Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid and Non-destructive Classification of New and Aged Maize Seeds Using Hyperspectral Image and Chemometric Methods

The aged seeds have a significant influence on seed vigor and corn growth. Therefore, it is vital for the planting industry to identify aged seeds. In this study, hyperspectral reflectance imaging (1,000–2,000 nm) was employed for identifying aged maize seeds using seeds harvested in different years. The average spectra of the embryo side, endosperm side, and both sides were extracted. The support vector machine (SVM) algorithm was used to develop classification models based on full spectra to evaluate the potential of hyperspectral imaging for maize seed detection and using the principal component analysis (PCA) and ANOVA to reduce data dimensionality and extract feature wavelengths. The classification models achieved perfect performance using full spectra with an accuracy of 100% for the prediction set. The performance of models established with the first three principal components was similar to full spectrum models, but that of PCA loading models was worse. Compared to other spectra, the two-band ratio (1,987 nm/1,079 nm) selected by ANOVA from embryo-side spectra achieved a better classification accuracy of 95% for the prediction set. The image texture features, including histogram statistics (HS) and gray-level co-occurrence matrix (GLCM), were extracted from the two-band ratio image to establish fusion models. The results demonstrated that the two-band ratio selected from embryo-side spectra combined with image texture features achieved the classification of maize seeds harvested in different years with an accuracy of 97.5% for the prediction set. The overall results indicated that combining the two wavelengths with image texture features could detect aged maize seeds effectively. The proposed method was conducive to the development of multi-spectral detection equipment.
Reproducibility of Lesion Count in Various Subregions on MRI Scans in Multiple Sclerosis

Purpose Lesion number and burden can predict the long-term outcome of multiple sclerosis, while the localization of the lesions is also a good predictive marker of disease progression. These biomarkers are used in studies and in clinical practice, but the reproducibility of lesion count is not well-known. Methods In total, five raters evaluated T2 hyperintense lesions in 140 patients with multiple sclerosis in six localizations: periventricular, juxtacortical, deep white matter, infratentorial, spinal cord, and optic nerve. Black holes on T1-weighted images and brain atrophy were subjectively measured on a binary scale. Reproducibility was measured using the intraclass correlation coefficient (ICC). ICCs were also calculated for the four most accurate raters to see how one outlier can influence the results. Results Overall, moderate reproducibility (ICC 0.5–0.75) was shown, which did not improve considerably when the most divergent rater was excluded. The areas that produced the worst results were the optic nerve region (ICC: 0.118) and atrophy judgment (ICC: 0.364). Comparing high- and low-lesion burdens in each region revealed that the ICC is higher when the lesion count is in the mid-range. In the periventricular and deep white matter area, where lesions are common, higher ICC was found in patients who had a lower lesion count. On the other hand, juxtacortical lesions and black holes that are less common showed higher ICC when the subjects had more lesions. This difference was significant in the juxtacortical region when the most accurate raters compared patients with low (ICC: 0.406 CI: 0.273–0.546) and high (0.702 CI: 0.603–0.785) lesion loads. Conclusion Lesion classification showed high variability by location and overall moderate reproducibility. The excellent range was not achieved, owing to the fact that some areas showed poor performance. Hence, putting effort toward the development of artificial intelligence for the evaluation of lesion burden should be considered.
Leucine-Rich Repeats and Transmembrane Domain 2 Controls Protein Sorting in the Striatal Projection System and Its Deficiency Causes Disturbances in Motor Responses and Monoamine Dynamics

The striatum is involved in action selection, and its disturbance can cause movement disorders. Here, we show that leucine-rich repeats and transmembrane domain 2 (Lrtm2) controls protein sorting in striatal projection systems, and its deficiency causes disturbances in monoamine dynamics and behavior. The Lrtm2 protein was broadly detected in the brain, but it was enhanced in the olfactory bulb and dorsal striatum. Immunostaining revealed a strong signal in striatal projection output, including GABAergic presynaptic boutons of the SNr. In subcellular fractionation, Lrtm2 was abundantly recovered in the synaptic plasma membrane fraction, synaptic vesicle fraction, and microsome fraction. Lrtm2 KO mice exhibited altered motor responses in both voluntary explorations and forced exercise. Dopamine metabolite content was decreased in the dorsal striatum and hypothalamus, and serotonin turnover increased in the dorsal striatum. The prefrontal cortex showed age-dependent changes in dopamine metabolites. The distribution of glutamate decarboxylase 67 (GAD67) protein and gamma-aminobutyric acid receptor type B receptor 1 (GABABR1) protein was altered in the dorsal striatum. In cultured neurons, wild-type Lrtm2 protein enhanced axon trafficking of GAD67-GFP and GABABR1-GFP whereas such activity was defective in sorting signal-abolished Lrtm2 mutant proteins. The topical expression of hemagglutinin-epitope-tag (HA)-Lrtm2 and a protein sorting signal abolished HA-Lrtm2 mutant differentially affected GABABR1 protein distribution in the dorsal striatum. These results suggest that Lrtm2 is an essential component of striatal projection neurons, contributing to a better understanding of striatal pathophysiology.
Increased Resilience of Peas Toward Root Rot Pathogens Can Be Predicted by the Nematode Metabolic Footprint

Legumes are important drivers of soil fertility, however, their frequent use in rotations fosters long-lived soil-borne pathogens that can seriously compromise legume root health and nitrogen fixation. To overcome this, the current study aims at improving the general soil suppressiveness toward pests and diseases by agroecosystem management that can be predicted by nematode-based bioindicators. Two long-term organically managed agroecosystems comparing plow and shallow non-inversion tillage were analyzed for free-living nematode communities. Soils out of these agroecosystems were evaluated further in a greenhouse assay for their ability to suppress pea root rot caused by Didymella pinodella, Fusarium avenaceum, and F. redolens. There was a general trend for higher levels of pea root rot disease severity following inoculations with single pathogens, however, this effect was heterogeneous among experiments and tillage systems. This was mainly due to an already very high resident population of D. pinodella in soil and the presence of seed-borne F. oxysporum determined by their high incidence in pea roots irrespective of the soil and inoculated pathogens. Additional inoculation with D. pinodella, for example, resulted in only 8.5% biomass reduction compared to the non-inoculated control, in both tillage systems. Similar biomass losses were recorded in non-inversion tilled soils inoculated with F. redolens. When analyzed across inoculation treatments, the pea root rot disease severity was only slightly reduced in non-inversion tilled soils when compared to the plough systems (11% in Exp 1 and, 9% in Exp 2), however in both experiments non-inversion tillage resulted in greater pea biomass (33 and 19% in Exp1 and 2, respectively). Furthermore, the metabolic, enrichment, and bacterivore carbon footprints of nematodes were 88, 81, and 97% higher, respectively, in the non-inversion tilled soils compared to the plough. The metabolic carbon footprint of nematodes correlated negatively with pea root rot disease severity (rho = −0.71, p = 0.047). Hence, non-inversion tillage was effective in controlling pea root rot. The use of nematode metabolic footprints for predicting soil health should be extended for various agroecosystems aiming for its general use in evaluating effects of agroecosystem management through researchers and potentially farm management advisors.
A Review of Healthy and Fibrotic Myocardium Microstructure Modeling and Corresponding Intracardiac Electrograms

Computational simulations of cardiac electrophysiology provide detailed information on the depolarization phenomena at different spatial and temporal scales. With the development of new hardware and software, in silico experiments have gained more importance in cardiac electrophysiology research. For plane waves in healthy tissue, in vivo and in silico electrograms at the surface of the tissue demonstrate symmetric morphology and high peak-to-peak amplitude. Simulations provided insight into the factors that alter the morphology and amplitude of the electrograms. The situation is more complex in remodeled tissue with fibrotic infiltrations. Clinically, different changes including fractionation of the signal, extended duration and reduced amplitude have been described. In silico, numerous approaches have been proposed to represent the pathological changes on different spatial and functional scales. Different modeling approaches can reproduce distinct subsets of the clinically observed electrogram phenomena. This review provides an overview of how different modeling approaches to incorporate fibrotic and structural remodeling affect the electrogram and highlights open challenges to be addressed in future research.
Subjective Well-Being and Bilateral Anterior Insula Functional Connectivity After Exercise Intervention in Older Adults With Mild Cognitive Impairment

While it is well known that exercise training is associated with improvement in subjective well-being among older adults, it is unclear if individuals with cognitive impairment experience the same effects elicited by exercise on subjective well-being. We further explored whether the bilateral anterior insula network may be an underlying neural mechanism for the exercise training-related improvements in subjective well-being. We investigated the effects of exercise training on subjective well-being in older adults (78.4 ± 7.1 years) with mild cognitive impairment (MCI; n = 14) and a cognitively normal (CN; n = 14) control group. We specifically assessed the relationship between changes in subjective well-being and changes in functional connectivity (FC) with the bilateral anterior insula from before to after exercise training. Cardiorespiratory fitness, subjective well-being, and resting-state fMRI were measured before and after a 12-week moderate-intensity walking intervention. A seed-based correlation analysis was conducted using the bilateral anterior insula as a priori seed regions of interest. The associations between bilateral anterior insula FC with other brain regions and subjective well-being were computed before and after exercise training, respectively, and the statistical difference between the correlations (before vs after exercise training) was evaluated. There was a significant Group (MCI vs CN) × Time (before vs after exercise training) interaction for subjective well-being, such that while those with MCI demonstrated significantly increased subjective well-being after exercise training, no changes in subjective well-being were observed in CN. Participants with MCI also showed an exercise training-related increase in the bilateral anterior insula FC. While there was no significant correlation between subjective well-being and bilateral anterior insula FC before exercise training, a positive association between subjective well-being and bilateral anterior insula FC was found in the MCI group after exercise training. Our findings indicate that 12 weeks of exercise training may enhance subjective well-being in older adults diagnosed with MCI and, further, suggest that increased bilateral anterior insula FC with other cortical regions may reflect neural network plasticity associated with exercise training-related improvements in subjective well-being.
Association Between Dietary Inflammatory Index and S-Klotho Plasma Levels in Middle-Aged and Elderly People

Background and Aims Soluble Klotho (S-Klotho) is a protein that has anti-aging properties. Dietary inflammation index (DII) is closely related to various age-related diseases. However, whether DII is related to S-Klotho plasma levels is still controversial. It was the goal of this study to examine the link between DII and S-Klotho in middle-aged and elderly people. Methods Between 2007 and 2016, five NHANES cycles were conducted, with 12,315 middle-aged and elderly (aged 40–79) participants having S-Klotho tests and submitting dietary recall data. The inflammatory potential of a diet was determined using the DII. To determine the plasma levels of S-Klotho, we employed a solid-phase sandwich enzyme-linked immunosorbent assay (ELISA). Results There was a negative correlation between DII and S-Klotho plasma levels. In the threshold effect analysis model, the breakpoint was DII=1.3, and the negative correlation was more obvious when DII < 1.3 (β = −10.6, p = 0.001). When DII > 1.3, the correlation disappeared (p = 0.355). There may be a threshold saturation effect. Conclusion In middle-aged and older individuals, there is a negative connection between the pro-inflammatory dietary pattern as evaluated by DII and the plasma level of S-Klotho. Given the rationale for the findings and the study's limitations, the fundamental mechanisms generating inflammation warrant additional exploration.
Beyond Maternal Tolerance: Education of Uterine Natural Killer Cells by Maternal MHC Drives Fetal Growth

Reproductive immunology has moved on from the classical Medawar question of 60 years ago “why doesn’t the mother reject the fetus? ”. Looking beyond fetal-maternal tolerance, modern reproductive immunology focuses on how the maternal immune system supports fetal growth. Maternal uterine natural killer (uNK) cells, in partnership with fetal trophoblast cells, regulate physiological vascular changes in the uterus of pregnant women and mice. These vascular changes are necessary to build the placenta and sustain fetal growth. NK cell functions in the uterus and elsewhere, including anti-viral and anti-tumour immunity mediated mostly by blood NK cells, are modulated by NK cell education, a quantifiable process that determines cellular activation thresholds. This process relies largely on interactions between self-MHC class I molecules and inhibitory NK cell receptors. By getting to know self, the maternal immune system sets up uNK cells to participate to tissue homeostasis in the womb. Placentation can be viewed as a form of natural transplantation unique in vertebrates and this raises the question of how uNK cell education or missing-self recognition affect their function and, ultimately fetal growth. Here, using combinations of MHC-sufficient and -deficient mice, we show that uNK cell education is linked to maternal and not fetal MHC, so that MHC-deficient dams produce more growth-restricted fetuses, even when the fetuses themselves express self-MHC. We also show that, while peripheral NK cells reject bone marrow cells according to the established rules of missing-self recognition, uNK cells educated by maternal MHC do not reject fetuses that miss self-MHC and these fetuses grow to their full potential. While these results are not directly applicable to clinical research, they show that NK education by maternal MHC-I is required for optimal fetal growth.
Association of Daily Eating Duration and Day-To-Day Variability in the Timing of Eating With Fatal Cancer Risk in Older Men

Meal timing has significant effects on health. However, whether meal timing is associated with the risk of developing and dying of cancer is not well-researched in humans. In the present study, we used data from 941 community-dwelling men aged 71 years who participated in the Uppsala Longitudinal Study of Adult Men to examine the association of meal timing with cancer morbidity and fatal cancer. The following meal timing variables were derived from 7-day food diaries: (i) daily eating duration, i.e., the time between the first and last eating episode of an arbitrary day; (ii) the calorically weighted midpoint of the daily eating interval, a proxy of when the eating window typically occurs during an arbitrary day; and (iii) the day-to-day variability in the timing of eating. We also assessed the reported daily energy intake reliability using the Goldberg method. During a mean observational period of 13.4 years, 277 men (29.4%) were diagnosed with cancer. Furthermore, 191 men (20%) died from cancer during 14.7 years of follow-up. As shown by Cox regression adjusted for potential confounders (e.g., smoking status and daily energy intake), men with reliable dietary reports whose daily eating intervals were on average 13 h long had a 2.3-fold greater fatal cancer risk than men whose daily eating windows were on average about 11 h long. We also found that men with an average day-to-day variability in the timing of eating of 48 to 74 min had a 2- to 2.2-fold higher fatal cancer risk than those with the lowest average day-to-day variability in the timing of eating (i.e., 23 min). No clear associations were found in men with inadequate dietary reports, emphasizing the need to consider the reliability of dietary records in nutritional epidemiology. To fully unlock its potential, studies are needed to test whether recommendations to time-restrict the 24-h eating interval and reduce day-to-day variability in the timing of eating can meaningfully alter the risk of death due to cancer.
The Influence of Ocean-Surface-Velocity-Dependent Wind Stress on the Dynamics of the Southern Ocean: the Near-Inertial and the Sub-Inertial Response

This thesis examines the consequences of the ocean-surface-velocity dependence of the wind stress (SVD) for the dynamics of the Southern Ocean. It does so by comparing the output from eddying ocean-model experiments that only differ in the way the wind stress is parameterized. The thesis consists of three separate research papers. The first paper assesses the influence of SVD on the near-inertial variability. It is shown that SVD leads to a substantial reduction of horizontally averaged near-inertial energy (NIE) and of horizontally averaged wind power input (WPI) into the near-inertial frequency band. The observed reduction of NIE and near-inertial WPI is explained by the fact that SVD, to leading order, adds a linear damping term to the momentum equation governing near-inertial oscillations in the mixed-layer. This damping term is inversely proportional to the mixed-layer depth and hence the effect of SVD on near-inertial oscillations is found to be largest if the mixed-layer is shallow. The second paper assesses the influence of SVD on sub-inertial time scales. It is found that SVD also substantially reduces sub-inertial WPI and mesoscale eddy kinetic energy (EKE). The largest effect of SVD on sub-inertial WPI and EKE is found along the path of the Antarctic Circumpolar Current (ACC). SVD is found to generally damp the amplitude of monthly to inter-annual variability in the model, without affecting the time-dependence of the wind stress, of WPI, and of the strength of the ACC. SVD is, however, found to have only a minor impact on the path and strength of the ACC. The third paper connects to the first one by focussing on the spatial and temporal distribution of NIE and near-inertial WPI in the Southern Ocean. The modelled near-inertial WPI is found to be mainly governed by the variability of the wind-stress at the local inertial frequency (IWSV). This relationship is used to indirectly examine the temporal evolution of near-inertial WPI on time scales much longer than those which can be directly examined with the model. It is found that from 1979 to 2011 IWSV over the Southern Ocean has increased substantially. Furthermore, the inter-annual variability of IWSV in the Southern Ocean is shown to be largely governed by the Southern Annular Mode.
A Commensal Streptococcus Dysregulates the Pseudomonas aeruginosa Nitrosative Stress Response

Chronic infections in the cystic fibrosis (CF) airway are composed of both pathogenic and commensal bacteria. However, chronic Pseudomonas aeruginosa infections are the leading cause of lung deterioration in individuals with CF. Interestingly, oral commensals can translocate to the CF lung and their presence is associated with improved lung function, presumably due to their ability to antagonize P. aeruginosa. We have previously shown that one commensal, Streptococcus parasanguinis, produces hydrogen peroxide that reacts with nitrite to generate reactive nitrogen intermediates (RNI) which inhibit P. aeruginosa growth. In this study, we sought to understand the global impact of commensal-mediated RNI on the P. aeruginosa transcriptome. RNA sequencing analysis revealed that S. parasanguinis and nitrite-mediated RNI dysregulated expression of denitrification genes in a CF isolate of P. aeruginosa compared to when this isolate was only exposed to S. parasanguinis. Further, loss of a nitric oxide reductase subunit (norB) rendered an acute P. aeruginosa isolate more susceptible to S. parasanguinis-mediated RNI. Additionally, S. parasanguinis-mediated RNI inactivated P. aeruginosa aconitase activity. Lastly, we report that P. aeruginosa isolates recovered from CF individuals are uniquely hypersensitive to S. parasanguinis-mediated RNI compared to acute infection or environmental P. aeruginosa isolates. These findings illustrate that S. parasanguinis hinders the ability of P. aeruginosa to respond to RNI, which potentially prevents P. aeruginosa CF isolates from resisting commensal and host-induced RNI in the CF airway.
Troponin T Is Negatively Associated With 3 Tesla Magnetic Resonance Peripheral Nerve Perfusion in Type 2 Diabetes

Objective The pathogenesis of diabetic polyneuropathy (DN) is poorly understood and given the increasing prevalence of DN, there is a need for clinical or imaging biomarkers that quantify structural and functional nerve damage. While clinical studies have found evidence of an association between elevated levels of troponin T (hsTNT) and N-terminal pro brain natriuretic peptide (proBNP) with microvascular compromise in type 2 diabetes (T2D), their implication in mirroring DN nerve perfusion changes remains unclear. The objective of this study was, therefore, to investigate whether hsTNT and proBNP assays are associated with MRI nerve perfusion in T2D. Methods In this prospective cross-sectional single-center case-control study, 56 participants (44 with T2D, 12 healthy control subjects) consented to undergo magnetic resonance neurography (MRN) including dynamic contrast-enhanced (DCE) perfusion imaging of the right leg. Using the extended Tofts model, primary outcome parameters that were quantified are the sciatic nerve’s microvascular permeability (Ktrans), the extravascular extracellular volume fraction (ve), and the plasma volume fraction (vp), as well as hsTNT and proBNP values from serological workup. Further secondary outcomes were clinical, serological, and electrophysiological findings. Results In T2D patients, hsTNT was negatively correlated with Ktrans (r=-0.38; p=0.012) and ve (r=-0.30; p=0.048) but not with vp (r=-0.16; p=0.294). HsTNT, Ktrans, and ve were correlated with peroneal nerve conduction velocities (NCVs; r=-0.44; p=0.006, r=0.42; p=0.008, r=0.39; p=0.014), and tibial NCVs (r=-0.38;p=0.022, r=0.33; p=0.048, r=0.37; p=0.025). No such correlations were found for proBNP. Conclusions This study is the first to find that hsTNT is correlated with a decrease of microvascular permeability and a reduced extravascular extracellular volume fraction of nerves in patients with T2D. The results indicate that hsTNT may serve as a potential marker for the assessment of nerve perfusion in future studies on DN.