cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57903/uj/mrtlsw
title: ZintegrUJ physics samples - Sand Simulation

description: Application: sand simulation This content was created as part of a project co-financed by the European Union within the framework of the European Social Fund POWER.03.05.00-00-Z309/17-00.
DOI: 10.5281/zenodo.10498386
title: Hyperspectral spectroscopic transmittance data collected in-vivo healthy and diseased tomato leaflets in controlled conditions - dataset I

description: Hyperspectral Spectroscopic Transmittance data collected in-vivo tomato leaflets in controlled conditions

Hyperspectral point-of-measurements (HS-POM) were collected in vivo from the adaxial side of healthy and diseased leaflets of nine tomato plants, in a dark room (in detail, three Control plants, three plants inoculated with Pseudomonas syringae pv. tomato, and three plants inoculated with Xanthomonas euvesicatoria). For each plant, spectral assessments were performed randomly on nine points of different leaflets, belonging to the 4th, 5th, and 6th expanded leaves.

Hyperspectral data were acquired using a Hamamatsu Photonics K.K. TM Series C11697MB spectrometer, which covers a wavelength range of 200-1100 nm with a spectral resolution of 0.6 nm. A transmission optical fiber bundle (FCR-7UVIR200-2-45-BX, Avantes, Eerbeek, The Netherlands) with a range of 200-2500 nm was used along with a stainless-steel slitted reflection probe that was positioned 0.5 cm above the sample surface to capture the leaflet's spectral signal and direct it to the spectrometer's entrance lens. A white LED light was placed underneath the leaflet to provide uniform illumination to its entire abaxial surface. The spectral range of the LED emits light from 390 to 800 nm. Therefore, the LED spectra were used as a reference to the spectral range measured by the spectrophotometer and to check measurement and light emission stability. The hyperspectral transmittance data were collected using specialized evaluation software (SpecEvaluationUSB2.exe, Hamamatsu Photonics K.K., Japan).

For more detailed description of the bacterial inoculation assays and the remain experimental conditions, please check:

Reis Pereira M, Santos FNd, Tavares F and Cunha M (2023) Enhancing host-pathogen phenotyping dynamics: early detection of tomato bacterial diseases using hyperspectral point measurement and predictive modeling. Front. Plant Sci. 14:1242201. doi: 10.3389/fpls.2023.1242201
DOI: 10.5281/zenodo.10498387
title: Hyperspectral spectroscopic transmittance data collected in-vivo healthy and diseased tomato leaflets in controlled conditions - dataset I

description: Hyperspectral Spectroscopic Transmittance data collected in-vivo tomato leaflets in controlled conditions

Hyperspectral point-of-measurements (HS-POM) were collected in vivo from the adaxial side of healthy and diseased leaflets of nine tomato plants, in a dark room (in detail, three Control plants, three plants inoculated with Pseudomonas syringae pv. tomato, and three plants inoculated with Xanthomonas euvesicatoria). For each plant, spectral assessments were performed randomly on nine points of different leaflets, belonging to the 4th, 5th, and 6th expanded leaves.

Hyperspectral data were acquired using a Hamamatsu Photonics K.K. TM Series C11697MB spectrometer, which covers a wavelength range of 200-1100 nm with a spectral resolution of 0.6 nm. A transmission optical fiber bundle (FCR-7UVIR200-2-45-BX, Avantes, Eerbeek, The Netherlands) with a range of 200-2500 nm was used along with a stainless-steel slitted reflection probe that was positioned 0.5 cm above the sample surface to capture the leaflet's spectral signal and direct it to the spectrometer's entrance lens. A white LED light was placed underneath the leaflet to provide uniform illumination to its entire abaxial surface. The spectral range of the LED emits light from 390 to 800 nm. Therefore, the LED spectra were used as a reference to the spectral range measured by the spectrophotometer and to check measurement and light emission stability. The hyperspectral transmittance data were collected using specialized evaluation software (SpecEvaluationUSB2.exe, Hamamatsu Photonics K.K., Japan).

For more detailed description of the bacterial inoculation assays and the remain experimental conditions, please check:

Reis Pereira M, Santos FNd, Tavares F and Cunha M (2023) Enhancing host-pathogen phenotyping dynamics: early detection of tomato bacterial diseases using hyperspectral point measurement and predictive modeling. Front. Plant Sci. 14:1242201. doi: 10.3389/fpls.2023.1242201
DOI: 10.14469/hpc/13612
title: B3LYP/Def2-TZVPP, GD3BJ, TS, chair, trans, G = -1451.040796

description: Gaussian 16 (C01) calculation
DOI: 10.57903/uj/ukpqc9
title: ZintegrUJ physics samples - Oscillators

description: Application: the evolution of the system governed by the stiff equation Application: one dimensional oscillator Application: ball motion with gravity, wind and air friction Application: pendulum motion in 3D This content was created as part of a project co-financed by the European Union within the framework of the European Social Fund POWER.03.05.00-00-Z309/17-00.
DOI: 10.57903/uj/g200az
title: ZintegrUJ physics samples - Articulated Bodies

description: An articulated body model Library: forward dynamics for articulated bodies Library: collisions for articulated bodies Application: simulation of articulated bodies This content was created as part of a project co-financed by the European Union within the framework of the European Social Fund POWER.03.05.00-00-Z309/17-00.
DOI: 10.57903/uj/vvji8n
title: ZintegrUJ physics samples - 3D Particles

description: Application: collisions of particles with a stationary plane Application: collisions of particles with a stationary sphere Application: collisions of particles with a test model (“test model” = “maskotka”) Application: the 90-degrees test Application: collisions between particles This content was created as part of a project co-financed by the European Union within the framework of the European Social Fund POWER.03.05.00-00-Z309/17-00.
DOI: 10.6084/m9.figshare.25018694
title: Supplementary Material for: Prognostic nutritional index after introduction of atezolizumab with bevacizumab predicts prognosis in advanced hepatocellular carcinoma: A multicenter study

description: Introduction: Atezolizumab plus bevacizumab (Atez/Bev) is the preferred treatment for advanced hepatocellular carcinoma (HCC). However, biomarkers of therapeutic efficacy have remained unclear. We took a retrospective approach to explore the role of prognostic nutritional index (PNI) for predicting the outcomes of Atez/Bev treatment.
Methods: One hundred twenty-five HCC patients were enlisted; these patients received Atez/Bev treatment and underwent dynamic computerized tomography/magnetic resonance imaging to determine the treatment response on at least one occasion between October 2020 and January 2023, and their PNI before treatment and at the beginning of the second cycle (PNI-2c) was evaluated.
Results: During the initial evaluation, 2 (2%), 28 (22%), 70 (56%), and 25 (20%) patients exhibited a complete response (CR), partial response (PR), stable disease (SD), and progressive disease (PD), respectively. Patients with non-PD tended to have higher PNI at baseline and PNI-2c than those with PD (p = 0.245 and 0.122, respectively), with optimal baseline PNI and PNI-2c cut-off values of 42.6 and 40.4, respectively. PNI at baseline could not be used to predict overall survival (OS) or progression-free survival (PFS). However, PNI-2c predicted OS and PFS (PNI-2c ≥ 40.4 vs. &lt; 40.4: 25.3 vs. 16.2 months, P = 0.008 for OS; 12.7 vs. 8.4 months, P = 0.036 for PFS). A multivariate analysis showed a significant association between PNI-2c and OS. 
Conclusions: PNI-2c is a predictor of prognosis in HCC patients treated with Atez/Bev therapy.
DOI: 10.57903/uj/qbvmmc
title: ZintegrUJ physics samples - Particles

description: Application: a particle system with penalty methods Application: stateless particle system Application: state-preserving particle system Application: a particle system with collisions Application: rendering with points Application: rendering with streaks Application: rendering with splats Application: rendering with sprites This content was created as part of a project co-financed by the European Union within the framework of the European Social Fund POWER.03.05.00-00-Z309/17-00.
DOI: 10.57903/uj/wevoyk
title: ZintegrUJ physics samples - Flocking

description: Application: flocking system This content was created as part of a project co-financed by the European Union within the framework of the European Social Fund POWER.03.05.00-00-Z309/17-00.
DOI: 10.6084/m9.figshare.25018694.v1
title: Supplementary Material for: Prognostic nutritional index after introduction of atezolizumab with bevacizumab predicts prognosis in advanced hepatocellular carcinoma: A multicenter study

description: Introduction: Atezolizumab plus bevacizumab (Atez/Bev) is the preferred treatment for advanced hepatocellular carcinoma (HCC). However, biomarkers of therapeutic efficacy have remained unclear. We took a retrospective approach to explore the role of prognostic nutritional index (PNI) for predicting the outcomes of Atez/Bev treatment.
Methods: One hundred twenty-five HCC patients were enlisted; these patients received Atez/Bev treatment and underwent dynamic computerized tomography/magnetic resonance imaging to determine the treatment response on at least one occasion between October 2020 and January 2023, and their PNI before treatment and at the beginning of the second cycle (PNI-2c) was evaluated.
Results: During the initial evaluation, 2 (2%), 28 (22%), 70 (56%), and 25 (20%) patients exhibited a complete response (CR), partial response (PR), stable disease (SD), and progressive disease (PD), respectively. Patients with non-PD tended to have higher PNI at baseline and PNI-2c than those with PD (p = 0.245 and 0.122, respectively), with optimal baseline PNI and PNI-2c cut-off values of 42.6 and 40.4, respectively. PNI at baseline could not be used to predict overall survival (OS) or progression-free survival (PFS). However, PNI-2c predicted OS and PFS (PNI-2c ≥ 40.4 vs. &lt; 40.4: 25.3 vs. 16.2 months, P = 0.008 for OS; 12.7 vs. 8.4 months, P = 0.036 for PFS). A multivariate analysis showed a significant association between PNI-2c and OS. 
Conclusions: PNI-2c is a predictor of prognosis in HCC patients treated with Atez/Bev therapy.
DOI: 10.6084/m9.figshare.25018706.v1
title: Unplugging experiments results from Robotized unplugging of a cylindrical peg press-fitted into a cylindrical hole

description: Experiments Data.xlsx (1.0)
DOI: 10.6084/m9.figshare.25018706
title: Unplugging experiments results from Robotized unplugging of a cylindrical peg press-fitted into a cylindrical hole

description: Experiments Data.xlsx (1.0)
DOI: 10.6084/m9.figshare.24981195
title: Contrasting response of root traits of arbuscular mycorrhizal and ectomycorrhizal trees to phosphorus availability in subtropical forests

description: The dataset includes a field survey and a soil P manipulation experiment in a subtropical forest, to investigate how root functional traits, mycorrhizal colonization and putative pathogen infection of arbuscular mycorrhizal and ectomycorrhizal tree seedlings respond to gradients of soil P.
DOI: 10.6084/m9.figshare.24981195.v1
title: Contrasting response of root traits of arbuscular mycorrhizal and ectomycorrhizal trees to phosphorus availability in subtropical forests

description: The dataset includes a field survey and a soil P manipulation experiment in a subtropical forest, to investigate how root functional traits, mycorrhizal colonization and putative pathogen infection of arbuscular mycorrhizal and ectomycorrhizal tree seedlings respond to gradients of soil P.
DOI: 10.21335/nmdc-1512912471
title: Gadoid eggs from haddock spawning ground survey 2022 identified to species by DNA analysis

description: Eggs were sampled at the haddock spawning ground survey for details se Johannesen et al (2022). The eggs were sorted on board using a stereomicroscope, and eggs with diameter of 1.2-1.6 mm were assumed to be gadoid eggs. The eggs were classified into egg development stages based on Thompson and Riley (1981). The samples were fixed in 98% alcohol after standard processing on board. All collected eggs classified as gadoid eggs, were subjected to genetic analysis at the laboratory at the Institute of Marine Research's station in Flødevigen. Eggs were set up for DNA extraction in a 96-well plate format using the Hamilton Star robot. Each plate had two negative controls randomized to ensure plate identity and orientation for further analyses. The chemistry and extraction method were provided by Omega Biotek and based on Mag-Bind® Blood and Tissue DNA HDQ Mag-Bind technology isolates DNA from enzymatically degraded cells in solution by binding small magnetic beads to DNA. This is further purified and eventually separated from the beads, resulting in a DNA extract. The concentration of DNA extracts was then measured using a fluorometric method on a ThermoFisher Fluoroskan Microplate Fluorometer with Quan IT kit dsDNA High Sensitivity (0.2-50ng). The samples were normalized to a concentration of &lt;= 5 ng/µl for further preparation of DNA libraries for sequencing. The target sequence is a universal mini barcode 295 bp sequence of the mitochondrial COI (cytochrome c oxidase subunit 1) developed for species identification of fish by Sultana et al (2018). Library preparation involves a two-step process with two rounds of PCR. In PCR1, the COI fragment is amplified, and in PCR2, each individual sample is tagged with a barcode (i5) while also receiving an index code (i7) representing the plate. This allows the identification of each sample after sequencing. Library preparation uses custom barcodes and indexes, not part of a commercial kit but developed based on a protocol described in Campbell et al (2015). The library underwent quality control by running it on an Agilent Bioanalyzer, providing a profile of the library through gel electrophoresis, and measuring concentrations on a Qubit fluorometer. Sequencing of the library was performed on an Illumina MiSeq using "paired end sequencing" with a MiSeq Reagent Kit v3 (600-cycle), including 5% PhiX as a control. Raw sequencing data in fastq format were processed in the R software (R Core Team 2023) and using the DADA2 module (Callahan et al. 2016). Quality-filtered sequences were then compared with a database consisting of COI sequences for gadoid fish using the R module rBLAST (Hahsler 2019). Successful species identification required a 100% match in the database for a single species.
For further details on the same methods applied to eggs sampled at the cod spawning survey in 2022, see Fuglebakk et al (in prep).
DOI: 10.5281/zenodo.10526883
title: Dataset related to article "Diagnostic accuracy of multiparametric MRI- and microultrasound-targeted biopsy in biopsy-naïve patients with a PI-RADS 5 lesion: a single-institutional study "

description: This record contains raw data related to article “Diagnostic accuracy of multiparametric MRI- and microultrasound-targeted biopsy in biopsy-naïve patients with a PI-RADS 5 lesion: a single-institutional study"

Abstract



 Purpose:  To evaluate the diagnostic accuracy of multiparametric magnetic resonance imaging (MRI)- and microultrasound (microUS)-guided targeted biopsy (TBx) in detecting prostate cancer (PCa) and clinically significant (cs) PCa among men with Prostate Imaging Reporting and Data System (PI-RADS 5) lesions and to compare this combined TBx (CTBx) strategy with CTBx plus systemic biopsy (SBx).

 Methods:  One hundred and thirty-six biopsy-naïve patients with PI-RADS 5 lesion at multiparametric MRI undergoing CTBx plus SBx were retrospectively evaluated. Analysis of diagnostic performance of microUS-TBx, MRI-TBx, CTBx, SBx and combined CTBx plus SBx was performed. Cost (downgrade, upgrade and biopsy core) to effectiveness (detection rate) was compared.

 Results:  CTBx achieved a comparable detection rate to CTBx plus SBx in diagnosis of PCa and csPCa (PCa: 78.7% [107/136] vs 79.4% [108/136]; csPCa: 67.6% [92/136] vs 67.6% [92/136]; p > 0.05) and outperformed SBx (PCa: 58.8% [80/136]; csPCa: 47.8% [65/136]; p < 0.001). Using CTB would have avoided 41.1% (56/136) unnecessary SBx, without missing any csPCa. The rate of any upgrading or csPCa upgrading was significantly higher by SBx than by CTBx [33/65 (50.8%) vs 17/65 (26.1%) and 20/65 (30.8%) vs 4/65 (6.15%), respectively, p < 0.05]. Considering csPCa detection rate, microUS showed high sensitivity and positive predictive value (94.6%, 87.9%, respectively), with lower specificity and negative predictive value (25.0% and 44.4%, respectively). At multivariable logistic regression models, positive microUS was identified as an independent predictor of csPCa (p = 0.024).

 Conclusions:  A combined microUS/MRI-TBx approach could be the ideal imaging tool for characterizing primary disease in PI-RADS five patients, allowing SBx to be avoided.
DOI: 10.5281/zenodo.10526884
title: Dataset related to article "Diagnostic accuracy of multiparametric MRI- and microultrasound-targeted biopsy in biopsy-naïve patients with a PI-RADS 5 lesion: a single-institutional study "

description: This record contains raw data related to article “Diagnostic accuracy of multiparametric MRI- and microultrasound-targeted biopsy in biopsy-naïve patients with a PI-RADS 5 lesion: a single-institutional study"

Abstract



 Purpose:  To evaluate the diagnostic accuracy of multiparametric magnetic resonance imaging (MRI)- and microultrasound (microUS)-guided targeted biopsy (TBx) in detecting prostate cancer (PCa) and clinically significant (cs) PCa among men with Prostate Imaging Reporting and Data System (PI-RADS 5) lesions and to compare this combined TBx (CTBx) strategy with CTBx plus systemic biopsy (SBx).

 Methods:  One hundred and thirty-six biopsy-naïve patients with PI-RADS 5 lesion at multiparametric MRI undergoing CTBx plus SBx were retrospectively evaluated. Analysis of diagnostic performance of microUS-TBx, MRI-TBx, CTBx, SBx and combined CTBx plus SBx was performed. Cost (downgrade, upgrade and biopsy core) to effectiveness (detection rate) was compared.

 Results:  CTBx achieved a comparable detection rate to CTBx plus SBx in diagnosis of PCa and csPCa (PCa: 78.7% [107/136] vs 79.4% [108/136]; csPCa: 67.6% [92/136] vs 67.6% [92/136]; p > 0.05) and outperformed SBx (PCa: 58.8% [80/136]; csPCa: 47.8% [65/136]; p < 0.001). Using CTB would have avoided 41.1% (56/136) unnecessary SBx, without missing any csPCa. The rate of any upgrading or csPCa upgrading was significantly higher by SBx than by CTBx [33/65 (50.8%) vs 17/65 (26.1%) and 20/65 (30.8%) vs 4/65 (6.15%), respectively, p < 0.05]. Considering csPCa detection rate, microUS showed high sensitivity and positive predictive value (94.6%, 87.9%, respectively), with lower specificity and negative predictive value (25.0% and 44.4%, respectively). At multivariable logistic regression models, positive microUS was identified as an independent predictor of csPCa (p = 0.024).

 Conclusions:  A combined microUS/MRI-TBx approach could be the ideal imaging tool for characterizing primary disease in PI-RADS five patients, allowing SBx to be avoided.
DOI: 10.34740/kaggle/dsv/7426536
title: US state_trends.csv
DOI: 10.6084/m9.figshare.25018732
title: Raw data from Beakiation: how a novel parrot gait expands the locomotor repertoire of living birds

description: Occupation of arboreal habitats poses myriad locomotor challenges, driving both anatomical and behavioural innovations across various tetrapod lineages. Here, we report and biomechanically assess a novel, beak-driven locomotor mode – ‘beakiation’ – by which parrots advance along the underside of narrow arboreal substrates. Using high speed videography and kinetic analyses, we describe the limb loading patterns and pendular mechanics of beakiation, and compare the biomechanical characteristics of this gait to other suspensory behaviours (namely, forelimb-driven brachiation and inverted quadrupedal walking). We report that the parrot beak experiences comparable force magnitudes (approx. 150% body weight in the normal plane; approx. 50% body weight in the fore-aft plane) to the forelimbs of brachiating primates. Parrot beakiation is also characterized by longer-than-expected pendular periods, similar to observations of gibbon brachiation. However, in terms of mechanical energy recovery, parrot beakiation is characterized by lower rates of energetic recovery than brachiating specialists: a product of its slower, more careful nature. The observation of this novel behaviour – which adds to a growing base of literature regarding beak-assisted locomotor strategies in birds – highlights the extraordinary behavioural plasticity of birds, the functional versatility of the avian beak, and the difficulties in reconstructing an animal's locomotor repertoire from morphological characteristics alone.
DOI: 10.6084/m9.figshare.25018732.v1
title: Raw data from Beakiation: how a novel parrot gait expands the locomotor repertoire of living birds

description: Occupation of arboreal habitats poses myriad locomotor challenges, driving both anatomical and behavioural innovations across various tetrapod lineages. Here, we report and biomechanically assess a novel, beak-driven locomotor mode – ‘beakiation’ – by which parrots advance along the underside of narrow arboreal substrates. Using high speed videography and kinetic analyses, we describe the limb loading patterns and pendular mechanics of beakiation, and compare the biomechanical characteristics of this gait to other suspensory behaviours (namely, forelimb-driven brachiation and inverted quadrupedal walking). We report that the parrot beak experiences comparable force magnitudes (approx. 150% body weight in the normal plane; approx. 50% body weight in the fore-aft plane) to the forelimbs of brachiating primates. Parrot beakiation is also characterized by longer-than-expected pendular periods, similar to observations of gibbon brachiation. However, in terms of mechanical energy recovery, parrot beakiation is characterized by lower rates of energetic recovery than brachiating specialists: a product of its slower, more careful nature. The observation of this novel behaviour – which adds to a growing base of literature regarding beak-assisted locomotor strategies in birds – highlights the extraordinary behavioural plasticity of birds, the functional versatility of the avian beak, and the difficulties in reconstructing an animal's locomotor repertoire from morphological characteristics alone.
DOI: 10.6084/m9.figshare.24833181
title: <b>Long-term stability of sapling dynamics is regulated by soil phosphorus availability in subtropical forest</b>

description: We collected annual dynamic data of 20,768 regenerating saplings, which were censused from 2008 to 2019 in a subtropical forest, to investigate how soil nutrients affect the temporal stability of productivity at both population and community levels.
DOI: 10.18112/openneuro.ds004572.v1.1.0
title: OTKA PLB-HYP Study1
DOI: 10.34740/kaggle/ds/4318874
title: Skin Lesions Classification Dataset
DOI: 10.34740/kaggle/ds/4321335
title: Kolkata's Culinary Map: Top 1000 TripAdvisor Picks
DOI: 10.5525/gla.researchdata.1564
title: Mid-infrared spectroscopy data from laboratory reared samples of Glossina spp

description: Mid-infrared spectral data from laboratory reared tsetse flies Glossina spp. used for sex and age prediction with MIRS toolbox.
DOI: 10.5281/zenodo.10527026
title: Observed data and processed data
DOI: 10.5281/zenodo.10527027
title: Observed data and processed data