cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31156945.v1
title: Supplementary Material for: Relapsing Intermediate Uveitis Following Resolved Syphilitic Retinitis in an HIV-Positive Patient: A Case Report

description: We report a case of intermediate uveitis as a delayed immune-mediated relapse following the successful treatment of syphilitic retinitis in an HIV-positive individual. A 30-year-old HIV-positive man presented with decreased vision in his left eye. Examination revealed left eye granulomatous anterior uveitis with, vitritis, retinal vasculitis, and optic disc edema. The patient was diagnosed with syphilitic uveitis, reactive for rapid plasma reagin(RPR), and initiated on intravenous penicillin by the internist. Topical corticosteroids were initiated, and oral corticosteroids were added after one week. Over two months, the lesions resolved clinically with decreasing RPR titers. After two months of complete remission and tapering of therapy, the patient presented with renewed disc edema, macular edema, vitreous cells, and snowballs suggestive of intermediate uveitis. The RPR titers showed a decreasing pattern. The patient responded well to oral corticosteroids, indicating a likely immune-mediated relapse rather than reinfection. This case highlights the need for continued surveillance, even after clinical resolution.
DOI: 10.5061/dryad.cj38k
title: Data from: Estimating the number of pulses in a mass extinction

description: Most previous work on the Signor-Lipps effect has focused on testing
 whether taxa in a mass extinction went extinct simultaneously or
 gradually. However, many authors have proposed scenarios in which taxa go
 extinct in distinct pulses. Little methodology has been developed for
 quantifying characteristics of such pulsed extinction events. Here we
 introduce a method for estimating the number of pulses in a mass
 extinction, based on the positions of fossil occurrences in a
 stratigraphic section. Rather than using a hypothesis test and assuming
 simultaneous extinction as the default, we reframe the question by asking
 what number of pulses best explains the observed fossil record. Using a
 two-step algorithm, we are able to estimate not just the number of
 extinction pulses, but also a confidence level or posterior probability
 for each possible number of pulses. In the first step, we find the maximum
 likelihood estimate for each possible number of pulses. In the second
 step, we calculate the Akaike Information Criterion (AIC) and Bayesian
 Information Criterion (BIC) weights for each possible number of pulses,
 and then apply a k-Nearest Neighbor classifier to these weights. This
 gives us a vector of confidence levels for the number of extinction pulses
 — for instance, we might be 80% confident that there was a single
 extinction pulse, 15% confident that there were two pulses, and 5%
 confidence that there were three pulses. Equivalently, we can state that
 we are 95% confidence that the number of extinction pulses is 1 or 2.
 Using simulation studies, we show that the method performs well in a
 variety of situations, although it has difficulty in the case of
 decreasing fossil recovery potential, and it is most effective for small
 numbers of pulses unless the sample size is large. We demonstrate the
 method using a dataset of Late Cretaceous ammonites.
description: R codeR code for estimating
 the number of pulses in a mass extinctioncode.Rsample datasetSeymour Island ammonite dataset from Macellari 1986dataset.txt
DOI: 10.6084/m9.figshare.31156948
title: Supplementary Material for: Slice-to-Volume Registration of the fetal thorax to assess observed/expected total fetal lungs volume in fetuses with congenital diaphragmatic hernia who underwent Fetoscopic Endoluminal Tracheal Occlusion

description: Objective: To evaluate the feasibility of slice-to-volume registration (SVR) of the fetal thorax in congenital diaphragmatic hernia (CDH), and to compare observed-to-expected total fetal lung volume (O/E TFLV) obtained from original and SVR MRI volumes for prediction of postnatal survival.
Methods: We retrospectively analyzed 35 fetuses with CDH undergoing MRI before and after fetoscopic endoluminal tracheal occlusion (FETO). High-resolution, motion-corrected SVR volumes were reconstructed using an automated pipeline. O/E TFLV was measured on both original and SVR volumes, and results were compared between survivors and non-survivors at 6 months of age. Agreement, correlation, and predictive accuracy were assessed using Pearson correlation and ROC analysis.
Results: Four cases (11.4%) were excluded due to uncorrectable artifacts or technical issues. SVR reconstruction required only three acquisitions versus a median of six for conventional imaging. Post-processing took a median of 14 minutes, and lung delineation was longer for SVR than for original volumes. O/E TFLV measurements showed good to very good agreement between original and SVR volumes (r=0.75 before and r=0.96 after FETO), with comparable predictive accuracy for survival (AUCoriginal=0.81–0.83 vs AUCSVR=0.83, p&gt;0.7).
Conclusion: SVR of the fetal thorax is feasible in CDH and provides reliable O/E TFLV measurements with prognostic accuracy comparable to conventional MRI, while reducing the need for repeated acquisitions.
DOI: 10.6084/m9.figshare.31156948.v1
title: Supplementary Material for: Slice-to-Volume Registration of the fetal thorax to assess observed/expected total fetal lungs volume in fetuses with congenital diaphragmatic hernia who underwent Fetoscopic Endoluminal Tracheal Occlusion

description: Objective: To evaluate the feasibility of slice-to-volume registration (SVR) of the fetal thorax in congenital diaphragmatic hernia (CDH), and to compare observed-to-expected total fetal lung volume (O/E TFLV) obtained from original and SVR MRI volumes for prediction of postnatal survival.
Methods: We retrospectively analyzed 35 fetuses with CDH undergoing MRI before and after fetoscopic endoluminal tracheal occlusion (FETO). High-resolution, motion-corrected SVR volumes were reconstructed using an automated pipeline. O/E TFLV was measured on both original and SVR volumes, and results were compared between survivors and non-survivors at 6 months of age. Agreement, correlation, and predictive accuracy were assessed using Pearson correlation and ROC analysis.
Results: Four cases (11.4%) were excluded due to uncorrectable artifacts or technical issues. SVR reconstruction required only three acquisitions versus a median of six for conventional imaging. Post-processing took a median of 14 minutes, and lung delineation was longer for SVR than for original volumes. O/E TFLV measurements showed good to very good agreement between original and SVR volumes (r=0.75 before and r=0.96 after FETO), with comparable predictive accuracy for survival (AUCoriginal=0.81–0.83 vs AUCSVR=0.83, p&gt;0.7).
Conclusion: SVR of the fetal thorax is feasible in CDH and provides reliable O/E TFLV measurements with prognostic accuracy comparable to conventional MRI, while reducing the need for repeated acquisitions.
DOI: 10.5061/dryad.v0vg627
title: Data from: Decreased mitochondrial metabolic requirements in fasting animals carry an oxidative cost

description: 1. Many animals experience periods of food shortage in their natural
 environment. It has been hypothesised that the metabolic responses of
 animals to naturally-occurring periods of food deprivation may have
 long-term negative impacts on their subsequent life-history. 2. In
 particular, reductions in energy requirements in response to fasting may
 help preserve limited resources but potentially come at a cost of
 increased oxidative stress. However, little is known about this trade-off
 since studies of energy metabolism are generally conducted separately from
 those of oxidative stress. 3. Using a novel approach that combines
 measurements of mitochondrial function with in vivo levels of hydrogen
 peroxide (H2O2) in brown trout (Salmo trutta), we show here that fasting
 induces energy savings in a highly metabolically active organ (the liver)
 but at the cost of a significant increase in H2O2, an important form of
 reactive oxygen species (ROS). 4. After a 2-week period of fasting, brown
 trout reduced their whole-liver mitochondrial respiratory capacities
 (state 3, state 4 and cytochrome c oxidase activity), mainly due to
 reductions in liver size (and hence the total mitochondrial content). This
 was compensated for at the level of the mitochondrion, with an increase in
 state 3 respiration combined with a decrease in state 4 respiration,
 suggesting a selective increase in the capacity to produce ATP without a
 concomitant increase in energy dissipated through proton leakage. However,
 the reduction in total hepatic metabolic capacity in fasted fish was
 associated with an almost two-fold increase in in vivo mitochondrial H2O2
 levels (as measured by the MitoB probe). 5. The resulting increase in
 mitochondrial ROS, and hence potential risk of oxidative damage, provides
 mechanistic insight into the trade-off between the short-term energetic
 benefits of reducing metabolism in response to fasting and the potential
 long-term costs to subsequent life-history traits.
description: Summary data
 FE-2017-00771
DOI: 10.6084/m9.figshare.31156951
title: Supplementary Material for: The vanishing colorectal tumour: lessons from an illustrative case report

description: Introduction
Colorectal cancer is the most frequent digestive neoplasia and is usually diagnosed by colonoscopy. Treatment is contingent on staging and other factors and generally includes a combination of endoscopic or surgical resection, chemotherapy and radiotherapy. 
Case Presentation
A 64 year-old female patient was diagnosed with an adenocarcinoma of the ascending colon following a colonoscopy performed due to anemia. After histological confirmation and staging she was submitted to a right hemicolectomy. However, the neoplasia was not present in the surgical specimen and follow up colonoscopy did not find any lesion in the remaining colon. Histopathological and endoscopic results were reappraised and the endoscopic list of the day of the index colonoscopy was reviewed with no potential error to be found. Finally, genetic concordance of the index biopsies and surgical specimen was confirmed. 
Discussion
Spontaneous regression of neoplasia is very rare, particularly in colorectal cancer. The mechanisms of this phenomenon are not well understood and are probably multifactorial. When the possibility of spontaneous regression is being considered, a very rigorous approach must be followed as errors, such as misidentification, are more likely. In this exemplary case we describe the steps taken to reach this surprising diagnosis.
DOI: 10.6084/m9.figshare.31156951.v1
title: Supplementary Material for: The vanishing colorectal tumour: lessons from an illustrative case report

description: Introduction
Colorectal cancer is the most frequent digestive neoplasia and is usually diagnosed by colonoscopy. Treatment is contingent on staging and other factors and generally includes a combination of endoscopic or surgical resection, chemotherapy and radiotherapy. 
Case Presentation
A 64 year-old female patient was diagnosed with an adenocarcinoma of the ascending colon following a colonoscopy performed due to anemia. After histological confirmation and staging she was submitted to a right hemicolectomy. However, the neoplasia was not present in the surgical specimen and follow up colonoscopy did not find any lesion in the remaining colon. Histopathological and endoscopic results were reappraised and the endoscopic list of the day of the index colonoscopy was reviewed with no potential error to be found. Finally, genetic concordance of the index biopsies and surgical specimen was confirmed. 
Discussion
Spontaneous regression of neoplasia is very rare, particularly in colorectal cancer. The mechanisms of this phenomenon are not well understood and are probably multifactorial. When the possibility of spontaneous regression is being considered, a very rigorous approach must be followed as errors, such as misidentification, are more likely. In this exemplary case we describe the steps taken to reach this surprising diagnosis.
DOI: 10.5061/dryad.7p51p
title: Data from: Social seeking declines in young adolescents

description: The desire to engage with others is an important motivational force
 throughout our lifespan. It is known that social behaviour and preferences
 change from childhood to adulthood, but whether this change is linked with
 any changes in social motivation is not known. We evaluated 255 typically
 developing participants from ages 4–20 years on a behavioural paradigm
 ‘Choose a Movie’ (CAM). On every trial, participants had a choice between
 viewing social or non-social movies presented with different levels of
 effort (key presses/screen touch required). Hence, participants chose not
 only the movie they would watch but also how much effort they would make.
 The difference between the effort levels of the chosen and not chosen
 stimuli helps in quantifying the motivation to seek it. This task could be
 used with all the age groups with minimal adaptations, allowing comparison
 between the groups. Results showed that children (4–8 years), older
 adolescents (12–16 years) and young adults (17–20 years) made more effort
 to look at social movies. Counterintuitively, this preference was not seen
 in young adolescents (around 9–12 years), giving a U-shaped developmental
 trajectory over the population. We present the first evidence for
 non-monotonic developmental change in social motivation in typical
 participants.
description: choose_a_movie_social_prefrence_data_Dubey_et_al
DOI: 10.5061/dryad.4br36
title: Data from: The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota

description: PCR amplification bias is a well-known problem in metagenomic analysis of
 arthropod communities. In contrast, variation of DNA degradation rates is
 a largely neglected source of bias. Differential degradation of DNA
 molecules could cause underrepresentation of taxa in a community
 sequencing sample. Arthropods are often collected by passive sampling
 devices, like malaise traps. Specimens in such a trap are exposed to
 varying periods of suboptimal storage and possibly different rates of DNA
 degradation. Degradation bias could thus be a significant issue, skewing
 diversity estimates. Here, we estimate the effect of differential DNA
 degradation on the recovery of community diversity of Hawaiian arthropods
 and their associated microbiota. We use a simple DNA size selection
 protocol to test for degradation bias in mock communities, as well as
 passively collected samples from actual Malaise traps. We compare the
 effect of DNA degradation to that of varying PCR conditions, including
 primer choice, annealing temperature and cycle number. Our results show
 that DNA degradation does indeed bias community analyses. However, the
 effect of this bias is of minor importance compared to that induced by
 changes in PCR conditions. Analyses of the macro and microbiome from
 passively collected arthropod samples are thus well worth pursuing.
description: Illumina read files for
 the Malaise trap samplesSample names include: 1.
 Sample ID, 2. body size category and 3. high or low molecular weight
 fractions (H/L). 16S and COI sequences were pooled for each
 sample.Malaise_Traps.tar.gzIllumina read files for PCR condition experimentSamples are named with a unique identifier followed by the used primer (ARF1/mICOIintF), followed by the according PCR conditions. a & b represent exact replicates, 51C an increase of annealing temperature by 5 °C and 22X a reduction of PCR cycle number by 10PCR_Conditions.tar.gzIllumina read files for DNA degradation experimentThe dataset contains read files of microbial 16S and arthropod COI amplicons. The sample name comprises 1. the amplified locus, 2. the DNA integrity (H/L) and 3. the temperature treatment (RT/FT)Laboratory_Degradation.tar.gzOTU_tablesOTU tables used for the analyses.
DOI: 10.6084/m9.figshare.31156954
title: Supplementary Material for: European Society for Paediatric Endocrinology (ESPE) and European Society of Endocrinology (ESE) Joint Clinical Practice Guidance for Healthcare Transition from Paediatric to Adult Endocrine Care

description: Background: The transition from paediatric to adult healthcare is a critical period for young individuals with endocrine conditions. Despite numerous published recommendations, Europe still lacks recent, comprehensive, evidence-based, and practically applicable guidelines for endocrine healthcare transition.
Objective: To develop European consensus guidance for transition from paediatric to adult care in endocrine conditions through a structured, evidence-based approach.
Methods: A systematic literature review identified 351 recommendations from 55 articles (2011-2023). Articles were included if they provided recommendations on transition from paediatric to adult care for patients with endocrine diseases or general (non-disease-specific) transition guidance. The guidance was developed by a core multidisciplinary group (n=7) and refined through focus groups with 18 experts from 10 European countries, representing both paediatric and adult care settings. Patient representatives have reviewed and approved it.
Results: The guidance includes recommendations across 11 domains: structure of transition service, patient empowerment, patient-professional relationship, multidisciplinary team organisation, healthcare provider education, timing and planning, care coordination, management of non-attendance, psychological support, parents/caregivers role and readiness tools. Each recommendation was rated as either 'recommend' (strong) or 'suggest' (conditional) based on expert consensus and available evidence.
Conclusion: This ESE-ESPE guidance provides a comprehensive, practical framework for endocrine healthcare transition, applicable across different European healthcare settings. The recommendations emphasise structured programs, care coordination, and patient-centred approaches to optimise transition outcomes.
DOI: 10.6084/m9.figshare.31156954.v1
title: Supplementary Material for: European Society for Paediatric Endocrinology (ESPE) and European Society of Endocrinology (ESE) Joint Clinical Practice Guidance for Healthcare Transition from Paediatric to Adult Endocrine Care

description: Background: The transition from paediatric to adult healthcare is a critical period for young individuals with endocrine conditions. Despite numerous published recommendations, Europe still lacks recent, comprehensive, evidence-based, and practically applicable guidelines for endocrine healthcare transition.
Objective: To develop European consensus guidance for transition from paediatric to adult care in endocrine conditions through a structured, evidence-based approach.
Methods: A systematic literature review identified 351 recommendations from 55 articles (2011-2023). Articles were included if they provided recommendations on transition from paediatric to adult care for patients with endocrine diseases or general (non-disease-specific) transition guidance. The guidance was developed by a core multidisciplinary group (n=7) and refined through focus groups with 18 experts from 10 European countries, representing both paediatric and adult care settings. Patient representatives have reviewed and approved it.
Results: The guidance includes recommendations across 11 domains: structure of transition service, patient empowerment, patient-professional relationship, multidisciplinary team organisation, healthcare provider education, timing and planning, care coordination, management of non-attendance, psychological support, parents/caregivers role and readiness tools. Each recommendation was rated as either 'recommend' (strong) or 'suggest' (conditional) based on expert consensus and available evidence.
Conclusion: This ESE-ESPE guidance provides a comprehensive, practical framework for endocrine healthcare transition, applicable across different European healthcare settings. The recommendations emphasise structured programs, care coordination, and patient-centred approaches to optimise transition outcomes.
DOI: 10.5061/dryad.0q35m
title: Data from: Trajectory energy minimisation for cell growth tracking and genealogy analysis

description: Cell growth experiments with a microfluidic device produce large-scale
 time-lapse image data, which contain important information on cell growth
 and patterns in their genealogy. To extract such information, we propose a
 scheme to segment and track bacterial cells automatically. In contrast
 with most published approaches, which often split segmentation and
 tracking into two independent procedures, we focus on designing an
 algorithm that describes cell properties evolving between consecutive
 frames by feeding segmentation and tracking results from one frame to the
 next one. The cell boundaries are extracted by minimizing the distance
 regularized level set evolution (DRLSE) model. Each individual cell was
 identified and tracked by identifying cell septum and membrane as well as
 developing a trajectory energy minimization function along time-lapse
 series. Experiments show that by applying this scheme, cell growth and
 division can be measured automatically. The results show the efficiency of
 the approach when testing on different datasets while comparing with other
 existing algorithms. The proposed approach demonstrates great potential
 for large-scale bacterial cell growth analysis.
description: data_paper.7zdata_paper.7zdata_paper.7zdata_paper.7zdata_paper.7z
DOI: 10.6084/m9.figshare.31156957
title: Supplementary Material for: Biocompatibility and Inflammatory Pathways of Silicone Oil in Complex Retinal Detachment: An In Vitro and Clinical Study

description: Introduction: This study aimed to characterize the inflammatory cytokine profile within silicone oil-associated fluid (SOAF) from eyes with complex rhegmatogenous retinal detachment (RRD) treated with silicone oil (SO) tamponade, comparing groups according to tamponade duration. Additionally, we aimed to assess in vitro the emulsification stability of SO in the presence of biological surfactant agents. Methods: This prospective multicenter study included 65 patients with complex RRD who underwent pars plana vitrectomy (PPV) with SO tamponade, divided into two groups according to tamponade duration (&lt;6 months vs ≥6 months), and 30 control eyes that underwent PPV for epiretinal membrane or full-thickness macular hole without SO. SOAF and undiluted vitreous samples were collected and analyzed for cytokine levels (IL-1α, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17, IP-10/CXCL10, IFNγ, TNFα, TGFβ1-3, and MCP-1) using multiplex bead-based immunoassays and ELISA. In vitro emulsification assays were performed using SOs of different viscosities and various biological surfactants. Results: The inflammatory composite score (mean z-score of log10-transformed IL-6, IL-8, and MCP-1) was significantly higher in RRD eyes than in controls (0.78 [0.35-1.16] vs -0.52 [-0.88-0.01]; p &lt; 0.0001), with no significant differences between tamponade-duration groups (0.82 [0.41-1.24] vs 0.76 [0.33-1.13]; p = 0.62). In SOAF, IL-6, IL-8, MCP-1, and TGF-β isoforms were elevated compared with vitreous controls. In vitro assays showed that stable emulsions formed in the presence of proteins (albumin or cell-culture supernatants), whereas lipidic or vitaminic surfactants produced unstable emulsions. Conclusion: Eyes with complex RRD exhibit a sustained pro-inflammatory and pro-fibrotic microenvironment within the perisilicone compartment, independent of tamponade duration. Proteins, particularly albumin, appear to act as key biological surfactants linking inflammation to SO emulsification. These findings highlight the need for targeted anti-inflammatory and anti-fibrotic strategies, as well as standardized tools for detecting subclinical emulsification.