Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Amount of Food in a Circular Dining Bowl from a Single Image

Unhealthy diet is a top risk factor causing obesity and numerous chronic diseases. To help the public adopt healthy diet, nutrition scientists need user-friendly tools to conduct Dietary Assessment (DA). In recent years, new DA tools have been developed using a smartphone or a wearable device which acquires images during a meal. These images are then processed to estimate calories and nutrients of the consumed food. Although considerable progress has been made, 2D food images lack scale reference and 3D volumetric information. In addition, food must be sufficiently observable from the image. This basic condition can be met when the food is stand-alone (no food container is used) or it is contained in a shallow plate. However, the condition cannot be met easily when a bowl is used. The food is often occluded by the bowl edge, and the shape of the bowl may not be fully determined from the image. However, bowls are the most utilized food containers by billions of people in many parts of the world, especially in Asia and Africa. In this work, we propose to premeasure plates and bowls using a marked adhesive strip before a dietary study starts. This simple procedure eliminates the use of a scale reference throughout the DA study. In addition, we use mathematical models and image processing to reconstruct the bowl in 3D. Our key idea is to estimate how full the bowl is rather than how much food is (in either volume or weight) in the bowl. This idea reduces the effect of occlusion. The experimental data have shown satisfactory results of our methods which enable accurate DA studies using both plates and bowls with reduced burden on research participants.
Analysis of seismic response in the city of Las Vegas, Nevada: A preliminary microzonation

Ground motion data recorded at 26 different locations in Las Vegas from six underground nuclear tests have been used to perform a preliminary microzonation of the city. The microzonation results are presented in the form of contour maps of the average observed seismic response throughout the city in 12 different frequency bands covering the period range from 0.16 to 6.0 sec. These data indicate that variations in long-period seismic response of as much as an order of magnitude can be expected at sites only a few kilometers apart in the city. Simple models of surface-wave propagation in the surface layer of alluvium of variable thickness can account for much of the observed variability. However, it appears that surface waves reflected back from the valley boundaries at the base of the surrounding mountain ranges also have a significant effect on the measured response.
Effects of PROtein enriched MEDiterranean Diet and EXercise on nutritional status and cognition in adults at risk of undernutrition and cognitive decline: the PROMED-EX Randomised Controlled Trial.

Introduction Undernutrition leading to unplanned weight loss is common in older age and has been linked to increased dementia risk in later life. Weight loss can precede dementia by a decade or more, providing a unique opportunity for early intervention to correct undernutrition and potentially prevent or delay cognitive impairment. The combined effects of diet and exercise on undernutrition have not yet been evaluated. The objective of this trial is to determine the effect of a protein-enriched Mediterranean diet, with and without exercise, on nutritional status and cognitive performance in older adults at risk of undernutrition and cognitive decline. Methods One hundred and five participants aged 60 years and over at risk of undernutrition and with subjective cognitive decline will be recruited to participate in a 6-month, single-blind, parallel-group randomised controlled trial. Participants will be block randomised into one of three groups: group 1—PROMED-EX (diet+exercise), group 2—PROMED (diet only) and group 3—standard care (control). The primary outcome is nutritional status measured using the Mini Nutritional Assessment. Secondary outcomes include cognitive function, nutritional intake, body composition, physical function and quality of life. Mechanistic pathways for potential diet and exercise-induced change in nutritional status and cognition will be explored by measuring inflammatory, metabolic, nutritional and metabolomic biomarkers. Ethics and dissemination The study is approved by the UK Office for Research Ethics Committee (ref: 21/NW/0215). Written informed consent will be obtained from participants prior to recruitment. Research results will be disseminated to the public via meetings and media and the scientific community through conference presentations and publication in academic journals. Trial registration number ClinicalTrials.gov Registry (NCT05166564).
Proximity extension assay-based discovery of biomarkers for disease activity in chronic inflammatory demyelinating polyneuropathy

Background Objective disease activity biomarkers are lacking in chronic inflammatory demyelinating polyneuropathy (CIDP), impacting treatment decisions in clinical care and outcomes in clinical trials. Using a proximity extension assay, we aimed to identify candidate serum protein biomarkers for disease activity in CIDP. Method We collected clinical data and serum of 106 patients with CIDP. Patients starting induction treatment (n=53) and patients on maintenance treatment starting treatment withdrawal (n=40) were assessed at baseline and at 6 months (or at relapse). Patients in remission (n=13) were assessed once. Clinical disease activity was defined based on improvement or deterioration by the minimal clinically important difference on the inflammatory Rasch-built Overall Disability Scale in combination with either grip strength or the Medical Research Council sum score. Using a proximity extension assay (Olink Explore platform), 1472 protein levels were analysed in serum. Candidate proteins were selected based on fold change>0.5 or <−0.5 and p<0.05 between clinically active and inactive disease. Longitudinal changes of candidate proteins between baseline and follow-up were analysed. Results We identified 48 candidate proteins that differed between clinically active and inactive disease on cross-sectional comparison. Five of these proteins (SUGT1, IRAK4, DCTN1, 5'-nucleotidase cytosolic IIIA (NT5C3A), glutaredoxin (GLRX)) also showed longitudinal changes consistent with disease activity changes. IRAK4 was also identified in a sensitivity analysis, using another definition for disease activity. Conclusion Our results indicate that IRAK4 and possibly SUGT1, DCTN1, NT5C3A and GLRX are candidate biomarkers for monitoring clinical disease activity in CIDP.
Extracellular nicotinamide phosphoribosyltransferase (eNAMPT) neutralization counteracts T cell immune evasion in breast cancer

Background Nicotinamide phosphoribosyltransferase (NAMPT) is a key intracellular enzyme that participates in nicotinamide adenine dinucleotide (NAD) homeostasis as well as a released cytokine (eNAMPT) that is elevated in inflammatory conditions and in cancer. In patients with breast cancer, circulating eNAMPT is elevated and its plasma levels correlate with prognosis and staging. In light of this, we investigated the contribution of eNAMPT in triple negative mammary carcinoma progression by investigating the effect of its neutralization via a specific neutralizing monoclonal antibody (C269). Methods We used female BALB/c mice injected with 4T1 clone 5 cells and female C57BL6 injected with EO771 cells, evaluating tumoral size, spleen weight and number of metastases. We injected two times a week the anti-eNAMPT neutralizing antibody and we sacrificed the mice after 28 days. Harvested tumors were analyzed by histopathology, flow cytometry, western blot, immunohistochemistry, immunofluorescence and RNA sequencing to define tumor characteristics (isolating tumor infiltrating lymphocytes and tumoral cells) and to investigate the molecular mechanisms behind the observed phenotype. Moreover, we dissected the functional relationship between T cells and tumoral cells using three-dimensional (3D) co-cultures. Results The neutralization of eNAMPT with C269 led to decreased tumor size and reduced number of lung metastases. RNA sequencing and functional assays showed that eNAMPT controlled T-cell response via the programmed death-ligand 1/programmed cell death protein 1 (PD-L1/PD-1) axis and its neutralization led to a restoration of antitumoral immune responses. In particular, eNAMPT neutralization was able to activate CD8+IFNγ+GrzB+ T cells, reducing the immunosuppressive phenotype of T regulatory cells. Conclusions These studies indicate for the first time eNAMPT as a novel immunotherapeutic target for triple negative breast cancer.
Effect of Witnessing House Raids and Arrests on Child Behavior: Evidence from Israeli-Palestinian Conflict

ABSTRACT This study utilizes self-reported data on exposure to conflict, collected in the West Bank, to examine the exposure effect of house raids or arrest of household members on child behavior. We show that exposed children are more likely to engage in violent behavior. We also show that the exposure effect is independent of gender and that its magnitude is greater for older children. We propose that altering personality traits, mainly exacerbating neuroticism is a channel through which exposure to conflict affects children’s behavior.
Frataxin Deficiency Drives a Shift from Mitochondrial Metabolism to Glucose Catabolism, Triggering an Inflammatory Phenotype in Microglia

Immunometabolism investigates the complex interplay between the immune system and cellular metabolism. This study highlights the effects of mitochondrial frataxin (FXN) depletion, which causes Friedreich’s ataxia (FRDA), a neurodegenerative condition characterized by coordination and muscle control deficiencies. Using single-cell RNA sequencing, we identified specific cell groups in the cerebellum of a FRDA mouse model, emphasizing a notable inflammatory microglial response. These FXN-deficient microglia cells exhibited enhanced inflammatory reactions. Furthermore, our metabolomic analyses revealed increased glycolysis and itaconate production in these cells, possibly driving the inflammation. Remarkably, butyrate treatment counteracted these immunometabolic changes, triggered an antioxidant response via the itaconate-Nrf2-GSH pathways, and dampened inflammation. The study also pinpointed Hcar2 (GPR109A) as a potential agent for butyrate anti-inflammatory impact on microglia. Tests on FRDA mice highlighted the neuroprotective attributes of butyrate intake, bolstering neuromotor performance. In essence, our findings shed light on how cerebellar microglia activation contributes to FRDA and highlight butyrate potential to alleviate neuroinflammation, rectify metabolic imbalances, and boost neuromotor capabilities in FRDA and similar conditions.
The Evolution of Saline Lakes in the Relict Drainage of the Yilgarn River, Western Australia

The Yilgarn River predecessor of the Swan River was a major river during the Tertiary before uplift of the Yilgarn Craton and the Darling Range Tectonic activity and climatic change associated with movementof theAustralian Plate caused this riversystem to dry up with the formation of riverine playa lakes in its abandoned channel Study of I saline lake sediments 2 paleochannel deposits and 3 older sedimentary formations reveal the history of this change The palynologic record within the river system shows that the most recent sediments were deposited in the present lake basins during the Quaternary During Pliocene time siliciclastic sediments and peat were deposited in the paleochannel system in the central part of the catchment Other sediments vary in age from Pliocene to Miocene The oldest sediments Eocene are preserved in crevices in uplifted areas of the Darling Range and at the base of paleochannels Saline lakes in the eastern part of the catchment are larger and contain more salt Lake areas decrease westward and the amount of halite contained in these lakes decreases substantially The surface of Lake Deborah is covered by a thick halite crust underlain by stratified lacustrine deposits of poorly consolidated salt clay and sand with intercalated salt and gypsum In Lake Deborah prolonged arid periods occurred when no salt was added to the lake For most of its history the lake has remained a NaCI repository Sodium chloride and other solutes are introduced by groundwater and surface inflow Brine migration from the lake is minimal due to the presence of thick mudstone layers at the bottom of the sedimentary sequence and the build up of sand dunes during arid periods This may explain why Lake Deborah is the most saline of the eastern lakes
Impact of gene selection criteria on transcriptomic ontology-based point of departure estimates

Apical effects are typically associated with changes in gene expression, which allows for the use of short- term in life transcriptomic studies to derive biologically relevant points of departure (POD). These methods offer cost savings over conventional toxicology assessments and can derive data from very short-term studies where apical effects may not yet be present. When there is limited or insufficient data for a conventional POD assessment, a transcriptomic screen could provide valuable data for deriving a cellular bioactivity POD for chemical screening and hazard assessment. We used existing transcriptomic data from published 5-day rat in vivo kidney and liver exposures to examine the effect of differential gene expression metrics for the selection of genes used for ontology pathway-based POD derivation. Williams Trend Test (WTT) indicate no gene expression dose-response in 6 instances and ANOVA in one, while DESeq2 detected differentially expressed genes in all instances. The three statistical metrics produced consistent POD values. One chemical (PFOA in liver) showed ontology enrichment indicative of a cytotoxic response at the highest dose, emphasizing the effect which too high a dose can have on the derivation of POD values if such response is not accounted for. Whether the choice of a gene selection metric combining both a statistical significance criterion as well as a minimum magnitude of change threshold affects the sensitivity of POD values depends on the specifics of the dose- response. Existing alternative and complementary analyses could be utilized with existing analyses pipelines to better inform analytical decisions when using transcriptomics and BMD for point of departure determinations.
An improved dehazing algorithm of aerial high-definition image

For unmanned aerial vehicle(UAV) images, the sensor can not get high quality images due to fog and haze weather. To solve this problem, An improved dehazing algorithm of aerial high-definition image is proposed. Based on the model of dark channel prior, the new algorithm firstly extracts the edges from crude estimated transmission map and expands the extracted edges. Then according to the expended edges, the algorithm sets a threshold value to divide the crude estimated transmission map into different areas and makes different guided filter on the different areas compute the optimized transmission map. The experimental results demonstrate that the performance of the proposed algorithm is substantially the same as the one based on dark channel prior and guided filter. The average computation time of the new algorithm is around 40% of the one as well as the detection ability of UAV image is improved effectively in fog and haze weather.
Mapping axon diameters and conduction velocity in the rat brain – different methods tell different stories of the structure-function relationship

The structure-function relationship of nerve fibers describes an empirically determined linear relationship between axon diameter, myelin thickness (i.e., g-ratio), and conduction velocity. We investigated the structure-function relationship with different modalities in axons projecting through the corpus callosum of the rodent brain. We measured transcallosal conduction times using optogenetically evoked local field potentials (LFP) and estimated conduction velocity after measuring the callosal length with diffusion magnetic resonance imaging (dMRI) based tractography. Tractography followed the same projection as the fluorescently labeled axons in the corpus callosum. In the same animal, axon diameters were quantified using transmission electron microscopy (TEM) and dMRI. Axon distributions of TEM indicated a bimodal population, where the larger axons shrink more than the smaller ones, when comparing the modes with cryo-TEM. When applying shrinkage-correction to axon diameters from TEM of dehydrated tissue, they were better aligned with estimates from dMRI obtained in the same animal. Measured LFPs predicted axon diameters that agree with the primary mode of the axon distribution, whereas the large axons estimated by dMRI predicted latencies too short to be measured by LFPs. Different modalities show different degrees of variations, being low between animals, suggesting that the variation is methodologically dominated - not anatomically. Our results show that modalities have different sensitivity profiles to the whole axon diameter distribution. Therefore, caution must be taken when interpreting a method’s prediction of a metric, as it may not represent the full but only a sub-part of the structure-function relationship of an axonal projection. Significance Statement We acquire both functional and structural metrics, namely conduction velocity, pathway length, axon diameter, and g-ratio in the same cohort of animals. The transcallosal conduction time was obtained from electrophysiological measurements after contralateral optogenetic stimulation in the rat motor cortex. Cryo-fixation of the tissue reveals different shrinkages for different sub-populations in the diameter distribution. Measured latencies correspond to the small axonal subpopulation with diameters extending up to the mode of the distribution obtained with electron microscopy. Diffusion-MRI primarily appears sensitive to the larger axons, obtained with histology, after correcting for diameter weighting and shrinkage. Different modalities can have very different sensitivities to the structure-function relationship of an axonal projection which must be accounted for in the interpretation.
microRNA-218-5p Coordinates Scaling of Excitatory and Inhibitory Synapses during Homeostatic Synaptic Plasticity

Homeostatic synaptic plasticity (HSP) is a fundamental neuronal mechanism that allows networks to compensate for prolonged changes in activity by adjusting synaptic strength. This process is crucial for maintaining stable brain function and has been implicated in memory consolidation during sleep. While scaling of both excitatory and inhibitory synapses plays an important role during homeostatic synaptic plasticity, molecules coordinating both of these processes are unknown. In this study, we investigate the role of miR-218-5p as a regulator of inhibitory and excitatory synapses in the context of picrotoxin (PTX)-induced homeostatic synaptic downscaling (HSD) in rat hippocampal neurons. Using enrichment analysis of miRNA-binding sites in differentially expressed genes changing upon PTX-induced HSD, we bioinformatically predicted and experimentally validated increased miR-218-5p activity upon PTX-treatment in the process compartment. By monitoring synapse structure in vitro with confocal microscopy, we demonstrate that inhibiting miR-218-5p activity exerts a dual effect during HSD: it prevents the downscaling of excitatory synapses and dendritic spines, while at the same time blocking inhibitory synapse upscaling. Furthermore, we identify the Neuroligin2 interacting molecule Mdga1 as a crucial target of miR-218-5p in the context of homeostatic upscaling of inhibitory synapses. By performing long-term electroencephalographic (EEG) recordings, we further revealed that local inhibition of miR-218-5p in the somatosensory cortex reduced local slow-wave activity (SWA) during non-rapid-eye-movement (NREM) sleep. In summary, this study uncovers miR-218-5p as a key player in coordinating inhibitory and excitatory synapses during homeostatic plasticity and sleep. Our findings contribute to a deeper understanding of how neural circuits maintain stability in the face of activity-induced perturbations, with potential implications for both physiological and pathological conditions. Significance Statement Homeostatic synaptic plasticity mechanisms evolved to keep neuronal firing rates within a physiological range in response to alterations in neural network activity. It has been proposed that similar mechanisms take place during sleep in a process that promotes memory consolidation and synaptic renormalization. In this study, posttranscriptional regulation of synaptic proteins by miR-218-5p has been identified to coordinate both excitatory and inhibitory synaptic scaling during activity-dependent homeostatic synaptic plasticity. Intriguingly, local inhibition of miR-218-5p in the cortex of mice resulted in reduced slow-wave activity, an EEG-signature of synchronous firing during non-rapid eye movement sleep and a hallmark correlate of sleep pressure. Overall, these findings propose a convergent, posttranscriptional mechanism to coordinate both excitatory and inhibitory synaptic strength in response to alterations in neuronal activity with potential implications for sleep.
Integrative analysis of the methylome and transcriptome of tomato fruit (Solanum lycopersicum L.) induced by postharvest handling

Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown, is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlated with ripening speed, and ripening indicators such as ethylene, ABA, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached ‘Turning’ (T) after storage under dark at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming), were compared to fresh-harvest fruit ‘FHT’. Fruit stored at 12.5°C, had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was longest. Fruit ripening at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in ABA. Clear differentiation between postharvest-ripened and ‘FHT’ was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in ‘FHT’ fruit, pointing to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.
Identification of single nucleotide genetic polymorphism sites using machine learning methods

The paper presents an algorithm for simulation modelling of nucleotide variations in the genomic DNA molecule. To identify single nucleotide genetic polymorphisms, it is proposed to use machine learning methods trained on simulated data. A comparative analysis of the effective classical and machine learning algorithms for identifying single nucleotide polymorphisms was performed on simulated data. The most optimal method for identifying single nucleotide genetic polymorphisms in DNA molecules at various experimental noise levels is the machine learning algorithm CART.