Miracle-dz/UniFAR-FTUs huggingface dataset:
Imaging of the Vulnerable Carotid Plaque

Panels A and B from Figure 1 are republished panels a and b from Figure 6 in the article “Imaging of the ulcerated carotid atherosclerotic plaque: a review of the literature” by V. Rafailidis et al., published in February 2017 in Insights into Imaging (DOI 10.1007/s13244-017-0543-8). Permission to republish the images has subsequently been obtained, with the request to provide a link to the Creative Commons Attribution 4.0 International License (creativecommons.org/licenses/by/4.0/).
Protein-Bound Uremic Toxins Lowering Effect of Sevelamer in Pre-Dialysis Chronic Kidney Disease Patients with Hyperphosphatemia: A Randomized Controlled Trial

P-cresyl sulfate and indoxyl sulfate are strongly associated with cardiovascular events and all-cause mortality in chronic kidney disease (CKD). This randomized controlled trial was conducted to compare the effects between sevelamer and calcium carbonate on protein-bound uremic toxins in pre-dialysis CKD patients with hyperphosphatemia. Forty pre-dialysis CKD patients with persistent hyperphosphatemia were randomly assigned to receive either 2400 mg of sevelamer daily or 1500 mg of calcium carbonate daily for 24 weeks. A significant decrease of total serum p-cresyl sulfate was observed in sevelamer therapy compared to calcium carbonate therapy (mean difference between two groups −5.61 mg/L; 95% CI −11.01 to −0.27 mg/L; p = 0.04). There was no significant difference in serum indoxyl sulfate levels (p = 0.36). Sevelamer had effects in terms of lowering fibroblast growth factor 23 (p = 0.01) and low-density lipoprotein cholesterol levels (p = 0.04). Sevelamer showed benefits in terms of retarding CKD progression. Changes in vascular stiffness were not found in this study.
Novel Synthetic Approach to Heteroatom Doped Polycyclic Aromatic Hydrocarbons: Optimizing the Bottom-Up Approach to Atomically Precise Doped Nanographenes

The success of the rational bottom-up approach to nanostructured carbon materials and the discovery of the importance of their doping with heteroatoms puts under the spotlight all synthetic organic approaches to polycyclic aromatic hydrocarbons. The construction of atomically precise heteroatom doped nanographenes has evidenced the importance of controlling its geometry and the position of the doping heteroatoms, since these parameters influence their chemical–physical properties and their applications. The growing interest towards this research topic is testified by the large number of works published in this area, which have transformed a once “fundamental research” into applied research at the cutting edge of technology. This review analyzes the most recent synthetic approaches to this class of compounds.
The Association between New World Alphasatellites and Bipartite Begomoviruses: Effects on Infection and Vector Transmission

Begomoviruses can be found in association with alphasatellites, which are capable of autonomous replication but are dependent on the helper begomovirus for systemic infection, encapsidation and vector transmission. Previous studies suggest that the presence of NW alphasatellites (genus Clecrusatellite) is associated with more severe symptoms. To better understand this interaction, we investigated the effects of two alphasatellites on infectivity, symptom development, viral DNA accumulation and vector transmission of three begomoviruses in three hosts. In tomato and Nicotiana benthamiana, all combinations were infectious. In Leonurus sibiricus, only the ToYSV/ToYSA combination was infectious. The presence of EuYMA increased symptom severity of EuYMV and ToYSV in N. benthamiana, and the presence of ToYSA was associated with more severe symptoms of ToYSV in N. benthamiana and L. sibiricus. EuYMA increased the accumulation of ToYSV in N. benthamiana but reduced the accumulation of EuYMV in tomato and of ToSRV in N. benthamiana. The presence of ToYSA decreased the accumulation of ToYSV in N. benthamiana and L. sibiricus. ToYSA negatively affected transmission of ToSRV by Bemisia tabaci MEAM1. Together, our results indicate that NW alphasatellites can interact with different begomoviruses, increasing symptom severity and interfering in the transmission of the helper begomovirus. Understanding this interaction is important as it may affect the emergence of diseases caused by begomovirus–alphasatellite complexes in the field.
ELTD1 Activation Induces an Endothelial-EMT Transition to a Myofibroblast Phenotype

ELTD1 is expressed in endothelial and vascular smooth muscle cells and has a role in angiogenesis. It has been classified as an adhesion GPCR, but as yet, no ligand has been identified and its function remains unknown. To establish its role, ELTD1 was overexpressed in endothelial cells. Expression and consequently ligand independent activation of ELTD1 results in endothelial-mesenchymal transistion (EndMT) with a loss of cell-cell contact, formation of stress fibres and mature focal adhesions and an increased expression of smooth muscle actin. The effect was pro-angiogenic, increasing Matrigel network formation and endothelial sprouting. RNA-Seq analysis after the cells had undergone EndMT revealed large increases in chemokines and cytokines involved in regulating immune response. Gene set enrichment analysis of the data identified a number of pathways involved in myofibroblast biology suggesting that the endothelial cells had undergone a type II EMT. This type of EMT is involved in wound repair and is closely associated with inflammation implicating ELTD1 in these processes.
The Bark of Picea abies L., a Waste from Sawmill, as a Source of Valuable Compounds: Phytochemical Investigations and Isolation of a Novel Pimarane and a Stilbene Derivative

In this work, the sawmill waste from Picea abies debarking was considered as source of valuable phytoconstituents. The extraction was performed using different ethanol/water mixtures, and characterization was obtained by LC-MSn. This latter revealed flavonoid glycosides, lignans, and procyanidins. Extraction with organic solvents (dichloromethane and methanol) and chromatographic separations of the obtained extracts by silica column followed by semi-preparative HPLC led to the isolation of polyphenols and terpenoids such as 21α-metoxy-serrat-14-en-3-one, 21α-hydroxy-serrat-14-en-3-one, pinoresinol, dehydroabietic acid, 15-hydroxy-dehydroabietic acid, 7-oxo-dehydroabietic acid, pimaric acid, 9β-pimara-7,15-dien-19-ol, 13-epi-manoyl oxide, taxifolin-3′-O-glucopyranoside, trans-astringin, and piceasides. Piceaside V and 9β-pimara-7-keto-19β-olide, two novel compounds identified for the first time in P. abies bark, were isolated, and their structures were elucidated using 1D and 2D NMR and MS techniques. The polyphenolic composition of the methanolic portion was also investigated using LC-MSn, and the piceaside content was estimated. To assess the antioxidant activity of main constituents, semi-preparative HPLC was performed on the methanolic extract, and the obtained fractions were assayed by using the DPPH test. Overall, this work shows the potential usefulness of P. abies bark as a source of valuable phytochemicals.
Proteomics analysis reveals digestion-resistant proteins from colostrum are associated with inflammatory and cytotoxic responses in intestinal epithelial cells.

BACKGROUND Though human milk feeding reduces the risk of necrotizing enterocolitis (NEC) in preterm infants compared with formula feeding, the exact risk reduction mechanism remains unknown. As NEC occurs at the distal small intestines where digestion has occurred, we applied proteomics to examine the extent to which colostrum proteins survive simulated infant in vitro digestion, and thus have potential to exert biological function. METHODS Ten preterm colostrum samples were left undigested or in vitro-digested, and lipopolysaccharide (LPS) binding protein, soluble cluster of differentiation 14, and tumor necrosis factor (TNF) receptors I and II were measured using ELISA in all undigested and in vitro-digested samples. Fully differentiated Caco-2 cells were exposed to digested colostrum samples prior to stimulation with LPS, TNF, or no stimulation. Inflammation (interleukin 8) and cytotoxicity (lactate dehydrogenase) were measured. Proteomic analyses of undigested and in vitro-digested samples were done using mass spectrometry. RESULTS We found that most proteins in colostrum are significantly, if not completely, degraded following in vitro digestion. We found select individual and combination digestion-resistant proteins that were positively correlated with LPS- and TNF-induced inflammation. CONCLUSIONS These results indicate the importance of considering the extent to which specific dietary compounds survive digestion to reach their site of claimed action (distal intestines), and that some digestion-resistant proteins may be contributing towards "low grade" inflammation that is necessary to promote intestinal growth and maturation during early infancy. This work provides the most detailed understanding of human milk protein degradation with simulated infant in vitro digestion to date. This article is protected by copyright. All rights reserved.
Gut Reactions: How Far Are We from Understanding and Manipulating the Microbiota Complexity and the Interaction with Its Host? Lessons from Autism Spectrum Disorder Studies

Autism is a group of neurodevelopmental disorders, characterized by early onset difficulties in social communication and restricted, repetitive behaviors and interests. It is characterized by familial aggregation, suggesting that genetic factors play a role in disease development, in addition to developmentally early environmental factors. Here, we review the role of the gut microbiome in autism, as it has been characterized in case-control studies. We discuss how methodological differences may have led to inconclusive or contradictory results, even though a disproportion between harmful and beneficial bacteria is generally described in autism. Furthermore, we review the studies concerning the effects of gut microbial-based and dietary interventions on autism symptoms. Also, in this case, the results are not comparable due to the lack of standardized methods. Therefore, autism-specific microbiome signatures and, consequently, possible microbiome-oriented interventions are far from being recognized. We argue that a multi-omic longitudinal implementation may be useful to study metabolic changes connected to microbiome changes.
Locality-Based Cache Management and Warp Scheduling for Reducing Cache Contention in GPU

GPGPUs has gradually become a mainstream acceleration component in high-performance computing. The long latency of memory operations is the bottleneck of GPU performance. In the GPU, multiple threads are divided into one warp for scheduling and execution. The L1 data caches have little capacity, while multiple warps share one small cache. That makes the cache suffer a large amount of cache contention and pipeline stall. We propose Locality-Based Cache Management (LCM), combined with the Locality-Based Warp Scheduling (LWS), to reduce cache contention and improve GPU performance. Each load instruction can be divided into three types according to locality: only used once as streaming data locality, accessed multiple times in the same warp as intra-warp locality, and accessed in different warps as inter-warp data locality. According to the locality of the load instruction, LWS applies cache bypass to the streaming locality request to improve the cache utilization rate, extend inter-warp memory request coalescing to make full use of the inter-warp locality, and combine with the LWS to alleviate cache contention. LCM and LWS can effectively improve cache performance, thereby improving overall GPU performance. Through experimental evaluation, our LCM and LWS can obtain an average performance improvement of 26% over baseline GPU.
Potential Novel Thioether-Amide or Guanidine-Linker Class of SARS-CoV-2 Virus RNA-Dependent RNA Polymerase Inhibitors Identified by High-Throughput Virtual Screening Coupled to Free-Energy Calculations

SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new pathogen from the family of Coronaviridae that caused a global pandemic of COVID-19 disease. In the absence of effective antiviral drugs, research of novel therapeutic targets such as SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) becomes essential. This viral protein is without a human counterpart and thus represents a unique prospective drug target. However, in vitro biological evaluation testing on RdRp remains difficult and is not widely available. Therefore, we prepared a database of commercial small-molecule compounds and performed an in silico high-throughput virtual screening on the active site of the SARS-CoV-2 RdRp using ensemble docking. We identified a novel thioether-amide or guanidine-linker class of potential RdRp inhibitors and calculated favorable binding free energies of representative hits by molecular dynamics simulations coupled with Linear Interaction Energy calculations. This innovative procedure maximized the respective phase-space sampling and yielded non-covalent inhibitors representing small optimizable molecules that are synthetically readily accessible, commercially available as well as suitable for further biological evaluation and mode of action studies.
A Time Division Multiplexing Inspired Lightweight Soft Exoskeleton for Hip and Ankle Joint Assistance

Exoskeleton robots are frequently applied to augment or assist the user’s natural motion. Generally, each assisted joint corresponds to at least one specific motor to ensure the independence of movement between joints. This means that as there are more joints to be assisted, more motors are required, resulting in increasing robot weight, decreasing motor utilization, and weakening exoskeleton robot assistance efficiency. To solve this problem, the design and control of a lightweight soft exoskeleton that assists hip-plantar flexion of both legs in different phases during a gait cycle with only one motor is presented in this paper. Inspired by time-division multiplexing and the symmetry of walking motion, an actuation scheme that uses different time-periods of the same motor to transfer different forces to different joints is formulated. An automatic winding device is designed to dynamically change the loading path of the assistive force at different phases of the gait cycle. The system is designed to assist hip flexion and plantar flexion of both legs with only one motor, since there is no overlap between the hip flexion movement and the toe-offs movement of the separate legs during walking. The weight of the whole system is only 2.24 kg. PD iterative control is accomplished by an algorithm that utilizes IMUs attached on the thigh recognizing the maximum hip extension angle to characterize toe-offs indirectly, and two load cells to monitor the cable tension. In the study of six subjects, muscle fatigue of the rectus femoris, vastus lateralis, gastrocnemius and soleus decreased by an average of 14.69%, 6.66%, 17.71%, and 8.15%, respectively, compared to scenarios without an exoskeleton.
Methacryloyl-GlcNAc Derivatives Copolymerized with Dimethacrylamide as a Novel Antibacterial and Biocompatible Coating

Improving medical implants with functional polymer coatings is an effective way to further improve the level of medical care. Antibacterial and biofilm-preventing properties are particularly desirable in the area of wound healing, since there is a generally high risk of infection, often with a chronic course in the case of biofilm formation. To prevent this we here report a polymeric design of polymer-bound N-acetyl-glucosamine-oligoethylene glycol residues that mimic a cationic, antibacterial, and biocompatible chitosan surface. The combination of easy to use, crosslinkable, thin, potentially 3D-printable polymethacrylate layering with antibacterial and biocompatible functional components will be particularly advantageous in the medical field to support a wide range of implants as well as wound dressings. Different polymers containing a N-acetylglucosamine-methacryloyl residue with oligoethylene glycol linkers and a methacryloyl benzophenone crosslinker were synthesized by free radical polymerization. The functional monomers and corresponding polymers were characterized by 1H, 13C NMR, and infrared (IR) spectroscopy. The polymers showed no cytotoxic or antiadhesive effects on fibroblasts as demonstrated by extract and direct contact cell culture methods. Biofilm formation was reduced by up to 70% and antibacterial growth by 1.2 log, particularly for the 5% GlcNAc-4EG polymer, as observed for Escherichia coli and Staphylococcus aureus as clinically relevant Gram-negative and Gram-positive model pathogens.
Robotic Spot Spraying of Harrisia Cactus (Harrisia martinii) in Grazing Pastures of the Australian Rangelands

Harrisia cactus, Harrisia martinii, is a serious weed affecting hundreds of thousands of hectares of native pasture in the Australian rangelands. Despite the landmark success of past biological control agents for the invasive weed and significant investment in its eradication by the Queensland Government (roughly $156M since 1960), it still takes hold in the cooler rangeland environments of northern New South Wales and southern Queensland. In the past decade, landholders with large infestations in these locations have spent approximately $20,000 to $30,000 per annum on herbicide control measures to reduce the impact of the weed on their grazing operations. Current chemical control requires manual hand spot spraying with high quantities of herbicide for foliar application. These methods are labour intensive and costly, and in some cases inhibit landholders from performing control at all. Robotic spot spraying offers a potential solution to these issues, but existing solutions are not suitable for the rangeland environment. This work presents the methods and results of an in situ field trial of a novel robotic spot spraying solution, AutoWeed, for treating harrisia cactus that (1) more than halves the operation time, (2) can reduce herbicide usage by up to 54% and (3) can reduce the cost of herbicide by up to $18.15 per ha compared to the existing hand spraying approach. The AutoWeed spot spraying system used the MobileNetV2 deep learning architecture to perform real time spot spraying of harrisia cactus with 97.2% average recall accuracy and weed knockdown efficacy of up to 96%. Experimental trials showed that the AutoWeed spot sprayer achieved the same level of knockdown of harrisia cactus as traditional hand spraying in low, medium and high density infestations. This work represents a significant step forward for spot spraying of weeds in the Australian rangelands that will reduce labour and herbicide costs for landholders as the technology sees more uptake in the future.
A Low Level of NaCl Stimulates Plant Growth by Improving Carbon and Sulfur Assimilation in Arabidopsis thaliana

High-salinity stress represses plant growth by inhibiting various metabolic processes. In contrast to the well-studied mechanisms mediating tolerance to high levels of salt, the effects of low levels of salts have not been well studied. In this study, we examined the growth of Arabidopsis thaliana plants under different NaCl concentrations. Interestingly, both shoot and root biomass increased in the presence of 5 mM NaCl, whereas more than 10 mM NaCl decreased plant biomass. To clarify the biological mechanism by which a low level of NaCl stimulated plant growth, we analyzed element accumulation in plants grown under different NaCl concentrations. In addition to the Na and Cl contents, C, S, Zn, and Cu contents were increased under 5 mM NaCl in shoots; this was not observed at higher NaCl concentrations. Adverse effects of high salinity, such as decreased levels of nitrate, phosphate, sulfate, and some cations, did not occur in the presence of 5 mM NaCl. An increase in C was possibly attributed to increased photosynthesis supported by Cl, Zn, and Cu, which also increased in shoots after NaCl application. Salt stress-responsive gene expression was enhanced under 20 mM NaCl but not at lower doses. Among the S metabolites analyzed, cysteine (Cys) was increased by 5 mM NaCl, suggesting that S assimilation was promoted by this dose of NaCl. These results indicate the usefulness of NaCl for plant growth stimulation.
FOXL2C134W: much ado about something!†

Recent studies have suggested that the unique FOXL2C134W mutation, which is pathognomonic for adult granulosa cell tumours of the ovary, is a tumour suppressor gene. In a recent issue of The Journal of Pathology, a detailed study by Pilsworth et al seeks to rebut the proposition that the FOXL2C134W mutation, which uniquely characterises adult granulosa cell tumours of the ovary, leads to reduced transcript levels with the implication that FOXL2 is a tumour suppressor gene. The study provides compelling evidence that both wild‐type and mutant FOXL2 transcripts and protein are expressed at equivalent levels. In the context of other recent studies, one is drawn to the conclusion that FOXL2C134W is a gain‐of‐function mutation whose impact is mediated through enhanced interactions with the SMAD transcription factor complex. © 2021 The Pathological Society of Great Britain and Ireland.
Therapeutic Potential of Various Plant-Based Fibers to Improve Energy Homeostasis via the Gut Microbiota

Obesity is due in part to increased consumption of a Western diet that is low in dietary fiber. Conversely, an increase in fiber supplementation to a diet can have various beneficial effects on metabolic homeostasis including weight loss and reduced adiposity. Fibers are extremely diverse in source and composition, such as high-amylose maize, β-glucan, wheat fiber, pectin, inulin-type fructans, and soluble corn fiber. Despite the heterogeneity of dietary fiber, most have been shown to play a role in alleviating obesity-related health issues, mainly by targeting and utilizing the properties of the gut microbiome. Reductions in body weight, adiposity, food intake, and markers of inflammation have all been reported with the consumption of various fibers, making them a promising treatment option for the obesity epidemic. This review will highlight the current findings on different plant-based fibers as a therapeutic dietary supplement to improve energy homeostasis via mechanisms of gut microbiota.
An Immunoenzymatic Method for the Determination of Ochratoxin A in Biological Liquids (Colostrum and Cow’s Milk)

Ochratoxins are mycotoxins that have been extensively studied lately due to the multiple toxic effects such as nephrotoxicity, hepatotoxicity, and carcinogenicity. These toxins contaminate plant and animal foods and after ingestion they reach into body fluids. The method of competitive direct enzyme immunoassay, in the solid phase, was validated through the determination of specific parameters (performance, linearity, recovery percentage, limit of detection, limit of quantification). The validated method was used to determine ochratoxin A in colostrum and cow’s milk. The method applied for the determination of ochratoxin A was linear for the concentration range of 0.0–0.5 ng/mL, the value for the regression coefficient (r) was 0.9838. Ochratoxin A was present in 91.67% of the colostrum and in 93.33% of cow’s milk samples. The linearity of the method, demonstrated for very low concentrations of analyte, the detection limit as well as the limit of quantification recommend the method for the determinations of micro-pollutants from foods, including biological fluids.