evident as the Matrigel was remodeled to provide an air interface; cultures were viable for more than one year. Immunofluorescence and electron microscopy (EM) identified an upper layer of mucociliary epithelium and a lower layer of highly organized extracellular matrix (ECM) interspersed with fibroblastic cells separated by a basement membrane. EM analysis of the mucosal construct after repetitive exposure to CSE revealed epithelial damage, loss of cilia, and ECM remodeling, as occurs <i>in vivo</i>. <b>Conclusions</b>: We have developed a robust bronchial mucosal model. The structural changes observed following CSE exposure suggest the model should have utility for drug discovery and preclinical testing, especially those targeting airway remodeling.
DOI: 10.6084/m9.figshare.4811539
title: Design and Rationale of the Metastatic Renal Cell Carcinoma (MaRCC) Registry: A Prospective Academic and Community-Based Study of Patients With Metastatic Renal Cell Cancer

description: The Metastatic Renal Cell Cancer Registry, a large, nationally representative, prospective registry of patients with metastatic renal cell carcinoma (mRCC), aims to understand real-world treatment patterns and outcomes of patients with mRCC in routine clinical practice across the United States. This observational study is designed to enroll 500 patients with previously untreated mRCC from approximately 60 academic and community treatment sites; as of December 7, 2016, 500 patients have enrolled at 54 sites. Key endpoints include real-world data on reasons for treatment initiation and discontinuation; treatment regimens; disease progression; patient-reported outcomes; and healthcare resource utilization in this patient population.
DOI: 10.6084/m9.figshare.4811539.v1
title: Design and Rationale of the Metastatic Renal Cell Carcinoma (MaRCC) Registry: A Prospective Academic and Community-Based Study of Patients With Metastatic Renal Cell Cancer

description: The Metastatic Renal Cell Cancer Registry, a large, nationally representative, prospective registry of patients with metastatic renal cell carcinoma (mRCC), aims to understand real-world treatment patterns and outcomes of patients with mRCC in routine clinical practice across the United States. This observational study is designed to enroll 500 patients with previously untreated mRCC from approximately 60 academic and community treatment sites; as of December 7, 2016, 500 patients have enrolled at 54 sites. Key endpoints include real-world data on reasons for treatment initiation and discontinuation; treatment regimens; disease progression; patient-reported outcomes; and healthcare resource utilization in this patient population.
DOI: 10.6084/m9.figshare.4811500
title: meta analysis virological success taieb.csv

description: <pre>PONE-D-16-35978R1 Virological success after 12 and 24 months of antiretroviral therapy in sub-Saharan Africa: comparing results of trials, cohorts and cross-sectional studies using a systematic review and meta-analysis<br>by Fabien Taieb, Yoann Madec, Amandine Cournil and Eric Delaporte<br></pre>
DOI: 10.6084/m9.figshare.4811485
title: Latihan Pemodelan Sederhana Metode Gaya Berat (Gravity)

description: Pemodelan sederhana metode gravity dengn model bola, silinder, dan lempeng. <br>
DOI: 10.6084/m9.figshare.4811500.v1
title: meta analysis virological success taieb.csv

description: <pre>PONE-D-16-35978R1 Virological success after 12 and 24 months of antiretroviral therapy in sub-Saharan Africa: comparing results of trials, cohorts and cross-sectional studies using a systematic review and meta-analysis<br>by Fabien Taieb, Yoann Madec, Amandine Cournil and Eric Delaporte<br></pre>
DOI: 10.6084/m9.figshare.4811449
title: Latihan Pemodelan Fixed & Continuous Metode Magnetik

description: Pemodelan sederhana metode magnetik dengan model kotak yang dibuat fixed dan continuous.<br>
DOI: 10.6084/m9.figshare.4811464
title: New Approach to the theory of Gravity: Global Relativity

description: Recently, it has been shown that general theory of relativity, in fact, can be independently derivedwithout using Einstein's general relativity equations. In the approach, the two most used solutions- the Schwarzschild and Reissner Nordstrom solutions - have been derived explicitly. Here, aneasy-to-understand self-contained introduction to the material is edited.The approach, as a matter of fact, is not an alternative to the theory, but another way demon-strating a di erent understanding of the theory of gravitation. Yet, gravity through the basic ideasof the approach is very comprehensible.
DOI: 10.6084/m9.figshare.4811449.v1
title: Latihan Pemodelan Fixed & Continuous Metode Magnetik

description: Pemodelan sederhana metode magnetik dengan model kotak yang dibuat fixed dan continuous.<br>
DOI: 10.6084/m9.figshare.4811422
title: Latihan Pemodelan Sederhana Metode Self-Potensial

description: Latihan pemodelan self-potensial sederhana untuk kasus bola, silinder, dan lempeng.<br>
DOI: 10.6084/m9.figshare.4811404
title: Childhood SES and brain structure: Volumes and related information

description: This accompanies the article "Childhood Socioeconomic Status and Childhood Maltreatment: Distinct Associations with Brain Structure" by Gwendolyn M. Lawson, Joshue S Camins, Laura Wisse, Jue Wu, Jeffrey T. Duda, Philip A. Cook, James C. Gee, and Martha J. Farah, available on PLOS One.<br>Expanded variable descriptions available in .sav file
DOI: 10.6084/m9.figshare.4811278
title: Metal(loid)-Contaminated Soils as a Source of Culturable Heterotrophic Aerobic Bacteria for Remediation Applications

description: Heavy metal–contaminated soils are a serious environmental problem. Herein, the culturable heterotrophic bacterial community present on two metal(loid)-contaminated sites in the Northern Portugal was investigated. The bacterial counts ranged from 5.96 to 7.69 and 7.04 to 7.51 (log CFU g<sup>−1</sup> soil) in Sites 1 and 3, respectively. The bacterial population was predominantly composed of <i>Firmicutes, Proteobacteria</i>, and <i>Actinobacteria</i> on both sites. The most represented genera in Site 1 were <i>Bacillus</i> (41%) and <i>Pseudomonas</i> (27%), whereas <i>Arthrobacter</i> (21%) and <i>Pseudomonas</i> (13%) were the most represented genera in Site 3. Several bacterial isolates showed tolerance to high concentrations of metal(loid)s, suggesting that both contaminated sites are a valuable source of metal(loid)-tolerant bacteria, which may be further used in bioremediation and/or phytoremediation processes.
DOI: 10.6084/m9.figshare.4811404.v1
title: Childhood SES and brain structure: Volumes and related information

description: This accompanies the article "Childhood Socioeconomic Status and Childhood Maltreatment: Distinct Associations with Brain Structure" by Gwendolyn M. Lawson, Joshue S Camins, Laura Wisse, Jue Wu, Jeffrey T. Duda, Philip A. Cook, James C. Gee, and Martha J. Farah, available on PLOS One.<br>Expanded variable descriptions available in .sav file
DOI: 10.6084/m9.figshare.4811167
title: Recaptured bat data from Reproductive seasonality, sex ratio and philopatry in Argentina's common vampire bats

description: First and second recaptures of banded bats
DOI: 10.6084/m9.figshare.4811173
title: Dispersal events from Reproductive seasonality, sex ratio and philopatry in Argentina's common vampire bats

description: Distance, sex, and time between recaptures of dispersed bats
DOI: 10.6084/m9.figshare.4811278.v1
title: Metal(loid)-Contaminated Soils as a Source of Culturable Heterotrophic Aerobic Bacteria for Remediation Applications

description: Heavy metal–contaminated soils are a serious environmental problem. Herein, the culturable heterotrophic bacterial community present on two metal(loid)-contaminated sites in the Northern Portugal was investigated. The bacterial counts ranged from 5.96 to 7.69 and 7.04 to 7.51 (log CFU g<sup>−1</sup> soil) in Sites 1 and 3, respectively. The bacterial population was predominantly composed of <i>Firmicutes, Proteobacteria</i>, and <i>Actinobacteria</i> on both sites. The most represented genera in Site 1 were <i>Bacillus</i> (41%) and <i>Pseudomonas</i> (27%), whereas <i>Arthrobacter</i> (21%) and <i>Pseudomonas</i> (13%) were the most represented genera in Site 3. Several bacterial isolates showed tolerance to high concentrations of metal(loid)s, suggesting that both contaminated sites are a valuable source of metal(loid)-tolerant bacteria, which may be further used in bioremediation and/or phytoremediation processes.
DOI: 10.6084/m9.figshare.4811161
title: Roost data from Reproductive seasonality, sex ratio and philopatry in Argentina's common vampire bats

description: Numbers of banded males and females recaptured in roosts
DOI: 10.6084/m9.figshare.4811167.v1
title: Recaptured bat data from Reproductive seasonality, sex ratio and philopatry in Argentina's common vampire bats

description: First and second recaptures of banded bats
DOI: 10.6084/m9.figshare.4811152
title: Near wall motion of undulatory swimmers in non-Newtonian fluids

description: We investigate the near-wall motion of an undulatory swimmer in both Newtonian and non-Newtonian fluids using a two-dimensional direct numerical simulation. Our results show that the undulatory swimmer has three types of swimming mode depending on its undulation amplitude. The swimmer can be strongly attracted to the wall and swim in close proximity of the wall, be weakly attracted to the wall with a relatively large distance away from the wall, or escape from the wall. The scattering angle of the swimmer and its hydrodynamic interaction with the wall are important in describing the near-wall swimming motion. The shear-thinning viscosity is found to increase the swimming speed and to slightly enhance the wall attraction by reducing the swimmer’s scattering angle. The fluid elasticity, however, leads to strong attraction of swimmer’s head towards the wall, reducing the swimming speed. The combined shear-thinning effect and fluid elasticity results in an enhanced swimming speed along the wall.
DOI: 10.6084/m9.figshare.4811161.v1
title: Roost data from Reproductive seasonality, sex ratio and philopatry in Argentina's common vampire bats

description: Numbers of banded males and females recaptured in roosts
DOI: 10.6084/m9.figshare.4811077
title: MOUtbhR RNA-seq functions analysis

description: RNA-seq pipeline analysis of mouse single end libraries.