cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24779724
title: Supplementary Material for: Alterations in serum miR-126-3p levels over time, a marker of pituitary insufficiency following head trauma

description: TBI is a condition caused by a head injury that poses a high risk of developing pituitary insufficiency in patients. We have previously reported alterations in miR-126-3p levels in sera from patients with TBI-induced pituitary deficiency. To investigate why TBI-induced pituitary deficiency develops in only some patients and to reveal the relationship of miR-126-3p with the hormone axes, we used mice epigenetically modified with miR-126-3p at the embryonic stage in this study. These modified mice were subjected to mild-TBI(mTBI) according to the Marmarou-weight-drop model. The alterations of miR-126-3p levels after mTBI of both wild-type and modified-miR-126-3p* lines of mice validated our human results. In addition, the hypothalamus, pituitary, and adrenal tissues were analyzed for the related transcripts and serum hormone levels. 
We report that mir-126-3p directly affects the upregulation of the Hypothamus-Pituitary-Adrenal (HPA) axis and ACTH secretion in the acute phase after mTBI. We have also demonstrated that miR-126-3p suppresses Gnrh transcripts in the hypothalamus and pituitary, but this is not reflected in FSH/LH serum levels. The increase in ACTH levels in the acute phase may indicate that the up-regulation of miR-126-3p has a protective effect on the HPA axis after TBI. Notably, the most prominent transcript response is found in the adrenals, highlighting their role in the pathophysiology of TBI. Our study revealed the role of miR-126-3p in TBI and pituitary deficiency developing after TBI, and the data obtained will significantly contribute to unraveling the mechanism of pituitary deficiency developing after TBI and developing new diagnostic and treatment strategies.
DOI: 10.6084/m9.figshare.24779724.v1
title: Supplementary Material for: Alterations in serum miR-126-3p levels over time, a marker of pituitary insufficiency following head trauma

description: TBI is a condition caused by a head injury that poses a high risk of developing pituitary insufficiency in patients. We have previously reported alterations in miR-126-3p levels in sera from patients with TBI-induced pituitary deficiency. To investigate why TBI-induced pituitary deficiency develops in only some patients and to reveal the relationship of miR-126-3p with the hormone axes, we used mice epigenetically modified with miR-126-3p at the embryonic stage in this study. These modified mice were subjected to mild-TBI(mTBI) according to the Marmarou-weight-drop model. The alterations of miR-126-3p levels after mTBI of both wild-type and modified-miR-126-3p* lines of mice validated our human results. In addition, the hypothalamus, pituitary, and adrenal tissues were analyzed for the related transcripts and serum hormone levels. 
We report that mir-126-3p directly affects the upregulation of the Hypothamus-Pituitary-Adrenal (HPA) axis and ACTH secretion in the acute phase after mTBI. We have also demonstrated that miR-126-3p suppresses Gnrh transcripts in the hypothalamus and pituitary, but this is not reflected in FSH/LH serum levels. The increase in ACTH levels in the acute phase may indicate that the up-regulation of miR-126-3p has a protective effect on the HPA axis after TBI. Notably, the most prominent transcript response is found in the adrenals, highlighting their role in the pathophysiology of TBI. Our study revealed the role of miR-126-3p in TBI and pituitary deficiency developing after TBI, and the data obtained will significantly contribute to unraveling the mechanism of pituitary deficiency developing after TBI and developing new diagnostic and treatment strategies.
DOI: 10.5281/zenodo.7669495
title: Tea bag index (TBI) for New Zealand sites

description: The file contains mean k and S value per GPS location, with as meta-data the starting date, duration and biome of the study.
description: These data are part of a larger dataset (http://www.teatime4science.org/).
Funded by OECD Co-operative Research Programme grant: Biological Resource Management for Sustainable Agricultural Systems. Directorate: T AD/CRP; Contract: JA00091460.
DOI: 10.5281/zenodo.7669496
title: Tea bag index (TBI) for New Zealand sites

description: The file contains mean k and S value per GPS location, with as meta-data the starting date, duration and biome of the study.
description: These data are part of a larger dataset (http://www.teatime4science.org/).
Funded by OECD Co-operative Research Programme grant: Biological Resource Management for Sustainable Agricultural Systems. Directorate: T AD/CRP; Contract: JA00091460.
DOI: 10.21227/31ws-jc64
title: MalariaSD: Malaria-Infected Cell Images dataset

description: The MalariaSD dataset encompasses diverse stages and classes of malaria parasites, including Plasmodium falciparum, Plasmodium malariae, Plasmodium vivax, and Plasmodium ovale, categorized into four phases: ring, schizont, trophozoite, and gametocyte. This resource aids researchers and healthcare professionals in gaining critical insights into malaria's epidemiology, diagnosis, and treatment.The MP-IDB, featuring high-quality malaria parasite images with the four stages, offers an opportunity for developing and evaluating novel image processing and analysis techniques to enhance malaria diagnosis accuracy and efficiency. In our proposed paper, we utilized these images to create a new dataset using stable diffusion and advanced image processing methods.Applying stable diffusion, we generated a dataset with 16 distinct classes, focusing on single-celled images. Through cropping and enhancement techniques, we produced refined images. This new dataset underwent training via stable diffusion, resulting in an additional 20 images for each class. Our efforts significantly increased the image count from an average of 12 to 40 images per class in the original dataset. This paper contributes to malaria research by expanding the dataset through stable diffusion and image processing. The augmented dataset provides a more comprehensive representation of malaria parasite stages and classes, empowering researchers and healthcare professionals to enhance their understanding of malaria's complexities and improve diagnostic methodologies.
DOI: 10.5281/zenodo.7669684
title: Tea bag index (TBI) for a field trial (olive orchard) in Ferrandina (Basilicata, Italy)

description: The file contains mean k and S value per GPS location, with as meta-data the starting date, duration and biome of the study.
DOI: 10.5281/zenodo.7669685
title: Tea bag index (TBI) for a field trial (olive orchard) in Ferrandina (Basilicata, Italy)

description: The file contains mean k and S value per GPS location, with as meta-data the starting date, duration and biome of the study.
DOI: 10.6084/m9.figshare.24772890
title: Supplementary Material for: C-X-C motif chemokine ligand 1 promotes colitis by modulating the gut microbiota

description: Introduction: C-X-C motif chemokine ligand 1 (CXCL1) is a potent neutrophil chemoattractant that plays a pivotal role in recruiting neutrophils during inflammatory conditions. This study explored the role of CXCL1 in modulating the gut microbiota, influencing neutrophil infiltration, and contributing to the development of colitis. 
Methods: We employed quantitative PCR to assess CXCL1 expression in colon samples. A mouse model of DSS-induced colitis was utilized to explore the progression of colitis in wild-type (WT) and CXCL1-deficient (CXCL1-/-) mice. 
Results: Colitis attenuation was evident in CXCL1-/- mice. Significant alterations were observed in the gut microbiome, as revealed by 16S rRNA gene sequencing. Furthermore, CXCL1-/- mice exhibited reduced gut permeability and diminished endotoxin levels in peripheral blood following DSS treatment compared to WT mice. In response to DSS treatment, WT mice showed a clear increase in neutrophil infiltration, while CXCL1-/- mice exhibited lower levels of infiltration. FMT using stools from CXCL1-/- mice alleviated DSS-induced colitis. Interestingly, FMT from patients with colitis increased CXCL1 and Ly6G expression in colons of gut-sterilized mice. Clinical data analysis revealed elevated CXCL1 and CD15 expression in patients with colitis, with a positive correlation between the severity of colitis and the expression of CXCL1 and CD15. 
Conclusion: These findings shed light on the pivotal role of CXCL1 in promoting colitis by modulating the gut microbiota.
DOI: 10.6084/m9.figshare.24923943
title: Supplementary Material for: X-linked lymphoproliferative syndrome: a spectrum of clinical and immunological profile and novel pathogenic variants from Chandigarh, India

description: Introduction: X-linked lymphoproliferative syndrome (XLP) is a rare primary immune deficiency. Two types of XLP have been described: XLP-1 and XLP-2.
Methods: We found 7 patients with XLP (3 had XLP-1 and 4 had XLP-2) after reviewing the data from Pediatric Immunodeficiency Clinic from 1997-2021.
Results: Mean age at diagnosis was 3.8 years and mean delay in diagnosis was 2.6 years. Five patients had recurrent episodes of infections. Four patients developed at least one episode of hemophagocytic lymphohistiocytosis (HLH) (2 with XLP-1 and 2 with XLP-2). Of these, 2 had recurrent HLH (both with XLP-2). Epstein-Barr virus (EBV) infection was detected in 2 (1 with XLP-1 and 1 with XLP-2). Both these patients had HLH. One child with XLP-2 had inflammatory bowel disease. Hypogammaglobulinemia was seen in 3 (2 with XLP-1 and 1 with XLP-2). Genetic analysis showed previously reported variants in 5, while 2 had novel variants (one in exon 7 of XIAP gene [c.1370dup p. Asn457Lysfs Ter16] and other had splice site variant in intron 1 of SH2D1A gene [c.138-2_138-1insG]). Episodes of HLH were managed with intravenous immunoglobulin (IVIg), methylprednisolone, oral prednisolone, cyclosporine and rituximab. Inflammatory bowel disease was managed using oral prednisolone and azathioprine. One patient underwent haploidentical hematopoietic stem cell transplantation (HSCT). One child with XLP-2 and WAS died because of fulminant pneumonia. 
Discussion/Conclusions: XLP should be considered as a strong possibility in any patient with features of HLH, repeated infections with hypogammaglobulinemia, persistent EBV infection and early onset IBD.
DOI: 10.6084/m9.figshare.24635511
title: Supplementary Material for: Individualized homeopathic medicines in the treatment of post-COVID-19 fatigue in adults: A single-blind, randomized, placebo-controlled trial

description: Introduction: The coronavirus disease (COVID-19) is leading to unknown and unusual health conditions that are challenging to manage. Post-COVID-19 fatigue is one of those challenges, becoming increasingly common as the pandemic evolves, as it impairs the quality of life of an individual. This trial attempts to identify the preliminary evidence of the efficacy of individualized homeopathic medicines (IHMs) against placebos in the treatment of post-COVID-19 fatigue in adults.
Methods: A 3-month, single-blind, randomized, placebo-controlled, parallel-arm trial was conducted at the outpatient department of The Calcutta Homoeopathic Medical College and Hospital, India. Sixty participants were randomized in a 1:1 ratio to receive either IHMs (n = 30) or identical-looking placebos (n = 30). The primary and secondary outcome measures were the Fatigue Assessment Scale (FAS) and Outcome in Relation to Impact on Daily Living (ORIDL), respectively, measured every month for up to 3 months. Comparative analysis was carried out on the intention-to-treat sample to detect group differences.
Results: Group differences in both the primary (FAS total: F1, 58 = 14.356, P &lt; 0.001) and secondary outcomes (ORIDL: F1, 58 = 210.986, P &lt; 0.001) after 3 months favored IHMs against placebos. Lycopodium clavatum (11.7%), Sulphur (11.7%), Arsenicum album (10%), and Thuja occidentalis (10%) were the most frequently indicated medicines. No harm, unintended effects, homeopathic aggravations, or any serious adverse events were reported from either of the groups. 
Conclusion: IHMs produced significantly better effects than placebos in the treatment of post-COVID-19 fatigue in adults. Definitive, robust trials may be undertaken to confirm the findings.
Trial registration: CTRI/2022/03/041316
DOI: 10.6084/m9.figshare.24635511.v1
title: Supplementary Material for: Individualized homeopathic medicines in the treatment of post-COVID-19 fatigue in adults: A single-blind, randomized, placebo-controlled trial

description: Introduction: The coronavirus disease (COVID-19) is leading to unknown and unusual health conditions that are challenging to manage. Post-COVID-19 fatigue is one of those challenges, becoming increasingly common as the pandemic evolves, as it impairs the quality of life of an individual. This trial attempts to identify the preliminary evidence of the efficacy of individualized homeopathic medicines (IHMs) against placebos in the treatment of post-COVID-19 fatigue in adults.
Methods: A 3-month, single-blind, randomized, placebo-controlled, parallel-arm trial was conducted at the outpatient department of The Calcutta Homoeopathic Medical College and Hospital, India. Sixty participants were randomized in a 1:1 ratio to receive either IHMs (n = 30) or identical-looking placebos (n = 30). The primary and secondary outcome measures were the Fatigue Assessment Scale (FAS) and Outcome in Relation to Impact on Daily Living (ORIDL), respectively, measured every month for up to 3 months. Comparative analysis was carried out on the intention-to-treat sample to detect group differences.
Results: Group differences in both the primary (FAS total: F1, 58 = 14.356, P &lt; 0.001) and secondary outcomes (ORIDL: F1, 58 = 210.986, P &lt; 0.001) after 3 months favored IHMs against placebos. Lycopodium clavatum (11.7%), Sulphur (11.7%), Arsenicum album (10%), and Thuja occidentalis (10%) were the most frequently indicated medicines. No harm, unintended effects, homeopathic aggravations, or any serious adverse events were reported from either of the groups. 
Conclusion: IHMs produced significantly better effects than placebos in the treatment of post-COVID-19 fatigue in adults. Definitive, robust trials may be undertaken to confirm the findings.
Trial registration: CTRI/2022/03/041316
DOI: 10.5281/zenodo.8005778
title: Spectroscopy and dynamics of the hydrated electron at the water/air interface

description: TR SFG data, least squares non-linear fit, computational trajectories and files
DOI: 10.5281/zenodo.8005779
title: Spectroscopy and dynamics of the hydrated electron at the water/air interface

description: TR SFG data, least squares non-linear fit, computational trajectories and files
DOI: 10.6084/m9.figshare.24793845
title: Supplementary Material for: Effect of SARS-CoV-2 incidence and immunisation rates on sporadic Creutzfeldt-Jakob disease incidence

description: Background
Recent case studies and media outlets have hypothesised an effect of SARS-CoV-2 infection and immunisation on the development or progression of neurodegenerative diseases such as Alzheimer’s disease or sporadic Creutzfeldt-Jakob disease (sCJD).
Objectives
This study aims to identify potential associations of SARS-COV-2 infections and SARS-COV-2 immunisation with sCJD incidence, disease duration, and age of onset.
Method 
We used data from a prospective sCJD surveillance study in Germany (2016 to 2022) and publicly available datasets of SARS-CoV-2 cases and vaccination numbers in Germany for the years 2020-2022. Associations of SARS-CoV-2 incidence and immunisation rates with sCJD incidence were assessed by comparing quarterly and annual cumulative sCJD incidences in the periods before (2016-2019) and during the pandemic (2020-2022).
Results 
We could not identify any time-related effect of SARS-CoV-2 incidence or immunisation rate on the sCJD incidence. Moreover, we did not find any sCJD incidence alterations before and during the SARS-CoV-2 pandemic on a federal or state level. The overall sCJD incidence was within expected ranges in the years 2020 to 2022. There were no changes in age of onset and clinical disease duration in these years.
Conclusions
We found no evidence supporting a short-term effect of the pandemic on sCJD incidence. However, considering the extended pre-clinical phase of sCJD, continued surveillance is needed to identify potential future incidence alterations.
DOI: 10.6084/m9.figshare.24793845.v1
title: Supplementary Material for: Effect of SARS-CoV-2 incidence and immunisation rates on sporadic Creutzfeldt-Jakob disease incidence

description: Background
Recent case studies and media outlets have hypothesised an effect of SARS-CoV-2 infection and immunisation on the development or progression of neurodegenerative diseases such as Alzheimer’s disease or sporadic Creutzfeldt-Jakob disease (sCJD).
Objectives
This study aims to identify potential associations of SARS-COV-2 infections and SARS-COV-2 immunisation with sCJD incidence, disease duration, and age of onset.
Method 
We used data from a prospective sCJD surveillance study in Germany (2016 to 2022) and publicly available datasets of SARS-CoV-2 cases and vaccination numbers in Germany for the years 2020-2022. Associations of SARS-CoV-2 incidence and immunisation rates with sCJD incidence were assessed by comparing quarterly and annual cumulative sCJD incidences in the periods before (2016-2019) and during the pandemic (2020-2022).
Results 
We could not identify any time-related effect of SARS-CoV-2 incidence or immunisation rate on the sCJD incidence. Moreover, we did not find any sCJD incidence alterations before and during the SARS-CoV-2 pandemic on a federal or state level. The overall sCJD incidence was within expected ranges in the years 2020 to 2022. There were no changes in age of onset and clinical disease duration in these years.
Conclusions
We found no evidence supporting a short-term effect of the pandemic on sCJD incidence. However, considering the extended pre-clinical phase of sCJD, continued surveillance is needed to identify potential future incidence alterations.
DOI: 10.15128/r23r074t97g
title: Recent advances in highly-efficient near infrared OLED emitters [dataset]

description: Near infrared (NIR) light (700–1400 nm) can be used in numerous biological/medical as well as technological applications. In this work we review the most recent examples of highly efficient NIR organic light-emitting diode (OLED) emitters among the most relevant types of luminophores: platinum(II), iridium(III), and osmium(II) complexes, unimolecular thermally activated delayed fluorescence (TADF) emitters and exciplexes, fluorescent dyes, and the emerging group of stable luminescent radicals. We dive into the structural design principles of emitters with improved NIR efficiency. In our discussion we consider unimolecular emission as well as that arising from aggregated luminophores as the latter often leads to a longer wavelength NIR. Our analysis of numerous emitters from various groups concludes, without a doubt, that platinum(II) complexes present superior efficiency in nearly all wavelengths from 700 to 1000 nm. We report on an apparent NIR boundary line, which appears to be a current limitation for NIR OLED efficiency. Presently, virtually only platinum(II) complexes exceed the efficiency limit set out by this boundary. So far efficient OLEDs, i.e. &gt;1% external quantum efficiency, emitting significantly beyond 1000 nm have not yet been reported.
DOI: 10.6084/m9.figshare.24968271
title: Averaged motion data for slow (meanVPdata_s) and fast (meanVPdata_f) reaching movements as a matlab file

description: The two files contain the motion data of eight planar reaching movements at two different speeds (400 and 800ms), recorded with VisualEyez and translated to Matlab. The experiment was approved by the institutional ethic committee and participants gave written consent. The single trials were normalised to contain 100 data-points and averaged for each movement and speed.
DOI: 10.6084/m9.figshare.24968271.v1
title: Averaged motion data for slow (meanVPdata_s) and fast (meanVPdata_f) reaching movements as a matlab file

description: The two files contain the motion data of eight planar reaching movements at two different speeds (400 and 800ms), recorded with VisualEyez and translated to Matlab. The experiment was approved by the institutional ethic committee and participants gave written consent. The single trials were normalised to contain 100 data-points and averaged for each movement and speed.
DOI: 10.6084/m9.figshare.24968247.v2
title: Basel phages annotation and clusters

description: <b>Table:</b><br>Annotation of Basel phages using current taxonomy information (Family, Subfamily, Genus) extracted from NCBI Taxonomy (version of DATE) and ICTV (sheet 1); The clustering results (sheet 2).<b>Figure:</b><br>Results of phages clustering visualised using C<i>omplexHeatmap</i>.
DOI: 10.5281/zenodo.10392792
title: Neural Field Arena - Classification

description: Neural fields (NeFs) have recently emerged as a versatile method for modeling signals of various modalities, including images, shapes, and scenes. Subsequently, many works have explored the use of NeFs as representations for downstream tasks, e.g. classifying an image based on the parameters of a NeF that has been fit to it. However, the impact of the NeF hyperparameters on their quality as downstream representation is scarcely understood and remains largely unexplored. This is partly caused by the large amount of time required to fit datasets of neural fields.

Thanks to fit-a-nef, a JAX-based library that leverages parallelization to enable fast optimization of large-scale NeF datasets, we performed a comprehensive study that investigates the effects of different hyperparameters --including initialization, network architecture, and optimization strategies-- on fitting NeFs for downstream tasks.Based on the proposed library and our analysis, we propose Neural Field Arena, a benchmark consisting of neural field variants of popular vision datasets, including MNIST, CIFAR, variants of ImageNet, and ShapeNetv2.Our library and the Neural Field Arena will be open-sourced to introduce standardized benchmarking and promote further research on neural fields.

The datasets that are currently available are the following:



MNIST, SIREN.

CIFAR10, SIREN,

MicroImageNet, SIREN.

ShapeNet, SIREN.


More datasets will be added in the future.
DOI: 10.5281/zenodo.10392793
title: Neural Field Arena - Classification

description: Neural fields (NeFs) have recently emerged as a versatile method for modeling signals of various modalities, including images, shapes, and scenes. Subsequently, many works have explored the use of NeFs as representations for downstream tasks, e.g. classifying an image based on the parameters of a NeF that has been fit to it. However, the impact of the NeF hyperparameters on their quality as downstream representation is scarcely understood and remains largely unexplored. This is partly caused by the large amount of time required to fit datasets of neural fields.

Thanks to fit-a-nef, a JAX-based library that leverages parallelization to enable fast optimization of large-scale NeF datasets, we performed a comprehensive study that investigates the effects of different hyperparameters --including initialization, network architecture, and optimization strategies-- on fitting NeFs for downstream tasks.Based on the proposed library and our analysis, we propose Neural Field Arena, a benchmark consisting of neural field variants of popular vision datasets, including MNIST, CIFAR, variants of ImageNet, and ShapeNetv2.Our library and the Neural Field Arena will be open-sourced to introduce standardized benchmarking and promote further research on neural fields.

The datasets that are currently available are the following:



MNIST, SIREN.

CIFAR10, SIREN,

MicroImageNet, SIREN.

ShapeNet, SIREN.


More datasets will be added in the future.