cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7409661
title: Supplementary Data for 'Altered body iron distribution and microcytosis in mice deficient in iron regulatory protein 2 (IRP2).'

description: Supplementary data for Galy, B., Ferring, D., Minana, B., Bell, O., Janser, H.G., Muckenthaler, M., Schümann, K. and Hentze, M.W., 2005. Altered body iron distribution and microcytosis in mice deficient in iron regulatory protein 2 (IRP2). <em>Blood</em>, <em>106</em>(7), pp.2580-2589.
description: {"references": ["Galy, B., Ferring, D., Minana, B., Bell, O., Janser, H.G., Muckenthaler, M., Sch\u00fcmann, K. and Hentze, M.W., 2005. Altered body iron distribution and microcytosis in mice deficient in iron regulatory protein 2 (IRP2). Blood, 106(7), pp.2580-2589."]}
DOI: 10.5281/zenodo.7407255
title: siphamia_roseigaster_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7407254
title: siphamia_roseigaster_decontaminated_gx.fasta.gz

description: .
DOI: 10.5281/zenodo.7409660
title: CAFA3 based dataset

description: Dataset based on CAFA3 database challenge. Functions presented in at least 50 and the duplicated proteins were removed from different sets. Each file contains the ontology (bp for Biological Process, cc for Cellular Component, and mf for Molecular Function) and the set (training, validation and test). For generated for augmentation, it has the identification of augmented_training.
DOI: 10.5281/zenodo.7409659
title: CAFA3 based dataset

description: Dataset based on CAFA3 database challenge. Functions presented in at least 50 and the duplicated proteins were removed from different sets. Each file contains the ontology (bp for Biological Process, cc for Cellular Component, and mf for Molecular Function) and the set (training, validation and test). For generated for augmentation, it has the identification of augmented_training.
DOI: 10.25934/pr00005579.2
title: Available IPD datapackage for study 'A Phase III, Randomized, Double-Blind, Placebo-Controlled, Multicenter Study To Evaluate the Efficacy and Safety Of Bevacizumab, and Associated Biomarkers, In Combination With Paclitaxel Compared With Paclitaxel Plus Placebo as First-line Treatment Of Patients With Her2-Negative Metastatic Breast Cancer'

description: This is a Phase III, randomized, double-blind, placebo-controlled multicenter study to evaluate the efficacy and safety of bevacizumab administered in combination with paclitaxel in patients with previously untreated, locally recurrent, or metastatic HER2-negative breast cancer. Patients will be randomized to one of two treatment arms: bevacizumab or placebo. All patients will be given an intravenous (IV) infusion of of paclitaxel (90 mg/m2) for 3 weeks during each 28-day cycle. bevacizumab or placebo (10 mg/kg) will be administered by IV infusion on Days 1 and 15 of each 28-day cycle. Patients will be treated until disease progression, unacceptable toxicity or death from any cause occurs.
DOI: 10.5281/zenodo.6826533
title: Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del/+-Del/+ - 5197_5212

description: We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration &gt; 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy &lt; 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.
DOI: 10.5281/zenodo.6826534
title: Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del/+-Del/+ - 5197_5212

description: We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration &gt; 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy &lt; 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.
DOI: 10.5281/zenodo.7409665
title: Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del/+-Del/+ - 5197_5212

description: We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration &gt; 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy &lt; 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.
DOI: 10.5281/zenodo.7405294
title: Open data for assessing habitats degree of conservation at plot level. An example dataset of forest structural attributes in Val d'Agri (Basilicata, Southern Italy)

description: We provide a georeferenced dataset of vertical and horizontal structure of forest types belonging to 4 habitat types, sensu Council Directive 92/43/EEC. The dataset includes structural indicators commonly linked to old-growth forests in Europe, in particular the amount of standing and lying deadwood. We collected data on 32 plots (24 of 225 m<sup>2</sup>, and 8 of 100 m<sup>2</sup>, according to different forests type) during spring and summer of 2022, in Val d’Agri (Basilicata, Southern Italy). The dataset we provide follows the common national standard for field data collection in forest habitat types, published by ISPRA in 2016 (https://www.isprambiente.gov.it/public_files/direttiva-habitat/Manuale-142-2016.pdf) with the aim to promote a greater homogeneity in assessment of habitat conservation status at Country and biogeographical level, as requested by the Habitats Directive. Data were acquired by using a free Android application (VegApp, (https://vegapp.de/), and standardized field survey forms. The selection of the location of the sample sites were spatially balanced by using the sofware QGis vers. 3.22 (http://qgis.osgeo.org) plots_Table1 shows the characteristics of the sample sites, and information on type of management, when available. plots_Table2 provides the description and the measuring unit of all the attributes included in the dataset at plot level. It includes parameters used for assessing old-growth forests, linking them to the main type forests management, in order to both select indicators useful for assessing the conservation degree of forest habitat types, and identify good practices for nature conservation in these ecosystems. plots_Table3 contains information on living trees and deadwood at plot level. Trees describes the dataset related to single-tree data, and it contains the following fields for all living trees, exceeding 10 cm DBH, occurring in the plots. The nomenclature follows the Italian checklist available at https://dryades.units.it/floritaly/ The shapefile "plots" contains the same information included in plots_Table1.
DOI: 10.5281/zenodo.7405293
title: Open data for assessing habitats degree of conservation at plot level. An example dataset of forest structural attributes in Val d'Agri (Basilicata, Southern Italy)

description: We provide a georeferenced dataset of vertical and horizontal structure of forest types belonging to 4 habitat types, sensu Council Directive 92/43/EEC. The dataset includes structural indicators commonly linked to old-growth forests in Europe, in particular the amount of standing and lying deadwood. We collected data on 32 plots (24 of 225 m<sup>2</sup>, and 8 of 100 m<sup>2</sup>, according to different forests type) during spring and summer of 2022, in Val d’Agri (Basilicata, Southern Italy). The dataset we provide follows the common national standard for field data collection in forest habitat types, published by ISPRA in 2016 (https://www.isprambiente.gov.it/public_files/direttiva-habitat/Manuale-142-2016.pdf) with the aim to promote a greater homogeneity in assessment of habitat conservation status at Country and biogeographical level, as requested by the Habitats Directive. Data were acquired by using a free Android application (VegApp, (https://vegapp.de/), and standardized field survey forms. The selection of the location of the sample sites were spatially balanced by using the sofware QGis vers. 3.22 (http://qgis.osgeo.org) plots_Table1 shows the characteristics of the sample sites, and information on type of management, when available. plots_Table2 provides the description and the measuring unit of all the attributes included in the dataset at plot level. It includes parameters used for assessing old-growth forests, linking them to the main type forests management, in order to both select indicators useful for assessing the conservation degree of forest habitat types, and identify good practices for nature conservation in these ecosystems. plots_Table3 contains information on living trees and deadwood at plot level. Trees describes the dataset related to single-tree data, and it contains the following fields for all living trees, exceeding 10 cm DBH, occurring in the plots. The nomenclature follows the Italian checklist available at https://dryades.units.it/floritaly/ The shapefile "plots" contains the same information included in plots_Table1.
DOI: 10.25934/pr00005788.1
title: Available IPD datapackage for study 'A Randomized, Multicenter, Adaptive Phase II/III Study To Evaluate The Efficacy And Safety Of Trastuzumab Emtansine (T-DM1) Versus Taxane (Docetaxel Or Paclitaxel) In Patients With Previously Treated Locally Advanced Or Metastatic HER2-Positive Gastric Cancer, Including Adenocarcinoma Of The Gastroesophageal Junction'

description: This multicenter, randomized, adaptive Phase II/III study will evaluate the efficacy and safety of trastuzumab emtansine (T-DM1) compared to standard taxane (docetaxel or paclitaxel) treatment in participants with human epidermal growth factor receptor 2 (HER2)-positive advanced gastric cancer. At the start of the trial (stage 1), participants will be randomized with a ratio 2:2:1 to one of three treatment arms: Arm A: trastuzumab emtansine 3.6 milligram per kilogram (mg/kg) per intravenous injection (IV) every 3 weeks; Arm B: trastuzumab emtansine 2.4 mg/kg IV every week; Arm C: standard taxane therapy (docetaxel 75 milligram per meter square [mg/m^2] IV every 3 weeks or paclitaxel 80 mg/m^2 kg IV every week per investigator choice). At the end of the first stage of the study, the dose and schedule of trastuzumab emtansine that will be used in the second stage of the study will be selected by an Independent Data Monitoring Committee (IDMC). The regimen selection analysis will be made after approximately 100 participants across all three study arms have been treated for at least 12 weeks. Once a trastuzumab emtansine regimen has been selected, Stage I participants who were assigned to the treatment arm which was selected for Stage II of the study and participants who were in the standard taxane group will continue to receive their assigned treatment regimen. Stage I participants who were assigned to the regimen that was not selected for further evaluation will continue to receive their assigned regimen and will continue to be followed for efficacy and safety. In Stage II of the study, additional participants will be recruited and randomized with a ratio 2:1 to either the selected regimen of trastuzumab emtansine or to the standard taxane therapy. Participants will receive study treatment until disease progression, unacceptable toxicity, initiation of another cancer therapy or withdrawal.
DOI: 10.25934/pr00005994.1
title: Available IPD datapackage for study 'A Phase III Prospective, Two-Cohort Non-Randomized, Multi-Centre, Multinational, Open-Label Study to Assess the Safety of Assisted- and Self-Administered Subcutaneous Trastuzumab as Therapy in Patients With Operable HER2-Positive Early Breast Cancer'

description: This multicenter, two-cohort, non-randomized, open-label study will evaluate the safety and tolerability of assisted and self-administered SC Herceptin as adjuvant therapy in participants with early HER2-positive breast cancer following tumor excision. Participants will receive Herceptin 600 milligrams (mg) SC every 3 weeks for 18 cycles, either by an assisted administration using a conventional syringe and needle/vial formulation (Cohort A) or with assisted and self-administration using a single-use injection device (SID) in selected participants (Cohort B).
DOI: 10.25403/upresearchdata.21682391
title: Captive, wild body temperature and heat dissipation behaviour for avian species in the Kalahari

description: Body temperature data collected for 9 South African desert bird species across a range of air temperatures. Birds were housed in large free flight aviaries (Tb data). Heat dissipation, shade seeking and activity behaviours were concurrently collected (Main Aviary Behaviour). These data were compared to free ranging behaviour collected for species in the wild community (Main Wild Behaviour).
DOI: 10.25403/upresearchdata.21682391.v1
title: Captive, wild body temperature and heat dissipation behaviour for avian species in the Kalahari

description: Body temperature data collected for 9 South African desert bird species across a range of air temperatures. Birds were housed in large free flight aviaries (Tb data). Heat dissipation, shade seeking and activity behaviours were concurrently collected (Main Aviary Behaviour). These data were compared to free ranging behaviour collected for species in the wild community (Main Wild Behaviour).
DOI: 10.25934/pr00006058.1
title: Available IPD datapackage for study 'A Randomized, Two-Arm, Open-Label, Multicenter Phase II Trial Assessing the Efficacy and Safety of Pertuzumab Given in Combination With Trastuzumab Plus an Aromatase Inhibitor in First Line Patients With HER2-Positive and Hormone Receptor-Positive Advanced (Metastatic or Locally Advanced) Breast Cancer'

description: This randomized, open-label, two-arm, multi-center, Phase II study will evaluate the efficacy and safety of pertuzumab in combination with trastuzumab plus an aromatase inhibitor (AI) in first-line participants with HER2-positive and hormone receptor-positive advanced breast cancer. Participants will be randomized to one of two treatment arms; Arm A (pertuzumab in combination with trastuzumab plus an AI) or Arm B (trastuzumab plus an AI). Participants may also receive induction chemotherapy (a taxane, either docetaxel or paclitaxel) at the investigator's discretion in combination with the assigned treatment arm. The anticipated time on study treatment is until disease progression, unacceptable toxicity, withdrawal of consent, or death whichever occurs first.
DOI: 10.6084/m9.figshare.21688391
title: Supplementary Material for: Treatment of congenital hypothyroidism – impact of secular changes in levothyroxine initial dose on early growth

description: Introduction: Newborn screening of congenital hypothyroidism (CH) has enabled early treatment with levothyroxine (LT4), ensuring normal growth and development. The initial LT4 dose recommendation has increased over decades. We evaluated whether the increased LT4 dosing influenced thyroid-stimulating hormone (TSH) and thyroxine (fT4) concentrations, growth, or treatment-related symptoms. Methods: LT4 doses, TSH, fT4, anthropometrics, and treatment-related symptoms until age two years were evaluated in 172 Finnish CH patients born between 1980 and 2018. The patients were grouped according to birth decade: 1980s (n = 19, mean LT4 starting dose 6.8 µg/kg/day), 1990s (n = 50, 7.4 µg/kg/day), 2000s (n = 59, 9.7 µg/kg/day) and 2010s (n = 44, 10.8 µg/kg/day) Results: TSH concentrations were higher during the first two years of life in children born in 1980s compared to children born later. TSH concentrations were often subnormal in children receiving higher LT4 doses (children born in 2000s and 2010s). However, symptoms of overtreatment were uncommon. Linear or head growth showed no differences between the groups during the first two years of life. Although growth was within the normal spectrum, children in all groups were shorter than their target length at two years and their weight-for-length was above the mean through the first two years of life. Discussion/Conclusion: Current treatment practice with higher LT4 dose normalizes TSH rapidly without significant increase in side effects. However, irrespective of initial LT4 dose, children were shorter than expected at 2 years of age. Effects of different initial LT4 dose on cognitive development urges further investigation.
DOI: 10.25377/sussex.21566013.v1
title: Dataset for paper: Consequences of approximating electron correlation effects

description: Data for paper published in Molecular Physics Nov 2022 The zip file contains 7 subdirectories containing (i) optimised wavefunctions (ii) static Coulomb hole data (fig 3), (iii) dynamic Coulomb hole data (fig 4 & 5), (iv) ‘exact’ electron correlation energy data (fig 6) (v) energy density data as a function of the intracule coordinate r (fig 7), (vi) energy density data as a function of the extracule coordinate R (fig 8), (vii) radial electron correlation energy distribution data using CS and LYP functional (fig 9). For more information about the data, please see the Data_readme_notes file in the zip folder. All data files (pd, sv, txt) are text files so can be opened in any text editor. Also included in some directories are the Latex files (.tex) used to generate the figures in the manuscript. This requires Latex software/editor. Abstract The effect of approximating electron correlation in few-electron systems is investigated using three wavefunctions: the many body wavefunction referred to as fully-correlated (FC), the Hartree Fock wavefunction (HF), and the Colle and Salvetti Jastrow-style wavefunction (CS) used in the derivation of the popular Lee, Yang and Parr (LYP) correlation functional. The electron correlation energy, static and dynamic Coulomb holes, various expectation values, and radial energy distributions (energy densities) are considered. It is shown that whilst the CS wavefunction can capture the behaviour of the wavefunction at the singularities of the Coulomb potential corresponding to the coalescence of two particles and decreases the area of the primary static Coulomb hole by nearly 30% compared to HF for He and Li++, it is unable to accurately model expectation values that depend on the whole of space and key features of the electron density behaviour in dynamic Coulomb holes and the energy density behaviour in energy distributions. These issues are amplified when considering the hydride ion and a system with the critical nuclear charge for binding. <br>
DOI: 10.25377/sussex.21566013
title: Dataset for paper: Consequences of approximating electron correlation effects

description: Data for paper published in Molecular Physics Nov 2022 The zip file contains 7 subdirectories containing (i) optimised wavefunctions (ii) static Coulomb hole data (fig 3), (iii) dynamic Coulomb hole data (fig 4 & 5), (iv) ‘exact’ electron correlation energy data (fig 6) (v) energy density data as a function of the intracule coordinate r (fig 7), (vi) energy density data as a function of the extracule coordinate R (fig 8), (vii) radial electron correlation energy distribution data using CS and LYP functional (fig 9). For more information about the data, please see the Data_readme_notes file in the zip folder. All data files (pd, sv, txt) are text files so can be opened in any text editor. Also included in some directories are the Latex files (.tex) used to generate the figures in the manuscript. This requires Latex software/editor. Abstract The effect of approximating electron correlation in few-electron systems is investigated using three wavefunctions: the many body wavefunction referred to as fully-correlated (FC), the Hartree Fock wavefunction (HF), and the Colle and Salvetti Jastrow-style wavefunction (CS) used in the derivation of the popular Lee, Yang and Parr (LYP) correlation functional. The electron correlation energy, static and dynamic Coulomb holes, various expectation values, and radial energy distributions (energy densities) are considered. It is shown that whilst the CS wavefunction can capture the behaviour of the wavefunction at the singularities of the Coulomb potential corresponding to the coalescence of two particles and decreases the area of the primary static Coulomb hole by nearly 30% compared to HF for He and Li++, it is unable to accurately model expectation values that depend on the whole of space and key features of the electron density behaviour in dynamic Coulomb holes and the energy density behaviour in energy distributions. These issues are amplified when considering the hydride ion and a system with the critical nuclear charge for binding. <br>