Miracle-dz/UniFAR-FTUs huggingface dataset:
On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions

Many ligands simultaneously interact with multiple protein chains in quaternary structure (QS). However, a significant number of previous studies on template-based modeling of protein-ligand interactions were based on monomeric structure (MS), which may suffer from incomplete binding information. The defects of using MS rather than QS have not been systematically studied before. In this work, based on molecular docking experiments and binding free energy estimations, we performed a large-scale comparison of the protein-ligand interactions in both forms of structures. We found that 1) about 18.6 percent biologically relevant ligands bind multiple chains in QS simultaneously. 2) For more than 95 percent complexes with multiple chains involved in the interactions, the binding free energy is lower for the QS form than the MS form. 3) For over 70 percent complexes with multi-chain binding pockets, docking with QS yields more accurate ligand conformations than with MS. While for about 1.82 percent complexes, accurate docking conformations were obtained by MS. Based on this work, it is encouraged to make use of QS rather than MS in future studies on protein-ligand interactions.
The Effects of Cannabidiol and Prognostic Role of TRPV2 in Human Endometrial Cancer

Several studies support, both in vitro and in vivo, the anti-cancer effects of cannabidiol (CBD), a transient receptor potential vanilloid 2 (TRPV2) ligand. TRPV2, often dysregulated in tumors, is associated with altered cell proliferation and aggressiveness. Endometrial cancer (EC) is historically divided in type I endometrioid EC and type II non-endometrioid EC, associated with poor prognosis. Treatment options with chemotherapy and combinations with radiation showed only limited efficacy. Since no data are reported concerning TRPV2 expression as well as CBD potential effects in EC, the aim of this study was to evaluate the expression of TRPV2 in biopsies and cell lines as well as the effects of CBD in in vitro models. Overall survival (OS), progression-free survival (PFS), cell viability, migration, and chemo-resistance have been evaluated. Results show that TRPV2 expression increased with the malignancy of the cancer tissue and correlated with shorter PFS (p = 0.0224). Moreover, in vitro TRPV2 over-expression in Ishikawa cell line increased migratory ability and response to cisplatin. CBD reduced cell viability, activating predominantly apoptosis in type I cells and autophagy in mixed type EC cells. The CBD improved chemotherapeutic drugs cytotoxic effects, enhanced by TRPV2 over-expression. Hence, TRPV2 could be considered as a marker for optimizing the therapy and CBD might be a useful therapeutic option as adjuvant therapy.
Mycotoxins in Feed and Food and the Role of Ozone in Their Detoxification and Degradation: An Update

Mycotoxins are secondary metabolites produced by some filamentous fungi, which can cause toxicity in animal species, including humans. Because of their high toxicological impacts, mycotoxins have received significant consideration, leading to the definition of strict legislative thresholds and limits in many areas of the world. Mycotoxins can reduce farm profits not only through reduced crop quality and product refusal, but also through a reduction in animal productivity and health. This paper briefly addresses the impacts of mycotoxin contamination of feed and food on animal and human health, and describes the main pre- and post-harvest systems to control their levels, including genetic, agronomic, biological, chemical, and physical methods. It so highlights (i) the lack of effective and straightforward solutions to control mycotoxin contamination in the field, at pre-harvest, as well as later post-harvest; and (ii) the increasing demand for novel methods to control mycotoxin infections, intoxications, and diseases, without leaving toxic chemical residues in the food and feed chain. Thus, the broad objective of the present study was to review the literature on the use of ozone for mycotoxin decontamination, proposing this gaseous air pollutant as a powerful tool to detoxify mycotoxins from feed and food.
Perfil de Uso de Aplicativos Móveis: Caracterização e Aplicações

The large amount of data generated by the advances of mobile technology makes the service providers get more and more interested in collecting and analyzing it. In this study, we investigate for the first time a real and largescale dataset related to the use of mobile applications to identify patterns of access, data traffic, period of use, and transition among services. The characterization results reveal that different services are consumed differently by their users. In addition to the characterization, the contributions of this work are two-fold. First, we propose and validate a synthetic data generator that can be used by other researchers. Also, we evaluate which metrics affect the prediction of the next application to be launched, reducing then the users' waiting time.
Fungal Community in Antarctic Soil Along the Retreating Collins Glacier (Fildes Peninsula, King George Island)

Glacial retreat is one of the most conspicuous signs of warming in Antarctic regions. Glacier soils harbor an active microbial community of decomposers, and under the continuous retraction of glaciers, the soil starts to present a gradient of physical, chemical, and biological factors reflecting regional changes over time. Little is known about the biological nature of fungi in Antarctic glacier soils. In this sense, this work aimed at studying the behavior of fungal community structure from samples of glacier soil collected after glacial retreat (Collins Glacier). A total of 309 fungi distributed in 19 genera were obtained from eleven soil samples. Representatives of the genera Pseudogymnoascus (Ascomycota) and Mortierella (Mortierellomycota) were the most abundant isolates in all samples. The data revealed the presence of filamentous fungi belonging to the phylum Basidiomycota, rarely found in Antarctica. Analysis of the generalized linear models revealed that the distance from the glacier as well as phosphorus and clay were able to modify the distribution of fungal species. Environmental variations proved to have influenced the genera Pseudogymnoascus and Pseudeutorium.
The Continuous Interaction Space: Integrating Gestures Above a Surface with Direct Touch

The advent of touch-sensitive and camera-based digital surfaces has spawned considerable development in two types of hand-based interaction techniques. In particular, people can interact: 1) directly on the surface via direct touch, or 2) above the surface via hand motions. While both types have value on their own, we believe much more potent interactions are achievable by unifying interaction techniques across this space. That is, the underlying system should treat this space as a continuum, where a person can naturally move from gestures over the surface to touches directly on it and back again. We illustrate by example, where we unify actions such as selecting, grabbing, moving, reaching, and lifting across this continuum of space. ACM Classification: H5.2 [Information interfaces and presentation]: User Interfaces. - Graphical user interfaces.
Magnetic Resonance-Guided Laser Interstitial Thermal Therapy for the Treatment of Nonlesional Insular Epilepsy in Pediatric Patients: Technical Considerations

Introduction: The insula presents anatomic challenges to surgical exploration and intervention. Open neurosurgical intervention is associated with high rates of complications despite improved seizure control. Minimally invasive techniques using novel energy delivery methods have gained popularity due to their relative safety and ability to overcome access-related barriers. The goal of this paper is to present an operative technical report and methodological considerations on the application of magnetic resonance-guided laser interstitial thermal therapy (MRgLITT) for the treatment of nonlesional, medically refractory, insular epilepsy in pediatric patients. Methods: Visualase laser probe(s) were implanted using ROSA robotic stereotactic guidance into the insula using a parasagittal trajectory. After confirmation of placement using intraoperative MRI, thermal energy was delivered under real-time MR guidance. Laser wire pullback was performed when the initial dose of thermal energy was insufficient to ablate the target in its entirety. Thermal ablation within the intended target was confirmed using gadolinium-enhanced brain MRI. Following removal of laser wires, a final T1-weighted axial brain MRI was performed to confirm no evidence of hemorrhage. Results: Three patients underwent MRgLITT of nonlesional insular epilepsy over an 11-month period. The epileptogenic focus was localized to the insula using stereoelectroencephalography. The anterior and middle portions of the insula were accessed using a parasagittal trajectory. Laser ablation was performed for up to 3 min using an output of 10.5 W. No complications were encountered, and all patients were discharged within 24 h after the surgery. At the most recent follow-up, all patients had an Engel I outcome without any new neurologic deficits. Conclusion: This small cohort shows that insular ablation can be achieved safely with promising seizure outcomes in the short term.
High-Precision Plane Detection Method for Rock-Mass Point Clouds Based on Supervoxel

In respect of rock-mass engineering, the detection of planar structures from the rock-mass point clouds plays a crucial role in the construction of a lightweight numerical model, while the establishment of high-quality models relies on the accurate results of surface analysis. However, the existing techniques are barely capable to segment the rock mass thoroughly, which is attributed to the cluttered and unpredictable surface structures of the rock mass. This paper proposes a high-precision plane detection approach for 3D rock-mass point clouds, which is effective in dealing with the complex surface structures, thus achieving a high level of detail in detection. Firstly, the input point cloud is fast segmented to voxels using spatial grids, while the local coplanarity test and the edge information calculation are performed to extract the major segments of planes. Secondly, to preserve as much detail as possible, supervoxel segmentation instead of traditional region growing is conducted to deal with scattered points. Finally, a patch-based region growing strategy applicable to rock mass is developed, while the completed planes are obtained by merging supervoxel patches. In this paper, an artificial icosahedron point cloud and four rock-mass point clouds are applied to validate the performance of the proposed method. As indicated by the experimental results, the proposed method can make high-precision plane detection achievable for rock-mass point clouds while ensuring high recall rate. Furthermore, the results of both qualitative and quantitative analyses evidence the superior performance of our algorithm.
Anatomical and hydraulic responses to desiccation in emergent conifer seedlings.

PREMISE The young seedling life stage is critical for reforestation after disturbance and for species migration under climate change, yet little is known regarding their basic hydraulic function or vulnerability to drought. Here, we sought to characterize responses to desiccation including hydraulic vulnerability, xylem anatomical traits, and impacts on other stem tissues that contribute to hydraulic functioning. METHODS Larix occidentalis, Pseudotsuga menziesii, and Pinus ponderosa (all ≤6 weeks old) were imaged using x-ray computed microtomography during desiccation to assess seedling biomechanical responses with concurrently measured hydraulic conductivity (ks ) and water potential (Ψ) to assess vulnerability to xylem embolism formation and other tissue damage. RESULTS In non-stressed samples for all species, pith and cortical cells appeared circular and well hydrated, but they started to empty and deform with decreasing Ψ which resulted in cell tearing and eventual collapse. Despite the severity of this structural damage, the vascular cambium remained well hydrated even under the most severe drought. There were significant differences among species in vulnerability to xylem embolism formation, with 78% xylem embolism in L. occidentalis by Ψ of -2.1 MPa, but only 47.7% and 62.1% in P. ponderosa and P. menziesii at -4.27 and -6.73 MPa, respectively. CONCLUSIONS Larix occidentalis seedlings appeared to be more susceptible to secondary xylem embolism compared to the other two species, but all three maintained hydration of the vascular cambium under severe stress, which could facilitate hydraulic recovery by regrowth of xylem when stress is relieved.
Application of Nanoemulsions (W/O) of Extract of Opuntia oligacantha C.F. Först and Orange Oil in Gelatine Films

Over the past decade, consumers have demanded natural, completely biodegradable active packaging serving as food containers. Bioactive plant compounds can be added to biopolymer-based films to improve their functionality, as they not only act as barriers against oxidation, microbiological, and physical damage, they also offer functionality to the food they contain. A water-in-oil (W/O) nanoemulsion was produced by applying ultrasound to xoconostle extract and orange oil, and was incorporated into gelatine films in different proportions 1:0 (control), 1:0.10, 1:0.25, 1:0.50, 1:0.75, and 1:1 (gelatine:nanoemulsion). The nanoemulsions had an average size of 118.80 ± 5.50 nm with a Z-potential of −69.9 ± 9.93 mV. The presence of bioactive compounds such as phenols, flavonoids, and betalains in the films was evaluated. The 1:1 treatment showed the highest presence of bioactive compounds, 41.31 ± 3.71 mg of gallic acid equivalent per 100 g (GAE)/100g for phenols, 28.03 ± 3.25 mg of quercetin equivalent per 100 g (EQ)/100g flavonoids and 0.014 mg/g betalains. Radical inhibition reached 72.13% for 2,20-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid (ABTS), and 82.23% for 1,1-diphenyl-2-picrylhydrazyl (DPPH). The color of the films was influenced by the incorporation of nanoemulsions, showing that it was significantly different (p < 0.05) to the control. Mechanical properties, such as tensile strength, Young’s modulus, and percentage elongation, were affected by the incorporation of nanoemulsified bioactive compounds into gelatine films. The obtained films presented changes in strength and flexibility. These characteristics could be favorable as packaging material.
Molecular Biology of Osteosarcoma

Osteosarcoma (OS) is the most frequent primary bone cancer in children and adolescents and the third most frequent in adults. Many inherited germline mutations are responsible for syndromes that predispose to osteosarcomas including Li Fraumeni syndrome, retinoblastoma syndrome, Werner syndrome, Bloom syndrome or Diamond–Blackfan anemia. TP53 is the most frequently altered gene in osteosarcoma. Among other genes mutated in more than 10% of OS cases, c-Myc plays a role in OS development and promotes cell invasion by activating MEK–ERK pathways. Several genomic studies showed frequent alterations in the RB gene in pediatric OS patients. Osteosarcoma driver mutations have been reported in NOTCH1, FOS, NF2, WIF1, BRCA2, APC, PTCH1 and PRKAR1A genes. Some miRNAs such as miR-21, -34a, -143, -148a, -195a, -199a-3p and -382 regulate the pathogenic activity of MAPK and PI3K/Akt-signaling pathways in osteosarcoma. CD133+ osteosarcoma cells have been shown to exhibit stem-like gene expression and can be tumor-initiating cells and play a role in metastasis and development of drug resistance. Although currently osteosarcoma treatment is based on adriamycin chemoregimens and surgery, there are several potential targeted therapies in development. First of all, activity and safety of cabozantinib in osteosarcoma were studied, as well as sorafenib and pazopanib. Finally, novel bifunctional molecules, of potential imaging and osteosarcoma targeting applications may be used in the future.
Influence of stage of maturity of grass silages on protein digestion and microbial protein synthesis in the rumen

In four change-over experiments, wilted grass silages, differing in growth stage at harvesting and as a consequence in cell wall content, were fed ad libitum to dairy cows in early and late lactation. Ruminal degradation rate of the crude protein fraction of the silages was investigated using nylon bag incubations. No significant relation between the degradation rate (%h-1) and the cell wall content of the silages was found. The soluble and undegradable fractions of the crude protein both increased with an increase in silage cell wall content. The soluble fraction was more closely related to dry matter content and date of harvesting than to cell wall content of the silages. The fraction of dietary protein escaping rumen fermentation increased with cell wall content.In duodenal protein, the fraction originating from the diet, estimated using amino acid profiles of dietary, microbial and duodenal protein, decreased with cell wall content.
Amino Acid Transporters in Plants: Identification and Function

Amino acid transporters are the main mediators of nitrogen distribution throughout the plant body, and are essential for sustaining growth and development. In this review, we summarize the current state of knowledge on the identity and biological functions of amino acid transporters in plants, and discuss the regulation of amino acid transporters in response to environmental stimuli. We focus on transporter function in amino acid assimilation and phloem loading and unloading, as well as on the molecular identity of amino acid exporters. Moreover, we discuss the effects of amino acid transport on carbon assimilation, as well as their cross-regulation, which is at the heart of sustainable agricultural production.
Dengue: A Minireview

Dengue, caused by infection of any of four dengue virus serotypes (DENV-1 to DENV-4), is a mosquito-borne disease of major public health concern associated with significant morbidity, mortality, and economic cost, particularly in developing countries. Dengue incidence has increased 30-fold in the last 50 years and over 50% of the world’s population, in more than 100 countries, live in areas at risk of DENV infection. We reviews DENV biology, epidemiology, transmission dynamics including circulating serotypes and genotypes, the immune response, the pathogenesis of the disease as well as updated diagnostic methods, treatments, vector control and vaccine developments.
The Development of a Skin Cancer Classification System for Pigmented Skin Lesions Using Deep Learning

Recent studies have demonstrated the usefulness of convolutional neural networks (CNNs) to classify images of melanoma, with accuracies comparable to those achieved by dermatologists. However, the performance of a CNN trained with only clinical images of a pigmented skin lesion in a clinical image classification task, in competition with dermatologists, has not been reported to date. In this study, we extracted 5846 clinical images of pigmented skin lesions from 3551 patients. Pigmented skin lesions included malignant tumors (malignant melanoma and basal cell carcinoma) and benign tumors (nevus, seborrhoeic keratosis, senile lentigo, and hematoma/hemangioma). We created the test dataset by randomly selecting 666 patients out of them and picking one image per patient, and created the training dataset by giving bounding-box annotations to the rest of the images (4732 images, 2885 patients). Subsequently, we trained a faster, region-based CNN (FRCNN) with the training dataset and checked the performance of the model on the test dataset. In addition, ten board-certified dermatologists (BCDs) and ten dermatologic trainees (TRNs) took the same tests, and we compared their diagnostic accuracy with FRCNN. For six-class classification, the accuracy of FRCNN was 86.2%, and that of the BCDs and TRNs was 79.5% (p = 0.0081) and 75.1% (p < 0.00001), respectively. For two-class classification (benign or malignant), the accuracy, sensitivity, and specificity were 91.5%, 83.3%, and 94.5% by FRCNN; 86.6%, 86.3%, and 86.6% by BCD; and 85.3%, 83.5%, and 85.9% by TRN, respectively. False positive rates and positive predictive values were 5.5% and 84.7% by FRCNN, 13.4% and 70.5% by BCD, and 14.1% and 68.5% by TRN, respectively. We compared the classification performance of FRCNN with 20 dermatologists. As a result, the classification accuracy of FRCNN was better than that of the dermatologists. In the future, we plan to implement this system in society and have it used by the general public, in order to improve the prognosis of skin cancer.
Health Related Quality of Life Following Coronary Revascularization: A Prospective Cross-sectional Study

Introduction Coronary Artery Bypass Grafting (CABG) and percutaneous coronary intervention (PCI) are invasive options for managing patients with coronary artery disease (CAD). CABG was first introduced in 1964 and it has been firmly recognized since then as a key surgical intervention for patients with intractable angina pectoris despite medications and myocardial infarction [1,2]. Percutaneous transluminal coronary angioplasty (PTCA) or percutaneous coronary intervention (PCI) established in 1979 by Andreas Gruentzig in Switzerland to treat stenotic coronary lesions of coronary arteries, the procedure then progressed technically and introduced devices like stents which improve not only long-term patency of treated lesions but also the prognosis of patients [3,4]. With the use of both revascularization methods (CABG and PCI), the relief of symptom and survival rates have increased [5]. The relative efficacy, benefits and risks of the two procedures have been compared in several studies [6-12]. In the latest published European and American guidelines, both CABG and PCI are accepted revascularization methods to reduce mortality and improve morbidity [13,14].
Structure–Biological Activity Relationships of Extra-Virgin Olive Oil Phenolic Compounds: Health Properties and Bioavailability

Extra-virgin olive oil is regarded as functional food since epidemiological studies and multidisciplinary research have reported convincing evidence that its intake affects beneficially one or more target functions in the body, improves health, and reduces the risk of disease. Its health properties have been related to the major and minor fractions of extra-virgin olive oil. Among olive oil chemical composition, the phenolic fraction has received considerable attention due to its bioactivity in different chronic diseases. The bioactivity of the phenolic compounds could be related to different properties such as antioxidant and anti-inflammatory, although the molecular mechanism of these compounds in relation to many diseases could have different cellular targets. The aim of this review is focused on the extra-virgin olive oil phenolic fraction with particular emphasis on (a) biosynthesis, chemical structure, and influence factors on the final extra-virgin olive oil phenolic composition; (b) structure–antioxidant activity relationships and other molecular mechanisms in relation to many diseases; (c) bioavailability and controlled delivery strategies; (d) alternative sources of olive biophenols. To achieve this goal, a comprehensive review was developed, with particular emphasis on in vitro and in vivo assays as well as clinical trials. This report provides an overview of extra-virgin olive oil phenolic compounds as a tool for functional food, nutraceutical, and pharmaceutical applications.