Miracle-dz/UniFAR-FTUs huggingface dataset:
Stormscapes: simulating cloud dynamics in the now

The complex interplay of a number of physical and meteorological phenomena makes simulating clouds a challenging and open research problem. We explore a physically accurate model for simulating clouds and the dynamics of their transitions. We propose first-principle formulations for computing buoyancy and air pressure that allow us to simulate the variations of atmospheric density and varying temperature gradients. Our simulation allows us to model various cloud types, such as cumulus, stratus, and stratoscumulus, and their realistic formations caused by changes in the atmosphere. Moreover, we are able to simulate large-scale cloud super cells – clusters of cumulonimbus formations – that are commonly present during thunderstorms. To enable the efficient exploration of these stormscapes, we propose a lightweight set of high-level parameters that allow us to intuitively explore cloud formations and dynamics. Our method allows us to simulate cloud formations of up to about 20 km × 20 km extents at interactive rates. We explore the capabilities of physically accurate and yet interactive cloud simulations by showing numerous examples and by coupling our model with atmosphere measurements of real-time weather services to simulate cloud formations in the now. Finally, we quantitatively assess our model with cloud fraction profiles, a common measure for comparing cloud types.
Convolutional neural network to identify symptomatic Alzheimer’s disease using multimodal retinal imaging

Background/Aims To develop a convolutional neural network (CNN) to detect symptomatic Alzheimer’s disease (AD) using a combination of multimodal retinal images and patient data. Methods Colour maps of ganglion cell-inner plexiform layer (GC-IPL) thickness, superficial capillary plexus (SCP) optical coherence tomography angiography (OCTA) images, and ultra-widefield (UWF) colour and fundus autofluorescence (FAF) scanning laser ophthalmoscopy images were captured in individuals with AD or healthy cognition. A CNN to predict AD diagnosis was developed using multimodal retinal images, OCT and OCTA quantitative data, and patient data. Results 284 eyes of 159 subjects (222 eyes from 123 cognitively healthy subjects and 62 eyes from 36 subjects with AD) were used to develop the model. Area under the receiving operating characteristic curve (AUC) values for predicted probability of AD for the independent test set varied by input used: UWF colour AUC 0.450 (95% CI 0.282, 0.592), OCTA SCP 0.582 (95% CI 0.440, 0.724), UWF FAF 0.618 (95% CI 0.462, 0.773), GC-IPL maps 0.809 (95% CI 0.700, 0.919). A model incorporating all images, quantitative data and patient data (AUC 0.836 (CI 0.729, 0.943)) performed similarly to models only incorporating all images (AUC 0.829 (95% CI 0.719, 0.939)). GC-IPL maps, quantitative data and patient data AUC 0.841 (95% CI 0.739, 0.943). Conclusion Our CNN used multimodal retinal images to successfully predict diagnosis of symptomatic AD in an independent test set. GC-IPL maps were the most useful single inputs for prediction. Models including only images performed similarly to models also including quantitative data and patient data.
Apparent inhibition of induced plant volatiles by a fungal pathogen prevents airborne communication between potato plants.

Plant communication in response to insect herbivory has been widely studied, whereas that involving pathogen attack has received much less attention. We tested for plant communication in potato (Solanum tuberosum) plants in response to leaf infection by the fungal pathogen Sclerotinia sclerotiorum. To this end, we measured the total amount and composition of volatile organic compounds (VOCs) produced by control and infected emitter plants, as well as tested for induced resistance of receiver plants exposed to VOCs from infected emitters. We further tested for changes in the expression of defensive genes due to pathogen infection. Fungal infection did not significantly affect the total amount or composition of VOCs produced by emitter plants. Correspondingly, we found no evidence of higher resistance to the pathogen in receiver plants exposed to VOCs from infected emitters relative to control emitters. Molecular analyses indicated that pathogen infection drove a downregulation of genes coding for VOC precursors, potentially explaining the absence of pathogen effects on VOC emissions and thus of communication. Overall, these results indicate no evidence of airborne communication between potato plants in response to fungal infection and point at pathogen inhibition of VOC emissions as a likely explanation for this result. This article is protected by copyright. All rights reserved.
A retrospective investigation of the added clinical value of SCT symptoms on neuropsychological assessments in youth with ADHD

ABSTRACT Some researchers believe that Sluggish Cognitive Tempo (SCT) should be its own psychiatric disorder. However, despite the abundance of literature describing its possible symptoms, evidence of its clinical impact on cognitive tests and some clinical comorbidities is still weak. This retrospective study aimed to analyze the added clinical value of exploring SCT symptoms prior to a neuropsychological assessment in a youth population diagnosed with an Attention-Deficit/Hyperactivity Disorder (ADHD). For this purpose, we used linear regressions to examine the association between different test results and SCT, as well as logistic regressions to examine the association between the existence of different diagnoses and SCT in a group of 295 ADHD patients [73 females, 24.7%], aged between 6 and 18 years [Mean (SD): 9.91 (3.12)]. Our results showed that parent-reported SCT symptoms did not help predict neuropsychological test outcomes. In addition, they did not predict Specific Learning Disorder (SLD) or Developmental Coordination Disorder (DCD), nor anxiety and depression when we controlled for age, Vanderbilt inattention and hyperactivity subscales, autism spectrum disorder, and intellectual disability. These results requestion the added-value of screening for SCT in similar clinical neuropsychological settings.
L‐lactate induces neurogenesis in the mouse ventricular‐subventricular zone via the lactate receptor HCA1

Adult neurogenesis occurs in two major niches in the brain: the subgranular zone of the hippocampal formation and the ventricular‐subventricular zone. Neurogenesis in both niches is reduced in ageing and neurological disease involving dementia. Exercise can rescue memory by enhancing hippocampal neurogenesis, but whether exercise affects adult neurogenesis in the ventricular‐subventricular zone remains unresolved. Previously, we reported that exercise induces angiogenesis through activation of the lactate receptor HCA1. The aim of the present study is to investigate HCA1‐dependent effects on neurogenesis in the two main neurogenic niches.
Imagined veridicality of social feedback amplifies early and late brain responses

ABSTRACT Higher social relevance has been shown to modulate event-related potentials (ERPs). It is unclear whether such modulations can be observed if one only imagines stimuli to be socially relevant. In a preregistered EEG study (N = 40), participants were presented neutral, positive and negative personality-descriptive adjectives, and given a subsequent feedback revealing whether or not the adjective described their personality. While it was emphasized that feedback occurred randomly, participants were asked either to treat the feedback information as randomly chosen or to imagine it represented a veridical social feedback. Imagined social context increased EPN, P3, and LPP amplitudes to feedback. Importantly, social context and emotional content interacted, resulting in enhanced processing of imagined social negative feedback for the N1 and EPN. These results demonstrate that social attributions can easily be elicited by instructions, modulating early and late processing stages, speaking for a strong affiliation motive.
Breast Milk-Derived Retinol Is a Potential Surrogate for Serum in the 13C-Retinol Isotope Dilution Test in Zambian Lactating Women with Vitamin A Deficient and Adequate Status.

BACKGROUND Vitamin A (VA) deficiency (VAD) affects ∼19 million pregnant women worldwide. The extent of VAD in Zambian women of reproductive age is unknown owing to lack of survey inclusion or the use of static serum retinol concentrations, a low-sensitivity biomarker. OBJECTIVES This cross-sectional study employed isotopic techniques to determine VA status with serum and milk among women aged 18-49 y (n = 197) either lactating with infants aged 0-24 mo or nonlactating with or without infants. METHODS Assistants were trained and piloted data collection. Demographic data, anthropometry, and relevant histories were obtained including malaria and anemia. For retinol isotope dilution (RID), baseline fasting blood and casual breast milk samples were collected before administration of 2.0 μmol 13C2-retinyl acetate and 24-h dietary recalls. On day 14, blood (n = 144) and milk (n = 66) were collected. Prevalence of total liver VA reserves (TLR) ≤0.10 μmol/g was defined as VAD with comparison to the DRI assumption of 0.07 μmol/g as minimally acceptable for North Americans. RESULTS When a 20% adjustment for dose lost to milk was made in the RID equation for lactation, mean total body VA stores (TBS) for lactating women were 25% lower than for nonlactating women (P < 0.01), which was not the case without adjustment (P = 0.3). Mean ± SD TLR for all women were 0.15 ± 0.11 μmol/g liver. Using retinol purified from breast milk instead of serum for RID analysis yielded similar TBS and TLR, which were highly correlated between methods (P < 0.0001). Serum retinol ≤0.70 μmol/L had 0% sensitivity using either VAD liver cutoff and milk retinol ≤1.0 μmol/L had 42% sensitivity for VAD at 0.10 μmol/g. CONCLUSIONS Determining accurate VA status among women of reproductive age, especially lactating women, forms a basis for extrapolation to the general population and informing policy development and program implementation.
Effects of amino acid modifications on the permeability of the pentameric sarcolipin channel

Sarcolipin (SLN) is an important transmembrane (TM) protein encoded by long noncoding RNA. SLN is expressed in the sarcoplasmic reticulum and regulates cardiac and skeletal muscle contractions. SLN forms a pentameric hydrophobic ligand‐gated ion channel. The protonation of Glu7 (protonated SLN, pSLN) and mutation of Thr18 to Ala18 (T18A) have been reported to exert a significant influence on the permeability of the channel. In this study, the altered permeability of both the pSLN and T18A pentameric channels was simulated. Combined with molecular dynamics simulation, the free‐energy landscape for single ions, computational electrophysiology, diffusion coefficient, and pore geometrical characteristic analyses were performed to further understand the properties of amino acid modifications in the SLN pentameric channel. The results suggest that both the pSLN and T18A pentameric channels form stable hydrophobic ligand‐gated channels. The TM voltage has a positive effect on the permeability of water molecules and ions. By using pSLN and T18A, our study provides helpful information on the pore‐forming mechanism of SLN and furthers our understanding of the regulatory mechanisms underlying the permeation of ions and water molecules in the pentameric SLN channel.
Ca2+‐regulated cell migration revealed by optogenetically engineered Ca2+ oscillations

The ability of a single Ca2+ ion to play an important role in cell biology is highlighted by the need for cells to form Ca2+ signals in the dimensions of space, time, and amplitude. Thus, spatial and temporal changes in intracellular Ca2+ concentration are important for determining cell fate. Optogenetic technology has been developed to provide more precise and targeted stimulation of cells. Here, U2OS cells overexpressing Ca2+ translocating channelrhodopsin (CatCh) were used to mediate Ca2+ influx through blue light illumination with various parameters, such as intensity, frequency, duty cycle, and duration. We identified that several Ca2+‐dependent transcription factors and certain kinases can be activated by specific Ca2+ waves. Using a wound‐healing assay, we found that low‐frequency Ca2+ oscillations increased cell migration through the activation of NF‐κB. This study explores the regulation of cell migration by Ca2+ signals. Thus, we can choose optical parameters to modulate Ca2+ waves and achieve activation of specific signaling pathways. This novel methodology can be applied to clarify related cell‐signaling mechanisms in the future.
Comparative analysis of the complete mitochondrial genomes of three rockfishes (Scorpaeniformes, Sebastiscus) and insights into the phylogenetic relationships of Sebastidae

Abstract Mitochondrial genome is a powerful molecule marker to provide information for phylogenetic relationships and revealing molecular evolution in ichthyological studies. Sebastiscus species, a marine rockfish, are of essential economic value. However, the taxonomic status and phylogenetic relationships of Sebastidae have been controversial so far. Here, the mitochondrial genomes (mitogenomes) of three species, S. tertius, S. albofasciatus, and S. marmoratus, were systemically investigated. The lengths of the mitogenomes’ sequences of S. tertius, S. albofasciatus, and S. marmoratus were 16910, 17056, and 17580 bp, respectively. It contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and one identical control region (D-loop) among the three species. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, which were most likely due to the difference in their living environment. The phylogenetic tree was constructed by Bayesian Inference (BI) and Maximum Likelihood (ML). Most interestingly, the results indicated that Sebastidae and Scorpaenidae were grouped into a separate branch, so the taxonomic status of Sebastidae should be classified into subfamily Sebastinae. Our results may lead to a taxonomic revision of Scorpaenoidei.
Plasma Total α-Synuclein and Neurofilament Light Chain: Clinical Validation for Discriminating Parkinson’s Disease from Normal Control

Background: A previously published paper (referred to as the original cohort) showed that using a cutoff value of 116.1 fg/mL for the plasma total α-synuclein concentrations could discriminate Parkinson’s disease (PD) patients from normal controls (NCs). In this study, another independent cohort (referred to as the validation cohort) was recruited to validate the agreement between the clinical diagnosis and the use of plasma total α-synuclein to identify PD patients. In addition to total α-synuclein, plasma neurofilament light chain (NfL) in the validation cohort was detected. Methods: Seventy PD patients and 33 NCs were enrolled in the validation cohort. A clinical diagnosis and the immunomagnetic reduction (IMR) assay for plasma total α-synuclein were performed for each participant. Thirty-three of 70 PD patients and 23 of 33 NCs were subjected to the plasma NfL assay via IMR. Results: The positive, negative, and overall percentages of agreement between the clinical diagnosis and plasma total α-synuclein diagnosis determined based on 116.1 fg/mL as the cutoff value were found to be 0.943, 0.818, and 0.903, respectively. The PD patients and NCs showed plasma NfL levels of 8.38 ± 4.19 pg/mL and 17.6 ± 7.95 pg/mL (p < 0.001), respectively. The cutoff value of the plasma NfL level used to differentiate PD patients from NCs was 12.8 pg/mL, with sensitivity and specificity values of 0.788 and 0.870, respectively. Conclusion: The results demonstrate the usefulness of the plasma total α-synuclein concentration to discriminate PD patients from NCs and reveal the elevation of the plasma NfL level in PD patients.
Self-Monitoring App Preferences for Sun Protection: Discrete Choice Experiment Survey Analysis

Background The availability and use of health apps continues to increase, revolutionizing the way mobile health interventions are delivered. Apps are increasingly used to prevent disease, improve well-being, and promote healthy behavior. On a similar rise is the incidence of skin cancers. Much of the underlying risk can be prevented through behavior change and adequate sun protection. Self-monitoring apps have the potential to facilitate prevention by measuring risk (eg, sun intensity) and encouraging protective behavior (eg, seeking shade). Objective Our aim was to assess health care consumer preferences for sun protection with a self-monitoring app that tracks the duration and intensity of sun exposure and provides feedback on when and how to protect the skin. Methods We conducted an unlabeled discrete choice experiment with 8 unique choice tasks, in which participants chose among 2 app alternatives, consisting of 5 preidentified 2-level attributes (self-monitoring method, privacy control, data sharing with health care provides, reminder customizability, and costs) that were the result of a multistep and multistakeholder qualitative approach. Participant preferences, and thus, the relative importance of attributes and their levels were estimated using conditional logit modeling. Analyses consisted of 200 usable surveys, yielding 3196 observations. Results Our respondents strongly preferred automatic over manually operated self-monitoring (odds ratio [OR] 2.37, 95% CI 2.06-2.72) and no cost over a single payment of 3 Swiss francs (OR 1.72, 95% CI 1.49-1.99). They also preferred having over not having the option of sharing their data with a health care provider of their choice (OR 1.66, 95% CI 1.40-1.97), repeated over single user consents, whenever app data are shared with commercial thirds (OR 1.57, 95% CI 1.31-1.88), and customizable over noncustomizable reminders (OR 1.30, 95% CI 1.09-1.54). While most participants favored thorough privacy infrastructures, the attribute of privacy control was a relatively weak driver of app choice. The attribute of self-monitoring method significantly interacted with gender and perceived personal usefulness of health apps, suggesting that female gender and lower perceived usefulness are associated with relatively weaker preferences for automatic self-monitoring. Conclusions Based on the preferences of our respondents, we found that the utility of a self-monitoring sun protection app can be increased if the app is simple and adjustable; requires minimal effort, time, or expense; and has an interoperable design and thorough privacy infrastructure. Similar features might be desirable for preventive health apps in other areas, paving the way for future discrete choice experiments. Nonetheless, to fully understand these preference dynamics, further qualitative or mixed method research on mobile self-monitoring-based sun protection and broader preventive mobile self-monitoring is required. International Registered Report Identifier (IRRID) RR2-10.2196/16087
Motivation for Critical Thinking in Nursing Students in Chile

Nursing education includes a constant challenge regarding the competencies that nurses must possess to provide high-quality nursing care. One of these competencies is critical thinking (CT), and motivation for critical thinking (MCT) has been identified as an element necessary to develop CT. Expectancy and value are important components of the MCT. This study aimed to analyze sociodemographic and academic factors related to MCT in Chilean nursing students. This study is an analytical–correlational, cross-sectional study conducted with 478 nursing students in Chile. The data were collected using an online questionnaire. The Critical Thinking Motivation Scale was used to measure MCT. Pearson’s square, Chi-square, means comparison test, and binomial logistic regression were used to analyze the data. The expectancy component of the MCT had the lowest scores on the scale. Age was associated with the cost subcomponent (p < .03), and high school was associated with the interest subcomponent (p < .01). Academic factors contributing to MCT were problem-based learning, professor motivation, and the inclusion of MCT in nursing disciplinary subjects. Strategies that improve CT and MCT should be implemented and evaluated periodically from the beginning of a nursing career. Faculty should be trained to motivate students to think critically.
Phase I feasibility study of Magnetic Resonance guided High Intensity Focused Ultrasound-induced hyperthermia, Lyso-Thermosensitive Liposomal Doxorubicin and cyclophosphamide in de novo stage IV breast cancer patients: study protocol of the i-GO study

Introduction In breast cancer, local tumour control is thought to be optimised by administering higher local levels of cytotoxic chemotherapy, in particular doxorubicin. However, systemic administration of higher dosages of doxorubicin is hampered by its toxic side effects. In this study, we aim to increase doxorubicin deposition in the primary breast tumour without changing systemic doxorubicin concentration and thus without interfering with systemic efficacy and toxicity. This is to be achieved by combining Lyso-Thermosensitive Liposomal Doxorubicin (LTLD, ThermoDox, Celsion Corporation, Lawrenceville, NJ, USA) with mild local hyperthermia, induced by Magnetic Resonance guided High Intensity Focused Ultrasound (MR-HIFU). When heated above 39.5°C, LTLD releases a high concentration of doxorubicin intravascularly within seconds. In the absence of hyperthermia, LTLD leads to a similar biodistribution and antitumour efficacy compared with conventional doxorubicin. Methods and analysis This is a single-arm phase I study in 12 chemotherapy-naïve patients with de novo stage IV HER2-negative breast cancer. Previous endocrine treatment is allowed. Study treatment consists of up to six cycles of LTLD at 21-day intervals, administered during MR-HIFU-induced hyperthermia to the primary tumour. We will aim for 60 min of hyperthermia at 40°C–42°C using a dedicated MR-HIFU breast system (Profound Medical, Mississauga, Canada). Afterwards, intravenous cyclophosphamide will be administered. Primary endpoints are safety, tolerability and feasibility. The secondary endpoint is efficacy, assessed by radiological response. This approach could lead to optimal loco-regional control with less extensive or even no surgery, in de novo stage IV patients and in stage II/III patients allocated to receive neoadjuvant chemotherapy. Ethics and dissemination This study has obtained ethical approval by the Medical Research Ethics Committee Utrecht (Protocol NL67422.041.18, METC number 18-702). Informed consent will be obtained from all patients before study participation. Results will be published in an academic peer-reviewed journal. Trial registration numbers NCT03749850, EudraCT 2015-005582-23.