Miracle-dz/UniFAR-FTUs huggingface dataset:
A Representational Similarity Analysis of Cognitive Control during Color-Word Stroop

Progress in understanding the neural bases of cognitive control has been supported by the paradigmatic color-word Stroop task, in which a target response (color name) must be selected over a more automatic, yet potentially incongruent, distractor response (word). For this paradigm, models have postulated complementary coding schemes: dorsomedial frontal cortex (DMFC) is proposed to evaluate the demand for control via incongruency-related coding, whereas dorsolateral PFC (DLPFC) is proposed to implement control via goal and target-related coding. Yet, mapping these theorized schemes to measured neural activity within this task has been challenging. Here, we tested for these coding schemes relatively directly, by decomposing an event-related color-word Stroop task via representational similarity analysis. Three neural coding models were fit to the similarity structure of multivoxel patterns of human fMRI activity, acquired from 65 healthy, young-adult males and females. Incongruency coding was predominant in DMFC, whereas both target and incongruency coding were present with indistinguishable strength in DLPFC. In contrast, distractor information was strongly encoded within early visual cortex. Further, these coding schemes were differentially related to behavior: individuals with stronger DLPFC (and lateral posterior parietal cortex) target coding, but weaker DMFC incongruency coding, exhibited less behavioral Stroop interference. These results highlight the utility of the representational similarity analysis framework for investigating neural mechanisms of cognitive control and point to several promising directions to extend the Stroop paradigm. SIGNIFICANCE STATEMENT How the human brain enables cognitive control — the ability to override behavioral habits to pursue internal goals — has been a major focus of neuroscience research. This ability has been frequently investigated by using the Stroop color-word naming task. With the Stroop as a test-bed, many theories have proposed specific neuroanatomical dissociations, in which medial and lateral frontal brain regions underlie cognitive control by encoding distinct types of information. Yet providing a direct confirmation of these claims has been challenging. Here, we demonstrate that representational similarity analysis, which estimates and models the similarity structure of brain activity patterns, can successfully establish the hypothesized functional dissociations within the Stroop task. Representational similarity analysis may provide a useful approach for investigating cognitive control mechanisms.
Verticillium dahliae Inoculation and in vitro Propagation Modify the Xylem Microbiome and Disease Reaction to Verticillium Wilt in a Wild Olive Genotype

Host resistance is the most practical, long-term and economically efficient disease control measure for Verticillium wilt in olive caused by the xylem-invading fungus Verticillium dahliae (Vd), and it is at the core of the integrated disease management. Plant’s microbiome at the site of infection may have an influence on the host reaction to pathogens; however, the role of xylem microbial communities in the olive resistance to Vd has been overlooked and remain unexplored to date. This research was focused on elucidating whether in vitro olive propagation may alter the diversity and composition of the xylem-inhabiting microbiome and if those changes may modify the resistance response that a wild olive clone shows to the highly virulent defoliating (D) pathotype of Vd. Results indicated that although there were differences in microbial communities among the different propagation methodologies, most substantial changes occurred when plants were inoculated with Vd, regardless whether the infection process took place, with a significant increase in the diversity of bacterial communities when the pathogen was present in the soil. Furthermore, it was noticeable that olive plants multiplied under in vitro conditions developed a susceptible reaction to D Vd, characterized by severe wilting symptoms and 100% vascular infection. Moreover, those in vitro propagated plants showed an altered xylem microbiome with a decrease in total OTU numbers as compared to that of plants multiplied under non-aseptic conditions. Overall, 10 keystone bacterial genera were detected in olive xylem regardless infection by Vd and the propagation procedure of plants (in vitro vs nursery), with Cutibacterium (36.85%), Pseudomonas (20.93%), Anoxybacillus (6.28%), Staphylococcus (4.95%), Methylobacterium-Methylorubrum (3.91%), and Bradyrhizobium (3.54%) being the most abundant. Pseudomonas spp. appeared as the most predominant bacterial group in micropropagated plants and Anoxybacillus appeared as a keystone bacterium in Vd-inoculated plants irrespective of their propagation process. Our results are first to show a breakdown of resistance to Vd in a wild olive that potentially maybe related to a modification of its xylem microbiome, and will help to expand our knowledge of the role of indigenous xylem microbiome on host resistance which can be of use to fight against main vascular diseases of olive.
The Use of Response Surface Method To Optimize The Ultrasound-assisted Extraction of Moringa Leaves

The Ultrasound-assisted extraction is one of the breakthrough in extraction techniques which offered the modest and more effective outcome based on several research influenced by some variables such as temperature, power and frequency, intensity, extraction time, preparation process, type and quantity of solvent. The objective of this study was to assess the effect of the three parameters including extraction time, solvent-to-solid ratio, and ethanol concentration each of which consists of three levels on the percentage of yield, total phenolic content and total flavonoid by using the Response Surface Method (RSM). This research used an ultrasound equipment which was set at frequency 20 kHz, amplitude 32% and the 0,5 of intensity. The experimental design of this research employed 40 runs of Response Surface Method constructed by Central Composite Design (CCD). The output showed that that the percentage of yield about 0.37-9.86%, the total phenolic compound ranged from 27.361-59.907 mg GAE/ml and the total flavonoid result varied from 5.568-67.384 mg/ml. In addition, the more ethanol concentration used the more phenolic and flavonoid content generated, however the yield production decreases. On the other hand the higher the solvent-to-solid ratio creates the high yield yet this variables showing no impact towards two other responses. The result of this study also revealed that extraction time has no effect on all the responses.
Élaboration d’une protection anti-oxydation pour matériaux composites SiC/SiC efficace à basse température

Ce memoire presente l’etude de protections anti-oxydation (PAO) de materiaux composites SiC/SiC. Ces materiaux sont dotes de proprietes specifiques (legerete, resistance aux chocs thermiques et tenue mecanique a haute temperature) par l’association de fibres et d’une matrice SiC liees par une interphase en carbone. Neanmoins, cette interphase s’oxyde des 400°C entrainant la decohesion entre les fibres et la matrice et ainsi la perte des proprietes mecaniques. En vue d’applications dans le domaine de l’aeronautique civile, la PAO doit etre operationnelle a basse temperature (400-650°C) et sur de longues periodes (de l’ordre de plusieurs milliers d’heures). Deux types de protections ont ete proposes et etudies: (i) une protection rigide formee par traitement thermique d’un melange entre une solution de phosphate d’aluminium et de silice. La structure du revetement a ensuite ete caracterisee par RMN, DRX et MEB et mise en relation avec l’efficacite de la protection. (ii) une protection dynamique basee sur l’utilisation de verres de phosphate formules afin de presenter des caracteristiques de viscosite optimales pour la PAO. Les formulations ont ete caracterisees par analyses thermiques (ATD, ATM, HSM) et par RMN. Une demarche raisonnee a ete mise en œuvre en correlant les proprietes thermiques aux caracteristiques structurales des oxydes utilises. Ces deux revetements etudies ameliorent la duree de vie du materiau, mais sans atteindre la specification attendue. Nous concluons que la protection dynamique est plus adaptee a l’application basse temperature et proposons des voies d’amelioration.
Botnet Detection Using DNS and HTTP Traffic Analysis

To perform a large scale attack on the victim, cyber attacker usually prepares thousands if not millions of infected computers to accomplish the goal. Once the infected computers, also called botnet, are ready, they will communicate with the Command and Control (C&C) server to obtain the instruction to perform their acts. Botnet tries to disguise their communication as regular traffic by using commonly used protocols such as HTTP so that their conversation with C&C is not blocked by the firewall. This research explores botnet's footprints using both HTTP and DNS protocols and analyzes their behaviors to select the most appropriate features of HTTP and DNS protocols to be used in our classification model. The developed model has been shown to provide 86% accuracy in distinguishing botnet from benign traffic on the enterprise network.
Biofilm Producing Rhizobacteria With Multiple Plant Growth-Promoting Traits Promote Growth of Tomato Under Water-Deficit Stress

Plant growth-promoting rhizobacteria (PGPR) not only enhance plant growth but also control phytopathogens and mitigate abiotic stresses, including water-deficit stress. In this study, 21 (26.9%) rhizobacterial strains isolated from drought-prone ecosystems of Bangladesh were able to form air–liquid (AL) biofilms in the glass test tubes containing salt-optimized broth plus glycerol (SOBG) medium. Based on 16S rRNA gene sequencing, Pseudomonas chlororaphis (ESR3 and ESR15), P. azotoformans ESR4, P. poae ESR6, P. fluorescens (ESR7 and ESR25), P. gessardii ESR9, P. cedrina (ESR12, ESR16, and ESR23), P. veronii (ESR13 and ESR21), P. parafulva ESB18, Stenotrophomonas maltophilia ESR20, Bacillus cereus (ESD3, ESD21, and ESB22), B. horikoshii ESD16, B. aryabhattai ESB6, B. megaterium ESB9, and Staphylococcus saprophyticus ESD8 were identified. Fourier transform infrared spectroscopy studies showed that the biofilm matrices contain proteins, polysaccharides, nucleic acids, and lipids. Congo red binding results indicated that these bacteria produced curli fimbriae and nanocellulose-rich polysaccharides. Expression of nanocellulose was also confirmed by Calcofluor binding assays and scanning electron microscopy. In vitro studies revealed that all these rhizobacterial strains expressed multiple plant growth-promoting traits including N2 fixation, production of indole-3-acetic acid, solubilization of nutrients (P, K, and Zn), and production of ammonia, siderophores, ACC deaminase, catalases, lipases, cellulases, and proteases. Several bacteria were also tolerant to multifarious stresses such as drought, high temperature, extreme pH, and salinity. Among these rhizobacteria, P. cedrina ESR12, P. chlororaphis ESR15, and B. cereus ESD3 impeded the growth of Xanthomonas campestris pv. campestris ATCC 33913, while P. chlororaphis ESR15 and B. cereus ESD21 prevented the progression of Ralstonia solanacearum ATCC® 11696TM. In a pot experiment, tomato plants inoculated with P. azotoformans ESR4, P. poae ESR6, P. gessardii ESR9, P. cedrina ESR12, P. chlororaphis ESR15, S. maltophilia ESR20, P. veronii ESR21, and B. aryabhattai ESB6 exhibited an increased plant growth compared to the non-inoculated plants under water deficit-stressed conditions. Accordingly, the bacterial-treated plants showed a higher antioxidant defense system and a fewer tissue damages than non-inoculated plants under water-limiting conditions. Therefore, biofilm-producing PGPR can be utilized as plant growth promoters, suppressors of plant pathogens, and alleviators of water-deficit stress.
RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer

Many mutagenic processes leave characteristic imprints on cancer genomes known as mutational signatures. These signatures have been of recent interest regarding their applicability in studying processes shaping the mutational landscape of cancer. In particular, pinpointing the presence of altered DNA repair pathways can have important therapeutic implications. However, mutational signatures of DNA repair deficiencies are often hard to infer. This challenge emerges as a result of deficient DNA repair processes acting by modifying the outcome of other mutagens. Thus, they exhibit non-additive effects that are not depicted by the current paradigm for modeling mutational processes as independent signatures. To close this gap, we present RepairSig, a method that accounts for interactions between DNA damage and repair and is able to uncover unbiased signatures of deficient DNA repair processes. In particular, RepairSig was able to replace three MMR deficiency signatures previously proposed to be active in breast cancer, with just one signature strikingly similar to the experimentally derived signature. As the first method to model interactions between mutagenic processes, RepairSig is an important step towards biologically more realistic modeling of mutational processes in cancer. The source code for RepairSig is publicly available at https://github.com/ncbi/RepairSig.
Motor Sequence Learning Deficits in Idiopathic Parkinson’s Disease Are Associated With Increased Substantia Nigra Activity

Previous studies have shown that persons with Parkinson’s disease (pwPD) share specific deficits in learning new sequential movements, but the neural substrates of this impairment remain unclear. In addition, the degree to which striatal dopaminergic denervation in PD affects the cortico-striato-cerebellar motor learning network remains unknown. We aimed to answer these questions using fMRI in 16 pwPD and 16 healthy age-matched control subjects while they performed an implicit motor sequence learning task. While learning was absent in both pwPD and controls assessed with reaction time differences between sequential and random trials, larger error-rates during the latter suggest that at least some of the complex sequence was encoded. Moreover, we found that while healthy controls could improve general task performance indexed by decreased reaction times across both sequence and random blocks, pwPD could not, suggesting disease-specific deficits in learning of stimulus-response associations. Using fMRI, we found that this effect in pwPD was correlated with decreased activity in the hippocampus over time. Importantly, activity in the substantia nigra (SN) and adjacent bilateral midbrain was specifically increased during sequence learning in pwPD compared to healthy controls, and significantly correlated with sequence-specific learning deficits. As increased SN activity was also associated (on trend) with higher doses of dopaminergic medication as well as disease duration, the results suggest that learning deficits in PD are associated with disease progression, indexing an increased drive to recruit dopaminergic neurons in the SN, however unsuccessfully. Finally, we found no differences between pwPD and controls in task modulation of the cortico-striato-cerebellar network. Notably, in both groups Bayesian model selection revealed cortico-cerebellar connections modulated by the task, suggesting that despite behavioral and activation differences, the same cortico-cerebellar circuitry is recruited for implementing the motor task.
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells

During affinity maturation, germinal center (GC) B cells alternate between proliferation and so-matic hypermutation in the dark zone (DZ) and affinity-dependent selection in the light zone (LZ). This anatomical segregation imposes that the vigorous proliferation that allows clonal expansion of positively-selected GC B cells takes place ostensibly in the absence of the signals that triggered selection in the LZ, as if by “inertia. ” We find that such inertial cycles specifically require the cell cycle regulator cyclin D3. Cyclin D3 dose-dependently controls the extent to which B cells proliferate in the DZ and is essential for effective clonal expansion of GC B cells in response to strong T follicular helper (Tfh) cell help. Introduction into the Ccnd3 gene of a Burkitt lymphoma-associated gain-of-function mutation (T283A) leads to larger GCs with increased DZ proliferation and, in older mice, to clonal B cell lymphoproliferation, suggesting that the DZ inertial cell cycle program can be coopted by B cells undergoing malignant transformation.
Selective vulnerability of supragranular layer neurons in schizophrenia

Schizophrenia is one of the most wide-spread mental brain disorders with complex and largely unknown etiology. To characterize the impact of schizophrenia at a cellular level, we performed single nucleus RNA sequencing of >190,000 neurons from the dorsolateral prefrontal cortex of patients with schizophrenia and matched controls (7 vs 11, respectively). In addition, to correlate data with cortical anatomy, >100,000 neurons were analyzed topographically by immunohistochemistry in an extended cohort of cases with schizophrenia and controls (10 vs 10). Compositional analysis of RNA sequencing data revealed reduction in relative abundance across all families of GABAergic neurons and a concomitant increase in principal neurons, which was most pronounced for supragranular subtypes (layers 2-3). Moreover, supragranular subtypes of GABAergic interneurons showed most dramatic transcriptomic changes. These results were substantiated by histological analysis, which revealed a reduction in the density of calretinin, calbindin and parvalbumin GABAergic interneurons particularly in layer 2. Common effect of schizophrenia on supragranular neuronal networks was underlined by downregulation of protein processing genes and upregulation of neuronal development/plasticity genes across supragranular subtypes of principal neurons and GABAergic interneurons. In situ hybridization and spatial transcriptomics further confirmed supragranular layer neuron vulnerability, revealing complexity of schizophrenia-affected cortical circuits. These point towards general network impairment within supragranular layers being a core substrate associated with schizophrenia symptomatology.
Monocyte Chemoattractant Protein 1 Promotes VEGF-A Expression in OSCC by Activating ILK and MEK1/2 Signaling and Downregulating miR-29c

Oral squamous cell carcinoma (OSCC) is an aggressive tumor that has a poor prognosis, with high levels of local invasion and lymph node metastasis. Vascular endothelial growth factor A (VEGF-A) plays essential roles in OSCC tumor angiogenesis and metastasis. Monocyte chemoattractant protein-1 (MCP-1, CCL2) is implicated in various inflammatory conditions and pathological processes, including oral cancer. The existing evidence has failed to confirm any correlation between MCP-1 or VEGF-A expression and OSCC angiogenesis. In this study, high expression levels of MCP-1 and VEGF-A were positively correlated with disease stage in patients with OSCC. In oral cancer cells, MCP-1 increased VEGF-A expression and subsequently promoted angiogenesis; miR-29c mimic reversed MCP-1 activity. We also found that MCP-1 modulated VEGF-A expression and angiogenesis through CCR2/ILK/MEK1/2 signaling. Ex vivo results of the chick embryo chorioallantoic membrane (CAM) assay revealed the angiogenic qualities of MCP-1, with increased numbers of visible blood vessel branches. Our data suggest that MCP-1 is a new molecular therapeutic target for the inhibition of angiogenesis and metastasis in OSCC.
Tackle Epithelial-Mesenchymal Transition With Epigenetic Drugs in Cancer

Epithelial-mesenchymal Transition (EMT) is a de-differentiation process in which epithelial cells lose their epithelial properties to acquire mesenchymal features. EMT is essential for embryogenesis and wound healing but is aberrantly activated in pathological conditions like fibrosis and cancer. Tumor-associated EMT contributes to cancer cell initiation, invasion, metastasis, drug resistance and recurrence. This dynamic and reversible event is governed by EMT-transcription factors (EMT-TFs) with epigenetic complexes. In this review, we discuss recent advances regarding the mechanisms that modulate EMT in the context of epigenetic regulation, with emphasis on epigenetic drugs, such as DNA demethylating reagents, inhibitors of histone modifiers and non-coding RNA medication. Therapeutic contributions that improve epigenetic regulation of EMT will translate the clinical manifestation as treating cancer progression more efficiently.
Evaluation of a P300-Based Brain-Machine Interface for a Robotic Hand-Orthosis Control

This work presents the design, implementation, and evaluation of a P300-based brain-machine interface (BMI) developed to control a robotic hand-orthosis. The purpose of this system is to assist patients with amyotrophic lateral sclerosis (ALS) who cannot open and close their hands by themselves. The user of this interface can select one of six targets, which represent the flexion-extension of one finger independently or the movement of the five fingers simultaneously. We tested offline and online our BMI on eighteen healthy subjects (HS) and eight ALS patients. In the offline test, we used the calibration data of each participant recorded in the experimental sessions to estimate the accuracy of the BMI to classify correctly single epochs as target or non-target trials. On average, the system accuracy was 78.7% for target epochs and 85.7% for non-target trials. Additionally, we observed significant P300 responses in the calibration recordings of all the participants, including the ALS patients. For the BMI online test, each subject performed from 6 to 36 attempts of target selections using the interface. In this case, around 46% of the participants obtained 100% of accuracy, and the average online accuracy was 89.83%. The maximum information transfer rate (ITR) observed in the experiments was 52.83 bit/min, whereas that the average ITR was 18.13 bit/min. The contributions of this work are the following. First, we report the development and evaluation of a mind-controlled robotic hand-orthosis for patients with ALS. To our knowledge, this BMI is one of the first P300-based assistive robotic devices with multiple targets evaluated on people with ALS. Second, we provide a database with calibration data and online EEG recordings obtained in the evaluation of our BMI. This data is useful to develop and compare other BMI systems and test the processing pipelines of similar applications.