Miracle-dz/UniFAR-FTUs huggingface dataset:
Graph Processing on FPGAs: Taxonomy, Survey, Challenges

Graph processing has become an important part of various areas, such as machine learning, computational sciences, medical applications, social network analysis, and many others. Various graphs, for example web or social networks, may contain up to trillions of edges. The sheer size of such datasets, combined with the irregular nature of graph processing, poses unique challenges for the runtime and the consumed power. Field Programmable Gate Arrays (FPGAs) can be an energy-efficient solution to deliver specialized hardware for graph processing. This is reflected by the recent interest in developing various graph algorithms and graph processing frameworks on FPGAs. To facilitate understanding of this emerging domain, we present the first survey and taxonomy on graph computations on FPGAs. Our survey describes and categorizes existing schemes and explains key ideas. Finally, we discuss research and engineering challenges to outline the future of graph computations on FPGAs.
Bicyclic Pyrrolidine-Isoxazoline γ Amino Acid: A Constrained Scaffold for Stabilizing α-Turn Conformation in Isolated Peptides

Unnatural amino acids have tremendously expanded the folding possibilities of peptides and peptide mimics. While α,α-disubstituted and β-amino acids are widely studied, γ-derivatives have been less exploited. Here we report the conformational study on the bicyclic unnatural γ amino acid, 4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-3-carboxylic acid 1. In model peptides, the (+)-(3aR6aS)-enantiomer is able to stabilize α-turn conformation when associated to glycine, as showed by 1H-NMR, FT-IR, and circular dichroism experiments, and molecular modeling studies. α-turn is a structural motif occurring in many biologically active protein sites, although its stabilization on isolated peptides is quite uncommon. Our results make the unnatural γ-amino acid 1 of particular interest for the development of bioactive peptidomimetics.
Estimating Physical Activity in Children Aged 8–11 Years Using Accelerometry: Contributions From Fundamental Movement Skills and Different Accelerometer Placements

Accelerometers are widely used to assess physical activity, but it is unclear how effective accelerometers are in capturing fundamental movement skills in children. This study examined the energy expenditure during different physical activities (PA) and calibrated triaxial accelerometry, worn at the wrist, waist and ankle, during children’s PA with attention to object control movement skills and cycling. Thirty children (14 girls) aged 8 to 11 years wore a GENEActiv accelerometer on their non-dominant wrist, dominant wrist, waist and ankle. Children undertook eight, 5-min bouts of activity comprising being lay supine, playing with Lego, slow walking, medium walking, medium paced running, overarm throwing and catching, instep passing a football and cycling at 35 W. VO2 was assessed concurrently using indirect calorimetry. Indirect calorimetry indicated that being lay supine and playing with Lego were classified as sedentary in nature (<1.5 METs), slow paced walking, medium placed walking and throwing and catching were classified as light (1.51–2.99 METs) and running, cycling and instep passing were classified as moderate intensity (>3 METs). ROC curve analysis indicated that discrimination of sedentary activity was excellent for all placements although the ankle performed better than other locations. This pattern was replicated for moderate physical activity (MPA) where the ankle performed better than other locations. Data were reanalyzed removing cycling from the data set. When this analysis was undertaken discrimination of sedentary activity remained excellent for all locations. For MPA discrimination of activity was considered good for waist and ankle placement and fair for placement on either wrist. The current study is the first to quantify energy expenditure in object control fundamental movement skills via indirect calorimetry in children aged 8–11 years whilst also calibrating GENEActiv accelerometers worn at four body locations. Results suggest throwing and catching is categorized as light intensity and instep kicking a football moderate intensity, resulting in energy expenditure equivalent to slow or medium paced walking or cycling and running, respectively. Ankle worn accelerometry appears to provide the most suitable wear location to quantify MPA including ambulatory activity, object control skills and cycling, in children aged 8–11 years.
Interactions Between Natural Herbicides and Lipid Bilayers Mimicking the Plant Plasma Membrane

Natural phytotoxic compounds could become an alternative to traditional herbicides in the framework of sustainable agriculture. Nonanoic acid, sarmentine and sorgoleone are such molecules extracted from plants and able to inhibit the growth of various plant species. However, their mode of action is not fully understood and despite clues indicating that they could affect the plant plasma membrane, molecular details of such phenomenon are lacking. In this paper, we investigate the interactions between those natural herbicides and artificial bilayers mimicking the plant plasma membrane. First, their ability to affect lipid order and fluidity is evaluated by means of fluorescence measurements. It appears that sorgoleone has a clear ordering effect on lipid bilayers, while nonanoic acid and sarmentine induce no or little change to these parameters. Then, a thermodynamic characterization of interactions of each compound with lipid vesicles is obtained with isothermal titration calorimetry, and their respective affinity for bilayers is found to be ranked as follows: sorgoleone > sarmentine > nonanoic acid. Finally, molecular dynamics simulations give molecular details about the location of each compound within a lipid bilayer and confirm the rigidifying effect of sorgoleone. Data also suggest that mismatch in alkyl chain length between nonanoic acid or sarmentine and lipid hydrophobic tails could be responsible for bilayer destabilization. Results are discussed regarding their implications for the phytotoxicity of these compounds.
Brain Segmentation From Computed Tomography of Healthy Aging and Geriatric Concussion at Variable Spatial Resolutions

When properly implemented and processed, anatomic T1-weighted magnetic resonance imaging (MRI) can be ideal for the noninvasive quantification of white matter (WM) and gray matter (GM) in the living human brain. Although MRI is more suitable for distinguishing GM from WM than computed tomography (CT), the growing clinical use of the latter technique has renewed interest in head CT segmentation. Such interest is particularly strong in settings where MRI is unavailable, logistically unfeasible or prohibitively expensive. Nevertheless, whereas MRI segmentation is a sophisticated and technically-mature research field, the task of automatically classifying soft brain tissues from CT remains largely unexplored. Furthermore, brain segmentation methods for MRI hold considerable potential for adaptation and application to CT image processing. Here we demonstrate this by combining probabilistic, atlas-based classification with topologically-constrained tissue boundary refinement to delineate WM, GM and cerebrospinal fluid (CSF) from head CT images. The feasibility and utility of this approach are revealed by comparison of MRI-only vs. CT-only segmentations in geriatric concussion victims with both MRI and CT scans. Comparison of the two segmentations yields mean Sørensen-Dice coefficients of 85.5 ± 4.6% (WM), 86.7 ± 5.6% (GM) and 91.3 ± 2.8% (CSF), as well as average Hausdorff distances of 3.76 ± 1.85 mm (WM), 3.43 ± 1.53 mm (GM) and 2.46 ± 1.27 mm (CSF). Bootstrapping results suggest that the segmentation approach is sensitive enough to yield WM, GM and CSF volume estimates within ~5%, ~4%, and ~3% of their MRI-based estimates, respectively. To our knowledge, this is the first 3D segmentation approach for CT to undergo rigorous within-subject comparison with high-resolution MRI. Results suggest that (1) standard-quality CT allows WM/GM/CSF segmentation with reasonable accuracy, and that (2) the task of soft brain tissue classification from CT merits further attention from neuroimaging researchers.
Mountains as Evolutionary Arenas: Patterns, Emerging Approaches, Paradigm Shifts, and Their Implications for Plant Phylogeographic Research in the Tibeto-Himalayan Region

Recently, the “mountain-geobiodiversity hypothesis” (MGH) was proposed as a key concept for explaining the high levels of biodiversity found in mountain systems of the Tibeto-Himalayan region (THR), which comprises the Qinghai–Tibetan Plateau, the Himalayas, and the biodiversity hotspot known as the “Mountains of Southwest China” (Hengduan Mountains region). In addition to the MGH, which covers the entire life span of a mountain system, a complementary concept, the so-called “flickering connectivity system” (FCS), was recently proposed for the period of the Quaternary. The FCS focuses on connectivity dynamics in alpine ecosystems caused by the drastic climatic changes during the past ca. 2.6 million years, emphasizing that range fragmentation and allopatric speciation are not the sole factors for accelerated evolution of species richness and endemism in mountains. I here provide a review of the current state of knowledge concerning geological uplift, Quaternary glaciation, and the main phylogeographic patterns (“contraction/recolonization,” “platform refugia/local expansion,” and “microrefugia”) of seed plant species in the THR. In addition, I make specific suggestions as to which factors future avenues of phylogeographic research should take into account based on the fundamentals presented by the MGH and FCS, and associated complementary paradigm shifts.
Elevated Plasma microRNA-105-5p Level in Patients With Idiopathic Parkinson’s Disease: A Potential Disease Biomarker

Parkinson’s disease (PD) is the second most common neurodegenerative disease, which still lacks a biomarker to aid in diagnosis and to differentiate diagnosis at the early stage of the disease. microRNAs (miRNAs) are small and evolutionary conserved non-coding RNAs that are involved in post-transcriptional gene regulation. Several miRNAs have been proposed as potential biomarkers in several diseases. In the present study, we screened miRNAs using a network vulnerability analysis, to evaluate their potential as PD biomarkers. We first extracted miRNAs that were differentially expressed between PD and healthy controls (HC) samples. Then we constructed the PD-specific miRNA-mRNA network and screened miRNA biomarkers using a new bioinformatics model. With this model, we identified miR-105-5p as a putative biomarker for PD. Moreover, we measured miR-105-5p levels in the plasma of patients with idiopathic PD (IPD) (n = 319), neurological disease controls (NDC, n = 305) and HC (n = 273) using reverse transcription real-time quantitative PCR (RT-qPCR). Our data clearly demonstrated that the plasma miR-105-5p level in IPD patients was significantly higher than those of HC (251%, p < 0.001) and NDC (347%, p < 0.001). There was no significant difference in miR-105-5p expression between IPD patients with or without anti-PD medications. Interestingly, we found that the plasma miR-105-5p expression level may be able to differentiate IPD from parkinsonian syndrome, essential tremor and other neurodegenerative diseases. We believe that a change in the plasma miR-105-5p level is a potential biomarker for IPD.
Scutellarin Exerts Hypoglycemic and Renal Protective Effects in db/db Mice via the Nrf2/HO-1 Signaling Pathway

This study investigated the hypoglycemic and renal protective effects of scutellarin (SCU) in db/db mice and elucidated the underlying mechanisms. The oral administration of metformin hydrochloride (Met) at 120 mg/kg and SCU at 25, 50, and 100 mg/kg over an eight-week period had hypoglycemic effects, demonstrated by decreases in body weight, blood glucose, food and water intake, and glycated hemoglobin activity and by augmented insulin levels and pyruvate kinase activity in the serum of db/db mice. SCU alleviated dyslipidemia by decreasing the levels of triglycerides and total cholesterol and enhancing the levels of high-density lipoprotein cholesterol in the serum of db/db mice. SCU reversed the overexpression of mRNA of renal damage markers (receptor for advanced glycation end products, neutrophil gelatinase-associated lipocalin, and kidney injury molecule 1), macrophage marker CD11b, and T cell marker CD3 in kidney of db/db mice. Pathological examination confirmed that SCU improved the organ structures of hyperglycemia-damaged livers, kidneys, and pancreas islets. Antibody array assay and enzyme-linked immunosorbent assay were combined to screen and analyze the regulatory effects of SCU on inflammatory factors and oxidative enzymes. SCU exerted anti-inflammatory effects by inhibiting the levels of proinflammatory cytokines (glycogen synthase kinase, intercellular adhesion molecule 2, and interleukin 1β and 2) and promoting anti-inflammatory cytokines (interleukin 4). SCU decreased the reactive oxygen species and malondialdehyde concentrations and increased the activity levels of antioxidative enzymes (superoxide dismutase, glutathione peroxidase, and catalase) in serum and kidneys. Furthermore, SCU upregulated the expression of nuclear factor erythroid 2-related factor 2 (Nrf2), which in turn improved heme oxygenase 1 (HO-1), superoxide dismutase 1 and 2, and catalase expression levels in kidneys. The study showed that SCU has at least partial hypoglycemic and renal protective effects in db/db mice, and the mechanism is the modulation of the Nrf2/HO-1 signaling pathway.
Attention to Monocular Images Bias Binocular Rivalry

When monocular images cannot be fused, perception alternates between the two (or more) possible images. This phenomenon, binocular rivalry (BR), is driven by the physical properties of the stimuli (size, contrast, spatial frequency, etc.) but it can also be modulated by attention to features of one of the rival stimuli (Chong et al., 2005; Dieter et al., 2016) and by attentional demands independent of the BR assessment (Paffen et al., 2008). Instead of the perceptually demanding tasks previously used to bias BR, we designed a simple counting task. We monocularly presented a number of trials (around 10 min) with a set of symbols and asked participants to count them. We found that after this task, dominance durations decreased for the unattended channel, and did not change for the attended channel. The results parallel those of Paffen et al. (2008) and square nicely with Levelt’s second proposition, suggesting that the counting task effectively increased the sensibility of one channel which led to increased strength of the images presented to that channel. Alternatively, the results could be explained assuming that the non-attended channel was inhibited during the counting task, and the inhibition was carried over to the BR task.
GABA-Producing Natural Dairy Isolate From Artisanal Zlatar Cheese Attenuates Gut Inflammation and Strengthens Gut Epithelial Barrier in vitro

Probiotic bacteria are recognized for their health-promoting properties, including maintenance of gut epithelial integrity and host immune system homeostasis. Taking into account the beneficial health-promoting effects of GABA, the presence of the gadB gene, encoding glutamate decarboxylase that converts L-glutamate to GABA, was analyzed in Lactic Acid Bacteria (LAB) natural isolates from Zlatar cheese. The results revealed that 52% of tested Lactobacillus spp. and 8% of Lactococcus spp. isolates harbor the gadB gene. Qualitative and quantitative analysis of GABA production performed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) revealed the highest GABA production by Lactobacillus brevis BGZLS10-17. Since high GABA-producing LAB natural isolates are the most valuable source of naturally produced GABA, the probiotic properties of BGZLS10-17 were characterized. This study demonstrated high adhesion of BGZLS10-17 strain to Caco-2 cells and the ability to decrease the adhesion of Escherichia coli ATCC25922 and Salmonella enterica C29039. Treatment of differentiated Caco-2 cells monolayer with BGZLS10-17 supernatant containing GABA alleviated inflammation (production of IL-8) caused by IL-1β and significantly stimulated the expression of tight junction proteins (zonulin, occludin, and claudin 4), as well as the expression of TGF-β cytokine leading to the conclusion that immunosuppression and strengthening the tight junctions can have significant role in the maintenance of intestinal epithelial barrier integrity. Taken together the results obtained in this study support the idea that using of GABA producing BGZLS10-17 probiotic strain could be a good strategy to modulate immunological response in various inflammatory diseases, and at the same time, it could be a good candidate for adjunct starter culture for production of GABA-enriched dairy foods and beverages offering new perspectives in designing the novel functional foods.
Contribution of Cytokines to Tissue Damage During Human Respiratory Syncytial Virus Infection

The human respiratory syncytial virus (hRSV) remains one of the leading pathogens causing acute respiratory tract infections (ARTIs) in children younger than 2 years old, worldwide. Hospitalizations during the winter season due to hRSV-induced bronchiolitis and pneumonia increase every year. Despite this, there are no available vaccines to mitigate the health and economic burden caused by hRSV infection. The pathology caused by hRSV induces significant damage to the pulmonary epithelium, due to an excessive inflammatory response at the airways. Cytokines are considered essential players for the establishment and modulation of the immune and inflammatory responses, which can either be beneficial or harmful for the host. The deleterious effect observed upon hRSV infection is mainly due to tissue damage caused by immune cells recruited to the site of infection. This cellular recruitment takes place due to an altered profile of cytokines secreted by epithelial cells. As a result of inflammatory cell recruitment, the amounts of cytokines, such as IL-1, IL-6, IL-10, and CCL5 are further increased, while IL-10 and IFN-γ are decreased. However, additional studies are required to elicit the mediators directly associated with hRSV damage entirely. In addition to the detrimental induction of inflammatory mediators in the respiratory tract caused by hRSV, reports indicating alterations in the central nervous system (CNS) have been published. Indeed, elevated levels of IL-6, IL-8 (CXCL8), CCL2, and CCL4 have been reported in cerebrospinal fluid from patients with severe bronchiolitis and hRSV-associated encephalopathy. In this review article, we provide an in-depth analysis of the role of cytokines secreted upon hRSV infection and their potentially harmful contribution to tissue damage of the respiratory tract and the CNS.
Lung Surfactant Lipids Provide Immune Protection Against Haemophilus influenzae Respiratory Infection

Non-typeable Haemophilus influenzae (NTHi) causes persistent respiratory infections in patients with chronic obstructive pulmonary disease (COPD), probably linked to its capacity to invade and reside within pneumocytes. In the alveolar fluid, NTHi is in contact with pulmonary surfactant, a lipoprotein complex that protects the lung against alveolar collapse and constitutes the front line of defense against inhaled pathogens and toxins. Decreased levels of surfactant phospholipids have been reported in smokers and patients with COPD. The objective of this study was to investigate the effect of surfactant phospholipids on the host-pathogen interaction between NTHi and pneumocytes. For this purpose, we used two types of surfactant lipid vesicles present in the alveolar fluid: (i) multilamellar vesicles (MLVs, > 1 μm diameter), which constitute the tensioactive material of surfactant, and (ii) small unilamellar vesicles (SUVs, 0.1 μm diameter), which are generated after inspiration/expiration cycles, and are endocytosed by pneumocytes for their degradation and/or recycling. Results indicated that extracellular pulmonary surfactant binds to NTHi, preventing NTHi self-aggregation and inhibiting adhesion of NTHi to pneumocytes and, consequently, inhibiting NTHi invasion. In contrast, endocytosed surfactant lipids, mainly via the scavenger receptor SR-BI, did not affect NTHi adhesion but inhibited NTHi invasion by blocking bacterial uptake in pneumocytes. This blockade was made possible by inhibiting Akt phosphorylation and Rac1 GTPase activation, which are signaling pathways involved in NTHi internalization. Administration of the hydrophobic fraction of lung surfactant in vivo accelerated bacterial clearance in a mouse model of NTHi pulmonary infection, supporting the notion that the lipid component of lung surfactant protects against NTHi infection. These results suggest that alterations in surfactant lipid levels in COPD patients may increase susceptibility to infection by this pathogen.
Involvement of the Dectin-1 Receptor upon the Effector Mechanisms of Human Phagocytic Cells against Paracoccidioides brasiliensis

Paracoccidioidomycosis (PCM), a systemic mycosis endemic in Latin America, occurs after inhalation of mycelial components of Paracoccidioides spp. When the fungus reaches the lungs and interacts with the alveolar macrophages and other cells, phagocytic cells such as neutrophils and monocytes are immediately recruited to the injured site. The interaction between surface molecules of pathogens and homologous receptors, present on the surface membrane of phagocytes, modulates the innate immune cell activation. Studies have shown the importance of fungal recognition by the Dectin-1 receptor, which can induce a series of cellular protective responses against fungi. The objective of the present study was to evaluate Dectin-1 receptor expression and the effector mechanisms of human monocytes and neutrophils activated or not with different cytokines, such as IFN-γ, TNF-α, and GM-CSF, followed by the challenge with Paracoccidioides brasiliensis (P. brasiliensis or Pb265). Therefore, analysis of Dectin-1 receptor expression was done by flow cytometry whereas the effector mechanisms were evaluated by fungal recovery by colony-forming unit (CFU) counting and hydrogen peroxide (H2O2) production. Our results showed that, after treatment with IFN-γ, TNF-α, and GM-CSF and challenge with Pb265, cells, especially monocytes, demonstrated an increase in Dectin-1 expression. Both types of cells treated with the cytokines exhibited a decreased fungal recovery and, conversely, an increased production of H2O2. However, when cultures were treated with an anti-Dectin-1 monoclonal antibody, to block the P. brasiliensis binding, a decrease in H2O2 production and an increase in fungal recovery were detected. This effect was observed in all cultures treated with the specific monoclonal antibody. These results show the involvement of the Dectin-1 receptor in fungal recognition and its consequent participation in the induction of the killing mechanisms against P. brasiliensis.