Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut

The aim of this study was to elucidate the ecological structure of the human gut temperate bacteriophage community and its role in inflammatory bowel disease (IBD). Temperate bacteriophages make up a large proportion of the human gut microbiota and are likely to play a role in IBD pathogenesis. However, many of these bacteriophages await characterization in reference databases. Therefore, we conducted a large-scale reconstruction of temperate bacteriophage and bacterial genomes from the whole-metagenome sequence data generated by the IBD Multi’omics Database project. By associating phages with their hosts via genome comparisons, we found that temperate bacteriophages infect a phylogenetically wide range of bacteria. The majority of variance in bacteriophage community composition was explained by variation among individuals, but differences in the abundance of temperate bacteriophages were identified between IBD and non-IBD patients. Of note, in active ulcerative colitis patients, temperate bacteriophages infecting Bacteroides uniformis and Bacteroides thetaiotaomicron—two species experimentally proven to be beneficial to gut homeostasis—were over-represented, whereas their hosts were under-represented in comparison with non-IBD patients. Supporting the mounting evidence that gut viral community plays a vital role in IBD, our results show potential association between temperate bacteriophages and IBD pathogenesis.
Antioxidants in Plants: A Valorization Potential Emphasizing the Need for the Conservation of Plant Biodiversity in Cuba

Plants are phytochemical hubs containing antioxidants, essential for normal plant functioning and adaptation to environmental cues and delivering beneficial properties for human health. Therefore, knowledge on the antioxidant potential of different plant species and their nutraceutical and pharmaceutical properties is of utmost importance. Exploring this scientific research field provides fundamental clues on (1) plant stress responses and their adaptive evolution to harsh environmental conditions and (2) (new) natural antioxidants with a functional versatility to prevent and treat human pathologies. These natural antioxidants can be valorized via plant-derived foods and products. Cuba contains an enormously rich plant biodiversity harboring a great antioxidant potential. Besides opening new avenues for the implementation of sustainable agroecological practices in crop production, it will also contribute to new strategies to preserve plant biodiversity and simultaneously improve nature management policies in Cuba. This review provides an overview on the beneficial properties of antioxidants for plant protection and human health and is directed to the valorization of these plant antioxidants, emphasizing the need for biodiversity conservation.
Rhythmic Convergence in Canadian French Varieties?

Studies of prosodic rhythm in a minority Ontario French using rhythm metrics did not demonstrate the effect of contact with English; moreover, they demonstrated an even more syllabletimed (French) pattern in this contact variety than in majority Canadian and European ones. To understand these results and further explore regional variation in Canadian French and the effect of linguistic contact, syllabic typology, length and duration of the stress group, syllable duration ratios, and vowel intensity are explored here through a comparison of a minority variety with a majority Canadian French (Quebec). Spontaneous samples show the same syllabic typology and distribution, stress group length and duration, similar syllable ratios, and a regular rhythmic pattern in both Canadian varieties. The analysis of intensity of stressed syllables, however, suggested divergence of the datasets from both traditional description of French and from each other. Thus, intensity accompanies primary stress in Ontario but not in Quebec, and both varieties use intensity to mark secondary stress. These results suggest a convergence to the neighboring English language and need to be confirmed in a controlled
Deep Learning to Predict Energy Expenditure and Activity Intensity in Free Living Conditions using Wrist-specific Accelerometry

ABSTRACT Wrist-worn accelerometers are more comfortable and yield greater compliance than hip-worn devices, making them attractive for free-living activity assessments. However, intricate wrist movements may require more complex predictive models than those applied to hip-worn devices. This study developed a novel deep learning method that predicts energy expenditure and physical activity intensity of adults using wrist-specific accelerometry. Triaxial accelerometers were worn by 119 participants on their wrist and hip for two weeks during waking hours. A deep learning model was developed from week 1 data of 60 participants and tested using week 2 data for: (i) the remaining 59 participants (Group UT), and (ii) participants used for training (Group TR). Estimates of physical activity were compared to a reference hip-specific method. Moderate-to-vigorous physical activity predicted by the wrist-model was not different to the reference method for participants in Group UT (5.9±3.1vs. 6.3±3.3 hour/week) and Group TR (6.9±3.7 vs. 7.2±4.2 hour/week). At 60-s epoch level, energy expenditure predicted by the wrist-model on Group UT was strongly correlated with the reference method (r=0.86, 95%CI: 0.84–0.87) and closely predicted activity intensity (83.7%, 95%CI: 80.9–86.5%). The deep learning method has application for wrist-worn accelerometry in free-living adults.
Upregulation of C-Reactive Protein by Placenta-Derived Mesenchymal Stem Cells Promotes Angiogenesis in A Rat Model with Cirrhotic Liver

Background and Objectives Liver cirrhosis is accompanied by abnormal vascular shunts. The Wnt pathway is essential for endothelial cell survival and proliferation. C-reactive protein (CRP), which is produced by hepatocyte, activates angiogenesis in cardiovascular diseases. Methods and Results The expression of CRP in CCl4-injured rat livers was detected using qRT-PCR and Western blotting after transplantation of placenta-derived mesenchymal stem cells (PD-MSCs) into rats. To determine whether CRP functions in hepatic regeneration by promoting angiogenesis through the Wnt pathway, we detected VEGF and β-catenin in liver tissues and BrdU and β-catenin in hepatocytes by immunofluorescence. The expression levels of CRP, Wnt pathway-related and angiogenic factors were increased in CCl4-injured and PD-MSCs transplanted rat livers. In vitro, the expression levels of Wnt signaling and angiogenic factors were decreased in siRNA-CRP-transfected rat hepatocytes. Conclusions CRP upregulation by PD-MSCs participates in vascular remodeling to promote liver regeneration via the Wnt signaling pathway during hepatic failure.
Temporal Attention Convolutional Network for Speech Emotion Recognition with Latent Representation

As the fundamental research of affective computing, speech emotion recognition (SER) has gained a lot of attention. Unlike with common deep learning tasks, SER was restricted by the scarcity of emotional speech datasets. In this paper, the vector quantization variational automatic encoder (VQ-VAE) was introduced and trained by massive unlabeled data in an unsupervised manner. Beneﬁting from the excellent invariant distribution encoding capability and discrete embedding space of VQ-VAE, the pre-trained VQ-VAE could learn latent representation from labeled data. The extracted latent representation could serve as the additional source data to make data abundantly available. While solving data lacking issue, sequence information modeling was also taken into account which was considered useful for SER. The proposed sequence model, temporal attention convolutional network (TACN) was simple yet good at learning contextual information from limited data which was not friendly to complicated structures of recurrent neural network (RNN) based sequence models. To validate the effectiveness of the latent representation, t-distributed stochastic neighbor embedding (t-SNE) was introduced to analyze the visualizations. To verify the performance of the proposed TACN, quantitative classiﬁcation results of all commonly used sequence models were provided. Our proposed model achieved state-of-the-art performance on IEMOCAP.
Differences in cortical activation patterns during action observation, action execution, and interpersonal synchrony between children with or without autism spectrum disorder (ASD): An fNIRS pilot study

Engaging in socially embedded actions such as imitation and interpersonal synchrony facilitates relationships with peers and caregivers. Imitation and interpersonal synchrony impairments of children with Autism Spectrum Disorder (ASD) might contribute to their difficulties in connecting and learning from others. Previous fMRI studies investigated cortical activation in children with ASD during finger/hand movement imitation; however, we do not know whether these findings generalize to naturalistic face-to-face imitation/interpersonal synchrony tasks. Using functional near infrared spectroscopy (fNIRS), the current study assessed the cortical activation of children with and without ASD during a face-to-face interpersonal synchrony task. Fourteen children with ASD and 17 typically developing (TD) children completed three conditions: a) Watch—observed an adult clean up blocks; b) Do—cleaned up the blocks on their own; and c) Together—synchronized their block clean up actions to that of an adult. Children with ASD showed lower spatial and temporal synchrony accuracies but intact motor accuracy during the Together/interpersonal synchrony condition. In terms of cortical activation, children with ASD had hypoactivation in the middle and inferior frontal gyri (MIFG) as well as middle and superior temporal gyri (MSTG) while showing hyperactivation in the inferior parietal cortices/lobule (IPL) compared to the TD children. During the Together condition, the TD children showed bilaterally symmetrical activation whereas children with ASD showed more left-lateralized activation over MIFG and right-lateralized activation over MSTG. Additionally, using ADOS scores, in children with ASD greater social affect impairment was associated with lower activation in the left MIFG and more repetitive behavior impairment was associated with greater activation over bilateral MSTG. In children with ASD better communication performance on the VABS was associated with greater MIFG and/or MSTG activation. We identified objective neural biomarkers that could be utilized as outcome predictors or treatment response indicators in future intervention studies.
A transcriptome-based classifier to determine molecular subtypes in medulloblastoma

Medulloblastoma is a highly heterogeneous pediatric brain tumor with five molecular subtypes, Sonic Hedgehog TP53-mutant, Sonic Hedgehog TP53-wildtype, WNT, Group 3, and Group 4, defined by the World Health Organization. The current mechanism for classification into these molecular subtypes is through the use of immunostaining, methylation, and/or genetics. We surveyed the literature and identified a number of RNA-Seq and microarray datasets in order to develop, train, test, and validate a robust classifier to identify medulloblastoma molecular subtypes through the use of transcriptomic profiling data. We have developed a GPL-3 licensed R package and a Shiny Application to enable users to quickly and robustly classify medulloblastoma samples using transcriptomic data. The classifier utilizes a large composite microarray dataset (15 individual datasets), an individual microarray study, and an RNA-Seq dataset, using gene ratios instead of gene expression measures as features for the model. Discriminating features were identified using the limma R package and samples were classified using an unweighted mean of normalized scores. We utilized two training datasets and applied the classifier in 15 separate datasets. We observed a minimum accuracy of 85.71% in the smallest dataset and a maximum of 100% accuracy in four datasets with an overall median accuracy of 97.8% across the 15 datasets, with the majority of misclassification occurring between the heterogeneous Group 3 and Group 4 subtypes. We anticipate this medulloblastoma transcriptomic subtype classifier will be broadly applicable to the cancer research and clinical communities.
A Patient-Centered Framework for Measuring the Economic Value of the Clinical Benefits of Digital Health Apps: Theoretical Modeling

Background As digital health tools such as smartphone apps evolve and enter clinical use, questions regarding their value must be addressed. Although there are scarce generalizable data on the value of health apps given their nascency and diverse use cases, it is possible to estimate the economic value of the clinical improvement they bring to patients using a quality-adjusted life-year (QALY)-based approach and generalized values from existing literature. Objective This paper aims to provide a patient-centered framework for assessing the economic value of the clinical benefits delivered by digital health apps. Methods We proposed a model based upon 5 levers: country-specific monetary value of a QALY, QALYs lost due to the condition, engagement rate of app users, average effect size of the app’s health impact, and duration of the app’s impact before remission. Results Using 2 digital health apps from the United States and United Kingdom as examples, we explored how this model could generate country-specific estimates of the economic value of the clinical benefits of health apps. Conclusions This new framework can help drive research priorities for digital health by elucidating the factors that influence the economic value.
Exploring Macroporosity of Additively Manufactured Titanium Metamaterials for Bone Regeneration with Quality by Design: A Systematic Literature Review

Additive manufacturing facilitates the design of porous metal implants with detailed internal architecture. A rationally designed porous structure can provide to biocompatible titanium alloys biomimetic mechanical and biological properties for bone regeneration. However, increased porosity results in decreased material strength. The porosity and pore sizes that are ideal for porous implants are still controversial in the literature, complicating the justification of a design decision. Recently, metallic porous biomaterials have been proposed for load-bearing applications beyond surface coatings. This recent science lacks standards, but the Quality by Design (QbD) system can assist the design process in a systematic way. This study used the QbD system to explore the Quality Target Product Profile and Ideal Quality Attributes of additively manufactured titanium porous scaffolds for bone regeneration with a biomimetic approach. For this purpose, a total of 807 experimental results extracted from 50 different studies were benchmarked against proposed target values based on bone properties, governmental regulations, and scientific research relevant to bone implants. The scaffold properties such as unit cell geometry, pore size, porosity, compressive strength, and fatigue strength were studied. The results of this study may help future research to effectively direct the design process under the QbD system.
Diagnosis and management of cutaneous melanoma.

BACKGROUND In the field of melanoma, clinical trials evaluating the impact of sentinel node biopsy, completion lymph node dissection and adjuvant medical therapies on patient outcomes have provided evidence that has changed practice significantly over the past five years. OBJECTIVE The aim of this article is to discuss key evidence that has informed new Cancer Council Australia melanoma management guidelines. DISCUSSION General practitioners play a critical role in melanoma diagnosis and follow-up. Complete excisional biopsy to achieve accurate tumour microstaging is essential for obtaining reliable prognostic information, planning further management and accessing adjuvant medical therapies. The management of patients with Stage III disease has changed dramatically over the past few years. Less surgery is now recommended, and patients may be offered potentially life-prolonging systemic therapies. Multidisciplinary discussion of management is recommended. Rapid advances in therapeutic options for patients with advanced melanoma have placed new emphasis on the importance of accurate staging and early management. Accordingly, the Australian national melanoma management guidelines have recently been updated. These evidence-based guidelines are now readily available on Cancer Council Australia's electronic Wiki platform, which facilitates regular further updating.
EFFECT OF TWO-FLUID NOZZLES ON THE STABILITY CHARACTERISTICS OF EMULSIONS PREPARED BY A HIGH-ENERGY METHOD (MICROFLUIDIZATION)

The atomization of oil in water emulsions is used in the food industry such as in the preparation of capsules, films and coatings among others. However, the passage through the atomization devices could have an influence on the properties of the emulsion and, consequently of the final product. In the present work, it was evaluated the influence of two fluid nozzles of different dimensions on stability parameters of oil in water emulsion produced by microfluidization and using gum Arabic as wall material. Results indicated that the droplet size, the polydispersity index and the Turbiscan stability index of atomized emulsions were affected by and Oswald ripening mechanism as compared with those of the original emulsion. The confocal laser scanning microscopy images confirmed that the passage of the emulsion through the atomization devices decreased the thickness of wall material of the droplets with respect to the original emulsion. It was concluded that, in the proper design of the final products prepared by atomization it must be considered its effect on the stability of the atomized emulsions by including during the processing, a suitable sampling-characterization on-line scheme.
Evaluation of Polyphenolic Profile and Antioxidant Activity of Pistacia lentiscus L. Leaves and Fruit Extract Obtained by Optimized Microwave-Assisted Extraction

Pistacia lentiscus L. is a Mediterranean shrub known for its health promoting effects attributed to a large extent to polyphenols accumulated in all parts of the plant. Microwave-assisted extraction is a green extraction technique enabling fast and effective isolation of plant polyphenols. Therefore, the aim of this research was to optimize the microwave-assisted extraction of polyphenols from Pistacia lentiscus L. leaves and fruit in terms of temperature, extraction time and microwave power and to evaluate their polyphenolic profile by UPLC/ESI-MS2 and antioxidant capacity by ORAC assay. Optimal extraction conditions for leaf polyphenols were 69 °C, 512 W and 12 min, while for fruit were slightly more intensive—75 °C, 602 W and 15 min. Obtained total phenolic content in leaves and fruit was similar to that obtained after 30 min of the heat-reflux method. The polyphenolic profile of extracts included 34 compounds, with myricetin glycosides being the most abundant compounds among flavonoids in Pistacia lentiscus L. leaves and fruit and gallic acid and its derivates among the phenolic acids. ORAC assay showed higher antioxidant capacity for Pistacia lentiscus L. leaves extract than for fruit, which is in correlation with their respective phenolic content.
A Kinematic Model of a Humanoid Lower Limb Exoskeleton with Hydraulic Actuators

Although it is well-established that exoskeletons as robots attached to the extremities of the human body increase their strength, limited studies presented a computer and mathematical model of a human leg hydraulic exoskeleton based on anthropometric data. This study aimed to examine lower limb joint angles during walking and running by using Inertial Measurement Units. The geometry and kinematic parameters were calculated. Twenty-six healthy adults participated in walking and running experiments. The geometric model of a human leg hydraulic exoskeleton was presented. Joint angle data acquired during experiments were used in the mathematical model. The position and velocity of exoskeleton actuators in each phase of movement were calculated using the MATLAB package (Matlab_R2017b, The MathWorks Company, Novi, MI, USA). The highest velocity of the knee actuator during walking and running was in the swing phase, 0.3 and 0.4 m/s, respectively. For the ankle and hip joints, the highest velocity of actuators occurred during the push-off phase. The results with 26 healthy subjects demonstrated that the system's compliance can be effectively adjusted while guiding the subjects walking in predefined trajectories. The developed mathematical model makes it possible to determine the position of lower limb segments and exoskeleton elements. The proposed model allows for calculating the position of the human leg and actuators’ characteristic points.
Phylogenetic relationship of hydrocarbon degrading fungi species in bioremediation

The study focussed on the phylogenetic relationship of hydrocarbon degrading fungi species in bioremediation. Hydrocarbon degrading fungi species were isolated from soil polluted with crude oil and treated with varying concentrations of agro-wastes. DNA sequencing was done on the consortia of fungi isolated. The evolutionary history was inferred by using the Maximum likelihood method based on the Tamura-Nei model. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was < 100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree was drawn to scale, with branch lengths measured in the number of substitutions per site. The phylogenetic relationship between the fungal species revealed that the organisms were grouped into two clusters, cluster 1 consist of Aspergillus oryzae, Aspergillus flavus, Talaromyces solicola, Penicillium purpurogenum, Penicillium citrium and Penicillium daleae while cluster 2 consist of Cunninghamella polymorpha and Cunninghamella bertholletiae. The results revealed that Aspergillus oryzae differs from Aspergillus flavus, while other organisms had high relationship with each other. The Cunninghamella polymorpha and Cunninghamella bertholletiae were highly related. The sequencing and phylogenetic of the fungi species revealed the specific identity of the organism and showed the similarity between the identified species.
EFFECTS OF NICOTINIC ACID ON PROTEIN OXIDATIVE MODIFICATIONS IN EXPERIMENTAL CHRONIC HEART FAILURE

A model of chronic heart failure experimental model was induced to rats based on the toxic effects of doxorubicin. The nature of changes in the content of protein peroxidation products (neutral and basic 2,4-dinitrophenylhydrazones) was established in cardiomyocytes and hepatocytes of rats which received weekly intramuscular doxorubicin for 5 weeks in a dose of 5 mg/kg body weight (bw) together with the daily intraperitoneal administration of nicotinic acid, 10 mg/kg bw. The obtained results pointed out reduced protein peroxidation in cardiomyocytes caused by nicotinic acid, in a chronic heart failure model in rats. This allows to consider nicotinic acid as a drug with a potential cardioprotective activity.