cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7328594
title: Spectral dataset of natural light fields measured in the Netherlands

description: This is a spectral dataset of natural light collected in the Netherlands. The data supplement contains the rural and city cubic irradiance spectra with associated wavelength spacing. We measured natural light fields for sunny weather in the shade and light for 24 rural and urban scenes across multiple days (in total 48 cubic measurements). We also measured natural light fields from dawn till dusk on a sunny day (in total 165 cubic measurements) and a cloudy day (in total 124 cubic measurements). This spectral light-field dataset provides comprehensive illumination statistics useful for understanding biological vision. The data reveal how perceptually meaningful aspects of the light, such as the direction, colour and diffuseness of the main light components, vary over space and time in ecologically valid conditions.
DOI: 10.5281/zenodo.7342499
title: Data for Apalachicola Bay oyster demographic analysis

description: Processed data describing the number and lengths of oysters sampled from long-term fisheries independent sampling in Apalachicola Bay, Florida. Original (raw) data collected by Florida Fish and Wildlife Conservation Commission and Florida Department of Agriculture and Consumer Services.
description: Raw data provided by Florida Fish and Wildlife Conservation Commission (FWC) Fish and Wildlife Research Institute (FWRI) scientists Ryan Gandy and Matthew Davis. Project funded by FWC award 20138-2101.
DOI: 10.5284/1044659
title: Newport Medieval Ship

description: The main aims of the Newport Medieval Ship Project are to document, analyse and describe this 15th-century vessel, and its associated artefacts and environmental finds. This archive comprises data gathered on site and during the post-excavation analysis phase. Digital documentation techniques, including contact digitising, laser scanning, digital photography and digital solid modelling have been utilised in order to create a detailed, accurate and versatile data set that lends itself to digital archiving and dissemination. The archive contains primary site records including scans of hand-drawn which have subsequently been digitised, scanned pro-forma records, and scans of pre-digital excavation photographs. During the post-excavation research phase, the hull timbers and artefacts were cleaned, recorded and analysed. The resulting records (timber drawings, solid models, and digital photographs) were used to create digital and physical models of selected hull timbers. Scaled models were then created and used to determine the original hull form of the medieval ship. The innovative use of digital recording and modelling has been held up as an example of best practice for similar nautical archaeology documentation projects throughout Europe. The archive also contains an extensive series of specialist reports, classified by function/artefact group or material type. These reports contain detailed analysis and, where appropriate, a catalogue. Many of the above-mentioned records contain information that has been entered in the comprehensive project database.
DOI: 10.5523/bris.9zxlt0cabbtq2wwiffr66mr8r
title: Supplementary material to Lombardi and De Luca "Derivation of fragility curves at design stage through Linear Time-History Analysis" Engineering Structures 2020

description: This is the supplementary material to Lombardi and De Luca "Derivation of fragility curves at design stage through Linear Time-HistoryAnalysis" Engineering Structures 2020. It includes the full geometry information about the case-study building (provided in xlsx and csv format) and the Matlab and OpenSees files employed to run the analyses described in the publication. It also include the OpenSees (.exe) version employed to run such analyses.
DOI: 10.5880/sfb806.58
title: Geodata of European loess domains

description: We present a new map of the distribution of aeolian sediments (mainly loess) and major potential source areas for Europe in Lehmkuhl et al. (accepted). The map was compiled combining geodata of different mapping approaches. Most of the used geodata stems from accurate national maps of 27 different countries. Problematic aspects such as different nomenclatures across administrative borders were carefully investigated and revised. The result is a seamless map, which comprises pedological, geological, and geomorphological data and can be used for paleoenvironmental and archeological studies and other applications. Further, we divided the loess areas into 6 main loess domains and 17 subdomains, to understand and explain the factors controlling their distribution and characteristics. For the subdivision we used the following criteria: (1) influence of silt production areas, (2) affiliation to subcatchments, as rivers are very important regional silt transport agents, (3) occurrence of past periglacial activity with characteristic overprinting of the deposits. Thes geodataset contains the borders of loess domains as published in Lehmkuhl et al. (accepted). A layer package file can be used to obtain the same visual appearance as published. The methdology is described in the referenced paper. References Lehmkuhl, F., Nett, J.J., Pötter, S., Schulte, P., Sprafke, T., Jary, Z., Antoine, P., Wacha, L., Wolf, D., Zerboni, A., Hošek, J., Marković, S.B., Obreht, I., Sümegi, P., Veres, D., Zeeden, C., Boemke, B.J., Schaubert, V., Viehweger, J., Hambach, U., accepted. Loess landscapes of Europe - mapping, geomorphology, and zonal differentiation. Earth-Science Reviews.
DOI: 10.6073/pasta/917b3947d91470eecf979e9297ed4d2e
title: Ice cover data for Falling Creek Reservoir and Beaverdam Reservoir, Vinton, Virginia, USA for 2013-2022

description: Ice cover was recorded at Falling Creek Reservoir and Beaverdam Reservoir (both located in Vinton, Virginia, USA) using multiple methods. The ice cover record for Falling Creek Reservoir began in the winter of 2013-2014 and Beaverdam Reservoir beginning in the winter of 2020-2021. Falling Creek Reservoir and Beaverdam Reservoir are owned and operated by the Western Virginia Water Authority as a primary and secondary drinking water source, respectively, for Roanoke, Virginia. These two reservoirs are some of the southernmost waterbodies in the United States that exhibit ice cover during the winter. Given incipient climate change, Falling Creek Reservoir and Beaverdam Reservoir's ice cover data represent an important record of warming for waterbodies in the southeastern United States. Ice cover presence was assessed using multiple methods: visual observation of ice spanning the deep hole (from an observer standing on a reservoir's dam); visual observation via an automated camera deployed near the deep hole; water temperature data from a profile of sensors deployed at a reservoir's deepest site; upwelling shortwave radiation and albedo measured by a meteorological station deployed on a metal structure located over Falling Creek Reservoirs's deep hole; and dissolved oxygen sensors deployed at multiple depths at the deep hole of both reservoirs.
DOI: 10.6084/m9.figshare.20020639.v1
title: Novel Gd(OH)3, GdOOH and Gd2O3 Nanorods: Microwave-Assisted Hydrothermal Synthesis and Optical Properties

description: We present a study of the controlled synthesis and optical properties of single-crystals Gd(OH)3, GdOOH and Gd2O3 nanorods. In this work, Gd(OH)3 nanorods were synthesized by a simple and fast microwave-assisted hydrothermal method. This process combined with the thermal decomposition oxidation of Gd(OH)3 nanorods as precursors enabled the preparation of single-crystalline GdOOH and Gd2O3 structures with well-defined morphology at low temperatures. The crystal structure dependence on the optical properties was investigated. We observed a green shift effect on the photoluminescence (PL) emission spectra from Gd(OH)3 to Gd2O3 nanorods, which can be attributed to different types of surface defects, as well as intrinsic properties that contribute significantly to the modified PL behavior.
DOI: 10.6084/m9.figshare.22059080
title: Supplementary Material for: Coupled mutual inhibition and mutual activation motifs as tools for cell-fate control

description: Multistability is central to biological systems as it plays a crucial role in adaptation, evolvability, and differentiation. The presence of positive feedback loops can enable multistability. The simplest of such feedback loops are a) a mutual inhibition loop (MI), b) a mutual activation loop (MA), and c) self-activation, all three of them known to give rise to bistability. However, the characteristic differences in the bistability exhibited by these motifs are relatively less understood. Here, we use dynamical simulations across a large ensemble of parameter sets and initial conditions to study the bistability characteristics of these motifs. Furthermore, we investigate the utility of these motifs for achieving coordinated expression through cyclic and parallel coupling amongst them. Our analysis revealed that MI-based architectures offer discrete and robust control over gene expression, multistability, and coordinated expression among multiple genes, as compared to MA-based architectures. We then devised a combination of MI and MA architectures to improve coordination and multistability. Such designs help improve our understanding of the control structures involved in robust cell-fate decisions and provide a way to achieve controlled decision-making in synthetic systems.
DOI: 10.6084/m9.figshare.24087144.v2
title: Three-Dimensional Venus Cloud Structure Simulated by a General Circulation Model

description: These are the simulation data (in HDF5 format) from OASIS, used to produce figures in the paper with the same title here. The data "regrid_avg_2696_3369_1.h5" is the temporal average of the regridded data, while "regrid_height_Venus_2900.h5" is the regridded result from an instantaneous moment.
DOI: 10.6084/m9.figshare.24265498.v1
title: Natural movies

description: Description of the data and file structureVarious types of natural scenes were obtained, categorized as flow (camera moving through space), pan (camera panning through space), still (fixed camera recording a still scene) and still moving (fixed camera recording an active scene). A total of 39 clips of 9.6 second duration were recorded at a frame rate of 120 FPS and a spatial extent of 720 × 1280. The dataset is divided into a training and validation set, both containing a balanced number of the different recording types (training set: 12 flow, 8 pan, 3 still and 8 still moving clips; validation set: 3 flow, 2 pan, 1 still and 2 still moving clips). All clips were preprocessed by converting the RGB channels to grayscale and bilinearly downsampling the spatial dimensions to 144 × 256.Code/SoftwareData is stored h5py format and can be accessed in Python as follows:<pre><pre>import h5py<br><br>root = "" # path to data<br>hf = h5py.File(f"{root}/natural.hdf5", "r")<br>dataset_name = "train" # or "test"<br>dataset = np.array(hf.get(dataset_name))<br>hf.close()</pre></pre>
DOI: 10.6084/m9.figshare.25188506
title: Supplementary Material for: Delineating the Disease Boundaries: Homozygous <i>CDC14A</i> Variants Underlying Nonsyndromic Hearing Loss and Hearing Impairment Infertile Male Syndrome

description: <b><i>Background:</i></b> Hereditary hearing loss is a genetically heterogeneous neurosensory disorder that affects many people. Deafness and infertility can coexist in some cases, creating the hearing impairment infertile male syndrome. There are several known molecular mechanisms that can cause deafness either on its own or in conjunction with infertility. <b><i>Methods and Results:</i></b> Here, we represent two consanguineous families (A, B), both families had clinical evidence of deafness, and family B also had infertility, so we referred to them as having nonsyndromic hearing loss (NSHL) and hearing impairment infertile male syndrome (HIIMS), respectively. These families’ genetic makeup was examined using an Affymetrix GeneChip 250K Nsp array followed by Sanger sequencing. In family A, we identified a novel homozygous stop gain variant [NM_003672.4; c.1000C&gt;T; p.(Gln334*)] and a homozygous missense variant [NM_003672.4; c.684C&gt;A; p.(Asn228Lys)] in family B in <i>CDC14A</i> gene (MIM#603504). In animal models, the <i>CDC14A</i> gene causes both hearing loss and infertility; in addition, it also causes NSHL and HIIMS in humans. <b><i>Conclusions:</i></b> Our study on the <i>CDC14A</i> gene has identified two novel variants, crucial for delineating disease boundaries. Variants in exon 10 and upstream cause HIIMS, and those in exon 11 and downstream are linked exclusively to hearing impairment. This precision enhances diagnostics and offers potential for targeted interventions, marking a significant advancement in understanding the genetic basis of these conditions.
DOI: 10.6084/m9.figshare.25265365
title: Supplementary Material for: Body mass index and outcomes in patients with Takotsubo syndrome: a nationwide retrospective cohort study

description: Background: Takotsubo syndrome (TTS) is a cardiac disorder that mimics acute coronary syndrome at presentation. While previous studies have demonstrated a relationship between body mass index (BMI) and outcomes in acute coronary syndrome, few have examined its relationship with TTS.
Methods: Using the Japanese Diagnosis Procedure Combination database, we retrospectively identified 14,551 patients admitted for TTS between 2010-2021. By applying multivariable regressions with restricted cubic splines, we examined the association between BMI and in-hospital mortality after adjusting for potential confounders. 
Results: Mean BMI was 21.1 kg/m2, classifying patients into severe underweight (&lt;16.0 kg/m2, 7.1%), mild/moderate underweight (16.0-18.4 kg/m2, 18.3%), normal weight (18.5-22.9 kg/m2, 46.8%), overweight (23.0-27.4 kg/m2, 22.2%), and obese (≥27.5 kg/m2, 5.6%) groups. Patients with severe or mild/moderate underweight were older and had a higher prevalence of impaired physical activity, malignancy, chronic pulmonary disease, and pneumonia. In-hospital mortality was the highest (9.4%) in the severe underweight group, followed by the mild/moderate underweight group (5.4%), with the lowest being in the obese group (2.1%). Severe underweight (adjusted odds ratio=2.05 [95% CI=1.54-2.73]) and mild/moderate underweight (1.26 [1.01-1.57]) were significantly associated with higher mortality compared with normal weight, while no significant association was noted with obesity. A nonlinear association between continuous BMI and mortality was observed, with mortality increasing when BMI decreased &lt;20.0 kg/m2 but nearly plateauing in BMI &gt;20 kg/m2.
Conclusions: The present nationwide analysis demonstrated a nonlinear association between BMI and in-hospital mortality of TTS. BMI is an easily available and clinically relevant marker for the risk stratification of TTS.
DOI: 10.6084/m9.figshare.25323583
title: Supplementary Material for: Neonatal Extracorporeal Membrane Oxygenation: Associations between Continuous Renal Replacement Therapy, Thrombocytopenia, and Outcomes

description: Introduction: The incidence of thrombocytopenia in neonates receiving extracorporeal membrane oxygenation (ECMO) with and without concurrent continuous renal replacement therapy (CRRT) and associated complications have not been well described. The primary aims of the current study were to (1) characterize thrombocytopenia in neonates receiving ECMO (including treated concurrently with CRRT) and (2) evaluate risk factors (including CRRT utilization) associated with severe thrombocytopenia. In a planned exploratory secondary aim, we explored the association of severe thrombocytopenia with outcomes in neonates receiving ECMO. 

Methods: We conducted a retrospective single-center chart review of neonates who received ECMO 07/01/14 - 03/01/20 and evaluated associations between CRRT, severe thrombocytopenia (platelet count &lt;50,000/mm3), and outcomes (ECMO duration, length of stay, and survival). 

Results: Fifty-two neonates received ECMO; 35 (67%) received concurrent CRRT. Severe thrombocytopenia occurred in 27 (52%) neonates overall and in 21 (60%) neonates who received concurrent CRRT. Underlying diagnosis, ECMO mode, care unit, and moderate/severe hemolysis differed between those who did and did not receive CRRT. CRRT-receivers experienced shorter hospital stays than CRRT non-receivers, but ECMO duration, length of intensive care unit (ICU) stay, and survival did not differ between groups. CRRT receipt was associated with severe thrombocytopenia. Exploratory classification and regression tree (CART) analysis suggests CRRT use, birthweight, and ICU location are all predictors of interest for severe thrombocytopenia.

Conclusions: In our cohort, CRRT use during ECMO was associated with severe thrombocytopenia, and patients who received ECMO with CRRT experienced shorter hospital stays than those who did not receive CRRT. Exploratory CART analysis suggests CRRT use, birthweight, and ICU location are all predictors for severe thrombocytopenia and warrant further investigations in larger studies.
DOI: 10.6084/m9.figshare.25506463
title: Refractive index and transmittance measurements of liquids from the visible to SWIR

description: Dataset containing the refractive indices of the liquids measured in this work, the reference materials used (and their refractive index uncertainties), and the percent transmittance of the liquids from 400 to 2000 nm.
DOI: 10.6084/m9.figshare.26267992
title: Supplementary Material for: A Reciprocal Relationship between Formal and Informal Social Engagement and Handgrip Strength of Older Adults in South Korea

description: Introduction: The relationship between social engagement and handgrip strength has been underexplored. Further, no prior research examined a plausible reciprocal association between them.

Methods: The study employed the seven waves of data (2006–2018) from the Korean Longitudinal Study of Aging (KLoSA) survey (7,927 respondents, mean age: 59 years old at Wave 1 [71 years old at Wave 7], women: 58%). It used ML-SEM, a cross-lagged panel model with fixed effects fitted by structural equation modeling with maximum likelihood estimation. In particular, the ML-SEM examined whether a reciprocal relationship existed between formal social engagement (number of association memberships and frequency of organizational activities)/informal social engagement (frequency of contact with familiar persons) and handgrip strength (the average of the four dynamometer measurements).

Results: The empirical analyses identified a systematic reciprocal association between formal social engagement and handgrip strength. Specifically, formal social engagement was positively associated with handgrip strength over time (the number of association memberships standardized coefficient: 0.012*, the frequency of organizational activities standardized coefficient: 0.022***). Conversely, handgrip strength was positively related to the number of memberships (the handgrip strength standardized coefficient: 0.025*) and the frequency of organizational activities (the handgrip strength standardized coefficient: 0.042**). 

Conclusion: The study thus supports the social causation proposition that formal social engagement in and through diverse associations may be positively associated with handgrip strength. It also validates the health selection argument that handgrip strength may increase the likelihood of formal social engagement.
DOI: 10.6084/m9.figshare.26317882
title: Supplementary Material for: Artificial Intelligence-driven Prediction Revealed CFTR Associated With Therapy Outcome Of Breast Cancer: A Feasibility Study

description: Introduction: In silico tools capable of predicting the functional consequences of genomic differences between individuals, many of which are AI-driven, have been the most effective over the past two decades for non-synonymous single nucleotide variants (nsSNVs). When appropriately selected for the purpose of the study, a high predictive performance can be expected. In this feasibility study, we investigate the distribution of nsSNVs with an allele frequency below 5%. To classify the putative functional consequence, a tier-based filtration led by AI-driven predictors and scoring system were implemented to the overall-decision making process, resulting in a list of prioritised genes. Methods: The study has been conducted on breast cancer patients of homogeneous ethnicity. Germline rare variants have been sequenced in genes that influence pharmacokinetic parameters of anticancer drugs or molecular signalling pathways in cancer. After AI-driven functional pathogenicity classification and data mining in pharmacogenomic (PGx) databases, variants were collapsed to the gene level and ranked according to their putative deleterious role. Results: In breast cancer patients, seven of the twelve genes prioritised based on the predictions were found to be associated with response to oncotherapy, histological grade, and tumour subtype. Most importantly, we showed that the group of patients with at least one rare nsSNVs in Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) had significantly reduced disease-free (Log Rank, p=0.002) and overall survival (Log Rank, p=0.006). Conclusion: AI-driven in silico analysis with PGx data mining provided an effective approach navigating for functional consequences across germline genetic background, which can be easily integrated into the overall decision-making process for future studies. The study revealed a statistically significant association with numerous clinicopathological parameters, including treatment response. Our study indicates that CFTR may be involved in the processes influencing the effectiveness of oncotherapy or in the malignant progression of the disease itself.
DOI: 10.6084/m9.figshare.26494207
title: Supplementary Material for: Phenotypic Discordance Among Siblings with Autosomal Recessive Polycystic Kidney Disease: Case Report and Review of the Literature

description: Missense variants in the PKHD1 gene are associated with the full spectrum of autosomal recessive polycystic kidney disease (ARPKD) severity and exhibit variable expressivity. The study of clinical expressivity is limited by the extensive allelic heterogeneity within the PKHD1 gene, which encodes a 4074-amino-acid protein. We report the case of adult siblings with biallelic missense PKHD1 variants, c.4870C&gt;T (p.Arg1624Trp) and c.8206T&gt;G (p.Trp2736Gly), who presented with discordant phenotypes. Patient A developed progressive chronic kidney disease and Caroli syndrome in childhood requiring combined liver and kidney transplantation, while patient B remains minimally affected in the fourth decade of life with normal kidney function and signs of medullary sponge kidney on renal imaging. We review previously reported cases of phenotypic discordance among siblings and suggest that genotypes composed of at least one hypomorphic missense variant are more likely to lead to phenotypic discordance.
DOI: 10.6084/m9.figshare.4047315.v2
title: RCUK open access block grant allocation 2013-18

description: Compilation of RCUK open access block grant allocations for five years, 2013/14 to 2017/18.* These funds were distributed to UK research institutions in order to pay article processing charges (APCs) to make RCUK-funded research outputs open access. The dataset includes figures for the amount provided to each eligible institution in each year. For year five (2017/18), the payments began to be made by RCUK every six months, so an additional sheet in the dataset shows the breadown into twice-yearly payments.<br><br>* Updated 23 April to include the fifth year (2017/18)<br>
DOI: 10.6084/m9.figshare.6534545
title: DATA - Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota

description: Data files supporting "Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota" to be published in PLoS-Biology