cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/d4n28458jd.1
title: Figures

description: Figures and figure legends for "Neuroprotective effects of cordycepin inhibit glutamate-induced apoptosis in hippocampal neurons"
DOI: 10.17632/g6b3rbkzkw.1
title: CPLEX code of the L-shaped method for wagon sizing and allocating wagon

description: In this research, a scenario-based two-stage stochastic programming model has been solved by using the L-shaped method. The model determines the optimal number of wagons and allocation of full and empty wagons during different time periods to optimize profit.
DOI: 10.17632/mgghc39cd6.1
title: Ego Relevance and Deception: Receivers (Burro & Castagnetti)

description: Code and data necessary to replicate "The Ego is No Fool: Absence of Motivated Belief Formation in Strategic Interactions"
DOI: 10.17632/mgghc39cd6.2
title: Ego Relevance and Deception: Receivers (Burro & Castagnetti)

description: Code and data necessary to replicate "The Ego is No Fool: Absence of Motivated Belief Formation in Strategic Interactions"
DOI: 10.17632/p9kb9xzbkp.1
title: Sample Dataset for Event Study - Covid19 Announcement and the Abnormal Return of Seaport Companies' Stock

description: Sample Dataset for Event Study - Covid19 Announcement and the Abnormal Return of Seaport Companies' Stock
DOI: 10.17632/sk565dkk6j.1
title: ethical threshold

description: data set of ethical threshold
DOI: 10.17632/sk565dkk6j.2
title: ethical threshold

description: data set of ethical threshold
DOI: 10.17632/z2fkd7y2gb.1
title: Active control of electro-visco-fingering in Hele-Shaw cells using Maxwell stress

description: The interfacial evolutions of electro-visco-fingering under an electric field.
DOI: 10.17632/p3xr562ph4.1
title: Active control of electro-visco-fingering in Hele-Shaw cells using Maxwell stress

description: Python code for analyzing the interfacial evolutions.
DOI: 10.5281/zenodo.10419468
title: Dataset to manuscript entitled "Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies" submitted to Scientifc Reports

description: This folder contains all raw data underlying the results presented in a manuscript, submitted to Scientifc Reports, and entitled:

Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies

 

Authored by:

Niusha Bagheri 1, Hongjian Chen 1, Mihailo Rabasovic 2, Jerker Widengren 1,*

1    Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center 106 91 Stockholm, Sweden

2 Laboratory for Biophysics, Institute of Physics Belgrade, Pregrevica 11811080 Zemun-Belgrade, Serbia

* Corresponding author (jwideng@kth.se)

 

The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. 

 

ABSTRACT

The amino acids tryptophan, tyrosine, and phenylalanine have been extensively used for different label-free protein studies, based on the intensity, lifetime, wavelength and/or polarization of their emitted fluorescence. Like most fluorescent organic molecules, these amino acids also tend to undergo transitions into dark meta-stable states, such as triplet and photo-radical states. While this may be perceived as a problem, these transitions are also highly environment-sensitive and can be used as an additional set of parameters, reflecting interactions, folding states, and immediate environments around the proteins. In this work, we applied the transient state monitoring (TRAST) technique, analyzing the average intensity of tyrosine emission under different excitation modulations, to characterize the photo physics of tyrosine for such readout purposes. By investigating how the dark state transitions of tyrosine varied with excitation intensity and solvent conditions we established a photophysical model for tyrosine. Next, we studied Calmodulin (containing two tyrosines), which upon calcium binding takes a more folded conformation. From these TRAST experiments, performed with 280nm time-modulated excitation, we show that tyrosine dark state transitions clearly change with the calmodulin conformation, and may thus represent a useful source of information for (label-free) analyses of protein conformations and interactions.
DOI: 10.5281/zenodo.10419469
title: Dataset to manuscript entitled "Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies" submitted to Scientifc Reports

description: This folder contains all raw data underlying the results presented in a manuscript, submitted to Scientifc Reports, and entitled:

Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies

 

Authored by:

Niusha Bagheri 1, Hongjian Chen 1, Mihailo Rabasovic 2, Jerker Widengren 1,*

1    Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center 106 91 Stockholm, Sweden

2 Laboratory for Biophysics, Institute of Physics Belgrade, Pregrevica 11811080 Zemun-Belgrade, Serbia

* Corresponding author (jwideng@kth.se)

 

The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. 

 

ABSTRACT

The amino acids tryptophan, tyrosine, and phenylalanine have been extensively used for different label-free protein studies, based on the intensity, lifetime, wavelength and/or polarization of their emitted fluorescence. Like most fluorescent organic molecules, these amino acids also tend to undergo transitions into dark meta-stable states, such as triplet and photo-radical states. While this may be perceived as a problem, these transitions are also highly environment-sensitive and can be used as an additional set of parameters, reflecting interactions, folding states, and immediate environments around the proteins. In this work, we applied the transient state monitoring (TRAST) technique, analyzing the average intensity of tyrosine emission under different excitation modulations, to characterize the photo physics of tyrosine for such readout purposes. By investigating how the dark state transitions of tyrosine varied with excitation intensity and solvent conditions we established a photophysical model for tyrosine. Next, we studied Calmodulin (containing two tyrosines), which upon calcium binding takes a more folded conformation. From these TRAST experiments, performed with 280nm time-modulated excitation, we show that tyrosine dark state transitions clearly change with the calmodulin conformation, and may thus represent a useful source of information for (label-free) analyses of protein conformations and interactions.
DOI: 10.17632/ccm76xs64y.1
title: Geophysical resistivity data

description: The Excel file consists of Geophysical resistivity data of our proposed area which include current electrode distance from the resistivity meter, potential electrode distance from the instrument, and resistance of the earth material with respect to depth
DOI: 10.5281/zenodo.7356907
title: LJ Speech - Aligned IPA transcriptions

description: Files:



	

	
grids.zip

	

		
contains TextGrids for all audio files containing three tiers words, phonemes and transcription

		

			
words contains the aligned normalized English words
			
phonemes contains IPA pronunciations transcribed using CMU dictionary which then were aligned with Montreal Forced Aligner. The pronunciations were then mapped from ARPAbet to IPA and duration marks were applied (without punctuation)
			
transcription contains unaligned phonemes including punctuation and word boundary labels (SIL0)
		
		
	
	
	

	
preview.png

	

		
preview of the first TextGrid opened in Praat
	
	
	

	
words-vocabulary.txt

	

		
contains all words from tier words
	
	
	

	
phonemes-vocabulary.txt

	

		
contains all phonemes from tier phonemes
	
	
	

	
transcription-vocabulary.txt

	

		
contains all phonemes/punctuation from tier transcription
	
	
	

	
phonemes-durations.pdf

	

		
contains the plotted phoneme duration distribution of tier phonemes
	
	
	

	
phonemes-durations-simple.pdf

	

		
contains the plotted phoneme duration distribution of tier phonemes if all duration markers are ignored
	
	
	

	
pronunciations.dict

	

		
contains the pronunciations for each word including punctuation and weights (occurrence)
	
	
	

	
script.sh

	

		
contains the script to reproduce all results
	
	



Phoneme duration marker:



	
˘ -> [0, 20) percentile
	
ˑ -> [80, 90) percentile
	
ː -> [90, inf) percentile



Silence marker:



	
SIL0 -> no silence
	
SIL1 -> [0, 33.33) percentile
	
SIL2 -> [33.33, 66.66) percentile
	
SIL3 -> [66.66, inf) percentile



 
description: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 416228727 – CRC 1410
DOI: 10.5281/zenodo.7356908
title: LJ Speech - Aligned IPA transcriptions

description: Files: <code>grids.zip</code> contains TextGrids for all audio files containing three tiers <code>words</code>, <code>phonemes</code> and <code>transcription</code> <code>words</code> contains the aligned normalized English words <code>phonemes</code> contains IPA pronunciations transcribed using CMU dictionary which then were aligned with Montreal Forced Aligner. The pronunciations were then mapped from ARPAbet to IPA and duration marks were applied (without punctuation) <code>transcription</code> contains unaligned phonemes including punctuation and word boundary labels (SIL0) <code>preview.png</code> preview of the first TextGrid opened in Praat <code>words-vocabulary.txt</code> contains all words from tier <code>words</code> <code>phonemes-vocabulary.txt</code> contains all phonemes from tier <code>phonemes</code> <code>transcription-vocabulary.txt</code> contains all phonemes/punctuation from tier <code>transcription</code> <code>phonemes-durations.pdf</code> contains the plotted phoneme duration distribution of tier <code>phonemes</code> <code>phonemes-durations-simple.pdf</code> contains the plotted phoneme duration distribution of tier <code>phonemes</code> if all duration markers are ignored <code>pronunciations.dict</code> contains the pronunciations for each word including punctuation and weights (occurrence) <code>script.sh</code> contains the script to reproduce all results Phoneme duration marker: <code>˘</code> -&gt; [0, 20) percentile <code>ˑ</code> -&gt; [80, 90) percentile <code>ː</code> -&gt; [90, inf) percentile Silence marker: <code>SIL0</code> -&gt; no silence <code>SIL1</code> -&gt; [0, 33.33) percentile <code>SIL2</code> -&gt; [33.33, 66.66) percentile <code>SIL3</code> -&gt; [66.66, inf) percentile
description: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 416228727 – CRC 1410
description: {"references": ["McAuliffe, M., Socolof, M., Mihuc, S., Wagner, M., & Sonderegger, M. (2017). Montreal Forced Aligner: Trainable Text-Speech Alignment Using Kaldi. Interspeech 2017, 498\u2013502. https://doi.org/10.21437/Interspeech.2017-1386"]}
DOI: 10.5281/zenodo.7499098
title: LJ Speech - Aligned IPA transcriptions

description: Files:



	

	
grids.zip

	

		
contains TextGrids for all audio files containing three tiers words, phonemes and transcription

		

			
words contains the aligned normalized English words
			
phonemes contains IPA pronunciations transcribed using CMU dictionary which then were aligned with Montreal Forced Aligner. The pronunciations were then mapped from ARPAbet to IPA and duration marks were applied (without punctuation)
			
transcription contains unaligned phonemes including punctuation and word boundary labels (SIL0)
		
		
	
	
	

	
preview.png

	

		
preview of the first TextGrid opened in Praat
	
	
	

	
words-vocabulary.txt

	

		
contains all words from tier words
	
	
	

	
phonemes-vocabulary.txt

	

		
contains all phonemes from tier phonemes
	
	
	

	
transcription-vocabulary.txt

	

		
contains all phonemes/punctuation from tier transcription
	
	
	

	
phonemes-durations.pdf

	

		
contains the plotted phoneme duration distribution of tier phonemes
	
	
	

	
phonemes-durations-simple.pdf

	

		
contains the plotted phoneme duration distribution of tier phonemes if all duration markers are ignored
	
	
	

	
pronunciations.dict

	

		
contains the pronunciations for each word including punctuation and weights (occurrence)
	
	
	

	
script.sh

	

		
contains the script to reproduce all results
	
	



Phoneme duration marker:



	
˘ -> [0, 20) percentile
	
ˑ -> [80, 90) percentile
	
ː -> [90, inf) percentile



Silence marker:



	
SIL0 -> no silence
	
SIL1 -> [0, 33.33) percentile
	
SIL2 -> [33.33, 66.66) percentile
	
SIL3 -> [66.66, inf) percentile



 
description: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 416228727 – CRC 1410
DOI: 10.17632/whwc5zkst5.1
title: A multi-GPU implementation of Real-Time Time-Dependent Auxiliary Density Functional Theory for the investigation of nanosystems irradiations

description: We report a new Multi-GPU (Graphical Processor Unit) implementation of real-time time-dependent Auxiliary Density Functional Theory (DFT) for simulations of attosecond electronic dynamics in molecular systems subjected to strong perturbations. Our code relies on the Kohn-Sham formalism of DFT and has been implemented in the deMon2k Fortran code. We expand single-particle wave functions (i.e molecular orbitals) as linear combinations of Gaussian-type-orbitals centered on atoms. The density matrix propagation is carried out on GPU while the Kohn-Sham potential is operated on CPUs (Central Processor Unit) with the help of variationally fitted densities. We propose a parallelization strategy using the MAGMA/CUDA libraries to calculate the exponential of dense Hermitian matrices entering the mathematical definition of the propagator, here using Taylor expansions. We report performance benchmarks on water droplets and on fullerenes (C50 to C540). They show a clear advantage of GPU over CPU (using the Scalapack library). The benchmarks also show the benefit of using more than one GPU for systems comprised of up to more than 10,000 basis functions. There, a speed-up of almost 40 between pure 40 CPU and four 4 GPU is obtained. Attosecond electron dynamics simulation in molecular systems comprised of several thousands of electrons becomes amenable to routine simulations in our code. We assess the accuracy of the GPU implementation considering various applications, namely, the calculation of extreme UV absorption spectra with non-Hermitian dynamics, the response of C180 to an electric perturbation, and finally the irradiation of a DNA/protein complex by a 0.4 MeV proton. The results demonstrate the robustness of the implementation. This work also paves the way for future even more efficient implementations.
DOI: 10.17632/dv7t7mrt3j.1
title: Target and Non-target Discovery Screening of Poly-and Per-Fluoroalkyl Substances (PFASs) in Environmental Biota-Samples

description: There are workflow and databases for non-target screening PFASs in complex environmental biota- samples using ultra-high performance liquid chromatography and quadrupole- orbitrap high-resolution mass spectrometer with software of Compound Discoverer. 
User can download these databases and import them into Mass Lists, Spectral Libraries and Compound Classes in Lists & Library of Compound Discoverer software, respectively, and then use the workflow to make non-target screening for PFASs.
DOI: 10.17632/pz735r8rw5.1
title: DADOS E MATERIAL: Artigo Turismo, stakeholders e fluxo informacional: panorama bibliométrico de pesquisa

description: Os conjuntos de dados gerados e/ou analisados durante o presente estudo.
DOI: 10.17632/kpn959nb2y.1
title: Magnitude of the carbon emission reduction from spatial spillovers

description: This dataset is associated with the article "Magnitude of the carbon emission reduction from spatial spillovers of disembodied technology in agricultural international trade".
DOI: 10.17632/kpn959nb2y.2
title: Magnitude of the carbon emission reduction from spatial spillovers

description: This dataset is associated with the article "Spatial spillovers of carbon emission reduction in agricultural international trade: new evidence from disembodied technology communications".
DOI: 10.17632/kpn959nb2y.3
title: Magnitude of the carbon emission reduction from spatial spillovers

description: This dataset is associated with the article "Spatial spillovers of carbon emission reduction in agricultural international trade: new evidence from disembodied technology communications".
DOI: 10.17632/tknt8f72y3.1
title: Data for “Markowitz inspects the foundation of multiple-objective portfolio selection: Justifying it by independent multivariate normal distributions”

description: The Matlab codes
DOI: 10.6084/m9.figshare.24894618
title: 20231223_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6084/m9.figshare.24894618.v1
title: 20231223_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.25573/data.24886395
title: Yeardley Descendants: Source Documents

description: Listing of source documents used to prove relationships between George Yeardley, his mother Rhoda Marston, down to their living descendants.
DOI: 10.25573/data.24886395.v1
title: Yeardley Descendants: Source Documents

description: Listing of source documents used to prove relationships between George Yeardley, his mother Rhoda Marston, down to their living descendants.
DOI: 10.25573/data.24886368
title: Yeardley Family Descendants Tree

description: Graphic display of two living matrilineal descendent lines from George Yeardley's mother, Rhoda Marston.
DOI: 10.25573/data.24886368.v1
title: Yeardley Family Descendants Tree

description: Graphic display of two living matrilineal descendent lines from George Yeardley's mother, Rhoda Marston.
DOI: 10.25573/data.24886284
title: Yeardley Family Summary

description: Life histories of George Yeardley's immediate family.
DOI: 10.17632/sk43xgzfdk.1
title: Planktonic foraminifera δ18O and concentrations of major and trace elements from IODP Hole U1432C

description: We investigate the last 230 kyr terrigenous input changes to the northeast SCS deep-sea based geochemical properties of Hole U1432C (3829 m water depth) retrieved by the International Ocean Discovery Program (IODP) Expedition 349. The dataset includes δ18O stable isotope signal obtained from planktonic foraminifera (Globigerinoides ruber white &gt; 150 µm) and elemental composition of the sediments.
DOI: 10.17632/yczy43n594.1
title: ASR indigenous language Wa'ikhana

description: This dataset includes a Wa'ikhana language model (waikhana_model.pt) for ASR inference, accompanied by a phoneme dictionary (dict.ltr.txt) and a lexicon (lexicon.txt)
DOI: 10.17632/yczy43n594.2
title: ASR indigenous language Wa'ikhana

description: This dataset includes a Wa'ikhana language model (waikhana_model.pt) for ASR inference, accompanied by a phoneme dictionary (dict.ltr.txt) and a lexicon (lexicon.txt)
DOI: 10.17632/yczy43n594.3
title: ASR indigenous language Wa'ikhana

description: This dataset includes a Wa'ikhana language model (waikhana_model.pt) for ASR inference, accompanied by a phoneme dictionary (dict.ltr.txt) and a lexicon (lexicon.txt)
DOI: 10.34740/kaggle/dsv/7261911
title: Mahanagar Yatayat Transport Dataset
DOI: 10.17632/tcbc4prhxv.1
title: The Holocene sedimentary evolution in northwest bohai strait,China

description: The database includes
DOI: 10.20383/102.0482
title: Floods on alluvial fans: implications for reworking rates, morphology and fan hazards: experimental dataset

description: This file contains data characterising four alluvial fan experiments conducted in UBC’s Biogeomorphology Experimental Laboratory. Run 1 had constant flow; Runs 2-4 had alternating five-minute “flood events” and five-minute low-flows, repeated throughout each experiment. The "flood events" in Run 2 had a constant flood flow; in Run 3 they had a moderate peak that tailed off slowly; in Run 4 they had a high peak that tailed of rapidly. All experiments had the same mean flow and the same constant sediment supply. For the three repeats of Runs 1-4 (12 experiments in total), this dataset contains information on fan gradient, lateral mobility rates, and erosion and deposition rates at each minute of the experiments. There is also data on the down-fan patterns of erosion and deposition, for the five-minute flood events and the intervening low-flow periods. Data provided are from 12-hours of experimental time and onwards (each experiment was around 20 hours long in total). These data are associated with the paper “Floods on alluvial fans: implications for reworking rates, morphology and fan hazards”, by Anya Leenman, Brett Eaton and Lucy MacKenzie (2021). The paper will be submitted to JGR: Earth Surface once this dataset is publicly available.
DOI: 10.5281/zenodo.10424311
title: Data for Study "Towards a transparent framework for assessing the revisions of national climate pledges after the Global Stocktake"

description: This is the data repository with global and country-level data for individual scenarios used in the study “Towards a transparent framework for assessing the revisions of national climate pledges after the Global Stocktake”.
DOI: 10.5281/zenodo.10424312
title: Data for Study "Towards a transparent framework for assessing the revisions of national climate pledges after the Global Stocktake"

description: This is the data repository with global and country-level data for individual scenarios used in the study “Towards a transparent framework for assessing the revisions of national climate pledges after the Global Stocktake”.
DOI: 10.48432/ordaws
title: LiDAR survey on 1000 hectares in Antimary, Acre, Brasil in 2011.

description: The LiDAR data Floresta Estadual do Antimary (ANT_A01_2011_LiDAR) refers to the survey carried out in the Antimary State Forest, Acre state, Brazil. The data were collected under the project Sustainable Landscapes, a project supported by the United States Agency for International Development (USAID) and US Department of State. The United States Forest Service working in collaboration with the Brazilian Agricultural Research Corporation (Embrapa) have made possible the provision of high accuracy LiDAR data aiming at developing new methods and generating knowledge in the field. This dataset contains: a. Classified LAS formatted point cloud data – compressed LAS files: LAZ format (vendor delivered); b. Digital Terrain Model (vendor delivered); c. Map of LiDAR coverage area and block boundaries; “Data were acquired by the Sustainable Landscapes Brazil project supported by the Brazilian Agricultural Research Corporation (Embrapa), the US Forest Service, USAID and the US Department of State."