Miracle-dz/UniFAR-FTUs huggingface dataset:
Combined Multi-Atlas and Multi-Layer Perception for Alzheimer's Disease Classification

Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disease. To distinguish the stage of the disease, AD classification technology challenge has been proposed in Pattern Recognition and Computer Vision 2021 (PRCV 2021) which provides the gray volume and average cortical thickness data extracted in multiple atlases from magnetic resonance imaging (MRI). Traditional methods either train with convolutional neural network (CNN) by MRI data to adapt the spatial features of images or train with recurrent neural network (RNN) by temporal features to predict the next stage. However, the morphological features from the challenge have been extracted into discrete values. We present a multi-atlases multi-layer perceptron (MAMLP) approach to deal with the relationship between morphological features and the stage of the disease. The model consists of multiple multi-layer perceptron (MLP) modules, and morphological features extracted from different atlases will be classified by different MLP modules. The final vote of all classification results obtains the predicted disease stage. Firstly, to preserve the diversity of brain features, the most representative atlases are chosen from groups of similar atlases, and one atlas is selected in each group. Secondly, each atlas is fed into one MLP to fetch the score of the classification. Thirdly, to obtain more stable results, scores from different atlases are combined to vote the result of the classification. Based on this approach, we rank 10th among 373 teams in the challenge. The results of the experiment indicate as follows: (1) Group selection of atlas reduces the number of features required without reducing the accuracy of the model; (2) The MLP architecture achieves better performance than CNN and RNN networks in morphological features; and (3) Compared with other networks, the combination of multiple MLP networks has faster convergence of about 40% and makes the classification more stable.
Intrinsic Connectivity Networks of Glutamate-Mediated Antidepressant Response: A Neuroimaging Review

Conventional monoamine-based pharmacotherapy, considered the first-line treatment for major depressive disorder (MDD), has several challenges, including high rates of non-response. To address these challenges, preclinical and clinical studies have sought to characterize antidepressant response through monoamine-independent mechanisms. One striking example is glutamate, the brain's foremost excitatory neurotransmitter: since the 1990s, studies have consistently reported altered levels of glutamate in MDD, as well as antidepressant effects following molecular targeting of glutamatergic receptors. Therapeutically, this has led to advances in the discovery, testing, and clinical application of a wide array of glutamatergic agents, particularly ketamine. Notably, ketamine has been demonstrated to rapidly improve mood symptoms, unlike monoamine-based interventions, and the neurobiological basis behind this rapid antidepressant response is under active investigation. Advances in brain imaging techniques, including functional magnetic resonance imaging, magnetic resonance spectroscopy, and positron emission tomography, enable the identification of the brain network-based characteristics distinguishing rapid glutamatergic modulation from the effect of slow-acting conventional monoamine-based pharmacology. Here, we review brain imaging studies that examine brain connectivity features associated with rapid antidepressant response in MDD patients treated with glutamatergic pharmacotherapies in contrast with patients treated with slow-acting monoamine-based treatments. Trends in recent brain imaging literature suggest that the activity of brain regions is organized into coherent functionally distinct networks, termed intrinsic connectivity networks (ICNs). We provide an overview of major ICNs implicated in depression and explore how treatment response following glutamatergic modulation alters functional connectivity of limbic, cognitive, and executive nodes within ICNs, with well-characterized anti-anhedonic effects and the enhancement of “top-down” executive control. Alterations within and between the core ICNs could potentially exert downstream effects on the nodes within other brain networks of relevance to MDD that are structurally and functionally interconnected through glutamatergic synapses. Understanding similarities and differences in brain ICNs features underlying treatment response will positively impact the trajectory and outcomes for adults suffering from MDD and will facilitate the development of biomarkers to enable glutamate-based precision therapeutics.
Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in ER (+) and/or PR (+) and HER2 (−) Breast Cancer

Background: Although intrinsic molecular subtype has been widely used, there remains great clinical heterogeneity of prognosis in the estrogen receptor (ER)- and/or progesterone receptor (PR)-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer (BC). Methods: The transcriptome expression data of messenger RNA (mRNA) were downloaded from The Cancer Genome Atlas (TCGA), Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), and the Gene Expression Omnibus (GEO) databases. Immune-related genes were acquired from the ImmPort database and additional literature search. Univariate Cox, LASSO regression, and multivariate Cox regression were used to screen prognostic immune-related genes and establish the risk signature. The correlation between the risk signature and clinical characteristics, the abundances of immune cells within the tumor microenvironment, and cancer phenotypes were further assessed. Results: Of note, 102 immune-related prognostic genes were identified in the METABRIC dataset by univariate Cox analysis. Consecutively, 7 immune-related genes (SHMT2, AGA, COL17A1, FLT3, SLC7A2, ATP6AP1, and CCL19) were selected to establish the risk signature by LASSO regression and multivariate Cox analysis. Its performance was further verified in TCGA and GSE21653 datasets. Multivariate Cox analysis showed that the risk signature was an independent prognostic factor. The 7-gene signature showed a significant correlation with intrinsic molecular subtypes and 70-gene signature. Furthermore, the CD4+ memory T cells were significantly higher in the low-risk group while a significantly higher proportion of M0-type macrophages was found in the high-risk group in both METABRIC and TCGA cohorts, which may have an influence on the prognosis. Furthermore, we found that the low-risk group may be associated with the immune-related pathway and the high-risk group was with the cell cycle-related pathway, which also showed an impact on the prognosis. Conclusion: These seven immune-related gene risk signatures provided an effective method for prognostic stratification in ER (+) and/or PR (+) and HER2 (−) BC.
Dynamic Phycobilin Pigment Variations in Diazotrophic and Non-diazotrophic Cyanobacteria Batch Cultures Under Different Initial Nitrogen Concentrations

Increased anthropogenic nutrient loading has led to eutrophication of aquatic ecosystems, which is the major cause of harmful cyanobacteria blooms. Element stoichiometry of cyanobacteria bloom is subject to nutrient availabilities and may significantly contribute to primary production and biogeochemical cycling. Phycobilisome is the antenna of the photosynthetic pigment apparatus in cyanobacteria, which contains phycobilin pigments (PBPs) and linker proteins. This nitrogen (N)-rich protein complex has the potential to support growth as a N-storage site and may play a major role in the variability of cyanobacteria N stoichiometry. However, the regulation of PBPs during bloom formation remains unclear. We investigated the temporal variation of N allocation into PBPs and element stoichiometry for two ubiquitous cyanobacteria species, Microcystis aeruginosa and Dolichospermum flos-aquae, in a batch culture experiment with different initial N availabilities. Our results indicated that the N allocation into PBPs is species-dependent and tightly regulated by the availability of nutrients fueling population expansion. During the batch culture experiment, different nutrient uptake rates led to distinct stoichiometric imbalances of N and phosphorus (P), which substantially altered cyanobacteria C: N and C: P stoichiometry. Microcystis invested cellular N into PBPs and exhibited greater flexibility in C: N and C: P stoichiometry than D. flos-aquae. The dynamics of such N-rich macromolecules may help explain the N stoichiometry variation during a bloom and the interspecific difference between M. aeruginosa and D. flos-aquae. Our study provides a quantitative understanding of the elemental stoichiometry and the regulation of PBPs for non-diazotrophic and diazotrophic cyanobacteria blooms.
Seed Moisture Isotherms, Sorption Models, and Longevity

Seed moisture sorption isotherms show the equilibrium relationship between water content and equilibrium relative humidity (eRH) when seeds are either losing water from a hydrated state (desorption isotherm) or gaining water from a dry state (adsorption isotherm). They have been used in food science to predict the stability of different products and to optimize drying and/or processing. Isotherms have also been applied to understand the physiological processes occurring in viable seeds and how sorption properties differ in relation to, for example, developmental maturity, degree of desiccation tolerance, or dormancy status. In this review, we describe how sorption isotherms can help us understand how the longevity of viable seeds depends upon how they are dried and the conditions under which they are stored. We describe different ways in which isotherms can be determined, how the data are modeled using various theoretical and non-theoretical equations, and how they can be interpreted in relation to storage stability.
A Multi-Species Comparison and Evolutionary Perspectives on Ion Regulation in the Antennal Gland of Brachyurans

Brachyurans inhabit a variety of habitats and have evolved diverse osmoregulatory patterns. Gills, antennal glands and a lung-like structure are important organs of crabs that maintain their homeostasis in different habitats. Species use different processes to regulate ions in the antennal gland, especially those with high terrestriality such as Grapsoidea and Ocypodoidea. Our phylogenetic generalized least square (PGLS) result also suggested that there is a correlation between antennal gland NKA activity and urine-hemolymph ratio for Na+ concentration in hypo-osmotic environments among crabs. Species with higher antennal gland NKA activity showed a lower urine-hemolymph ratio for Na+ concentration under hypo-osmotic stress. These phenomenon may correlate to the structural and functional differences in gills and lung-like structure among crabs. However, a limited number of studies have focused on the structural and functional differences in the antennal gland among brachyurans. Integrative and systemic methods like next generation sequencing and proteomics method can be useful for investigating the differences in multi-gene expression and sequences among species. These perspectives can be combined to further elucidate the phylogenetic history of crab antennal glands.
The Body Scaling Effect and Its Impact on Physics Plausibility

In this study we investigated the effect of body ownership illusion-based body scaling on physics plausibility in Virtual Reality (VR). Our interest was in examining whether body ownership illusion-based body scaling could affect the plausibility of rigid body dynamics similarly to altering VR users' scale by manipulating their virtual interpupillary distance and viewpoint height. The procedure involved the conceptual replication of two previous studies. We investigated physics plausibility with 40 participants under two conditions. In our synchronous condition, we used visuo-tactile stimuli to elicit a body ownership illusion of inhabiting an invisible doll-sized body on participants reclining on an exam table. Our asynchronous condition was otherwise similar, but the visuo-tactile stimuli were provided asynchronously to prevent the onset of the body ownership illusion. We were interested in whether the correct approximation of physics (true physics) or physics that are incorrect and appearing as if the environment is five times larger instead (movie physics) appear more realistic to participants as a function of body scale. We found that movie physics did appear more realistic to participants under the body ownership illusion condition. However, our hypothesis that true physics would appear more realistic in the asynchronous condition was unsupported. Our exploratory analyses revealed that movie physics were perceived as plausible under both conditions. Moreover, we were not able to replicate previous findings from literature concerning object size estimations while inhabiting a small invisible body. However, we found a significant opposite effect regarding size estimations; the object sizes were on average underestimated during the synchronous visuo-tactile condition when compared to the asynchronous condition. We discuss these unexpected findings and the potential reasons for the results, and suggest avenues for future research.
Projection of Damaged Visual and Language Regions on Low Trail Making Test Part-B Performance in Stroke Patients

Background The Trail Making Test Part-B (TMT-B) is an attention functional test to investigate cognitive dysfunction. It requires the ability to recognize not only numbers but also letters. We analyzed the relationship between brain lesions in stroke patients and their TMT-B performance. Methods From the TMT-B, two parameters (score and completion time) were obtained. The subjects were classified into several relevant groups by their scores and completion times through a data-driven analysis (k-means clustering). The score-classified groups were characterized by low (≤10), moderate (10 < score < 25), and high (25) scores. In terms of the completion time, the subjects were classified into four groups. The lesion degree in the brain was calculated for each of the 116 regions classified by automated anatomical labeling (AAL). For each group, brain sites with a significant difference (corrected p < 0.1) between each of the 116 regions were determined by a Wilcoxon Rank–Sum significant difference test. Results Lesions at the cuneus and the superior occipital gyrus, which are mostly involved in visual processing, were significant (corrected p < 0.1) in the low-score group. Furthermore, the moderate-score group showed more-severe lesion degrees (corrected p < 0.05) in the regions responsible for the linguistic functions, such as the superior temporal gyrus and the supramarginal gyrus. As for the completion times, lesions in the calcarine, the cuneus, and related regions were significant (corrected p < 0.1) in the fastest group as compared to the slowest group. These regions are also involved in visual processing. Conclusion The TMT-B results revealed that the subjects in the low-score group or the slowest- group mainly had damage in the visual area, whereas the subjects in the moderate-score group mainly had damage in the language area. These results suggest the potential utility of TMT-B performance in the lesion site.
Age and Gender Differences in Cardiovascular Autonomic Failure in the Transgenic PLP-syn Mouse, a Model of Multiple System Atrophy

Multiple system atrophy (MSA) is a rare and progressive neurodegenerative disorder. Autonomic failure (AF) is one main clinical feature which has a significant impact on health-related quality of life. The neuropathological hallmark of MSA is the abnormal accumulation of α-synuclein in oligodendrocytes forming glial cytoplasmic inclusions. Only little is known about gender and age differences in AF in MSA. This study was carried out in 6 and 12 months old transgenic PLP-α-syn and WT male and female mice. Heart rate variability (HRV) was assessed both in time, frequential and non-linear domains. Baroreflex sensitivity (BRS) was estimated by the sequence method. Duration of ventricular depolarization and repolarization (QT/QTc intervals) were evaluated from the ECG signals. Three-way ANOVA (genotype x gender x age) with Sidak's method post-hoc was used to analyze data. BRS was significantly changed in PLP-α-syn mice and was age-dependent. QT and QTc intervals were not significantly modified in PLP-α-syn mice. An impaired HRV was observed at 12 months of age in PLP-α-syn female but not in male mice, indicative of cardiovascular AF.
Clinical Manifestations and Molecular Backgrounds of Parkinson's Disease Regarding Genes Identified From Familial and Population Studies

Over the past 20 years, numerous robust analyses have identified over 20 genes related to familial Parkinson's disease (PD), thereby uncovering its molecular underpinnings and giving rise to more sophisticated approaches to investigate its pathogenesis. α-Synuclein is a major component of Lewy bodies (LBs) and behaves in a prion-like manner. The discovery of α-Synuclein enables an in-depth understanding of the pathology behind the generation of LBs and dopaminergic neuronal loss. Understanding the pathophysiological roles of genes identified from PD families is uncovering the molecular mechanisms, such as defects in dopamine biosynthesis and metabolism, excessive oxidative stress, dysfunction of mitochondrial maintenance, and abnormalities in the autophagy–lysosome pathway, involved in PD pathogenesis. This review summarizes the current knowledge on familial PD genes detected by both single-gene analyses obeying the Mendelian inheritance and meta-analyses of genome-wide association studies (GWAS) from genome libraries of PD. Studying the functional role of these genes might potentially elucidate the pathological mechanisms underlying familial PD and sporadic PD and stimulate future investigations to decipher the common pathways between the diseases.
Investigating How Auditory and Visual Stimuli Promote Recovery After Stress With Potential Applications for Workplace Stress and Burnout: Protocol for a Randomized Trial

Background Work-related stress is one of the top sources of stress amongst working adults. Relaxation rooms are one organizational strategy being used to reduce workplace stress. Amongst healthcare workers, relaxation rooms have been shown to improve perceived stress levels after 15 min of use. However, few studies have examined physiological and cognitive changes after stress, which may inform why relaxation rooms reduce perceived stress. Understanding the biological mechanisms governing why perceived stress improves when using a relaxation room could lead to more effective strategies to address workplace stress. Objective The purpose of this research study is to understand how physiological measures, cognitive performance, and perceived stress change after acute stress and whether certain sensory features of a relaxation room are more effective at promoting recovery from stress. Methods 80 healthy adults will perform a stress induction task (Trier Social Stress Test, TSST) to evaluate how physiological and cognitive responses after stress are affected by sensory features of a relaxation room. After the stress induction task, participants will recover for 40 min in a MindBreaks™ relaxation room containing auditory and visual stimuli designed to promote relaxation. Participants will be randomized into four cohorts to experience auditory and visual stimuli; auditory stimuli; visual stimuli; or no stimuli in the room. Measures of heart rate and neural activity will be continuously monitored using wearable devices. Participants will perform working memory assessments and rate their perceived stress levels throughout the experiment. These measures will be compared before and after the stress induction task to determine how different sensory stimuli affect the rate at which individuals recover. Results Recruitment started in December 2021 and will continue until December 2022 or until enrollment is completed. Final data collection and subsequent analysis are anticipated by December 2022. We expect all trial results will be available by early 2023. Discussion Findings will provide data and information about which sensory features of a relaxation room are most effective at promoting recovery after acute stress. This information will be useful in determining how these features might be effective at creating individualized and organizational strategies for mitigating the effects of workplace stress.
Scaffolding learner writing strategies in an ESL secondary class in the seychelles: A sociocultural perspective

This research draws on the metaphor of scaffolding from sociocultural theory to explore how an English as a Second Language (ESL) teacher provided scaffolded instruction to his ESL students during writing lessons. Evidence in this study suggests that the teacher mostly made use of two main types of instructional scaffolding: bridging and modeling. As evidenced in this study, these two types of scaffolding may lead eventually to students' use of writing strategies, but were not adequate to foster and sustain writing strategies development. The teacher attempted to teach many writing skills at a time and his scaffolding focused on a wide collection of writing strategies (e.g., charts, plan, graduated questions and thinking-prompt). However, evidence also suggests that he did not give enough attention to how he could systematically support writing strategy development in his students. The study sheds light on the complex process that mastering the teaching of writing strategies requires and the vital role that the teacher ought to play in the development and understanding and use of writing strategies. The study underlines that teaching writing strategies requires thoughtful planning of how to support strategy development in students, and has to be co-constructed and practised by both the teacher and students.
Study of influence of ascorbic acid, reducing sugars and methyldopa on betalains content in Celosia cristata callus

Aim. The aim of the present work is to investigate the influence of reducing sugars, ascorbic acid and methyl DOPA as one of the DOPA decarboxylase inhibitors on total amount and spectrum of betalains in the callus culture of cockscomb Celosia cristata L. (Amaranthaceae). Methods. Tissue culture methods, analytical high-performance liquid chromatography (HPLC), spectrophotometry. Results. Adding of some reducing sugars (1 % of glucose, arabinose or rhamnose) to the media does not increase the total betalains content. Ascorbic acid at a concentration of 5 mM also does not significantly affect the amount of betalains, but considerably inhibit the callus growth. Moreover, ascorbic acid causes significant decreasing of the dopamine content and the normalized concentration of the main betacyanin pigment of the callus – amaranthin. Investigations have begun to study the effects of DOPA-decarboxylase inhibitors on the content of betalains and dopamine. Increased level of betalains in the callus in the presence of all used concentrations of methylDOPA was aobserved. The necessity of use of ascorbic acid or another stabilizer of methylDOPA in order to prevent oxidation of this inhibitor has been established. Conclusions. The data obtained suggest that methylDOPA as well as, probably, other inhibitors of DOPA decarboxylase can influence on betalains level in callus culture, so their use may be a potential strategy for these pigments content increasing. Keywords: Celosia cristata L. betalains, dopamine, callus culture.