Miracle-dz/UniFAR-FTUs huggingface dataset:
Mucosal Barrier and Th2 Immune Responses Are Enhanced by Dietary Inulin in Pigs Infected With Trichuris suis

Diet composition may play a crucial role in shaping host immune responses and commensal gut microbiota populations. Bioactive dietary components, such as inulin, have been extensively studied for their bioactive properties, particularly in modulating gut immune function and reducing inflammation. It has been shown that colonization with gastrointestinal parasitic worms (helminths) may alleviate chronic inflammation through promotion of T-helper cell type (Th) 2 and T-regulatory immune responses and alterations in the gut microbiome. In this study, we investigated if dietary inulin could modulate mucosal immune function in pigs during colonization with the porcine whipworm Trichuris suis. T. suis infection induced a typical Th2-biased immune response characterized by transcriptional changes in Th2- and barrier function-related genes, accompanied by intestinal remodeling through increased epithelial goblet and tuft cell proliferation. We observed that inulin also up-regulated Th2-related immune genes (IL13, IL5), and suppressed Th1-related pro-inflammatory genes (IFNG, IL1A, IL8) in the colon. Notably, inulin augmented the T. suis-induced responses with increased transcription of key Th2 and mucosal barrier genes (e.g., IL13, TFF3), and synergistically suppressed pro-inflammatory genes, such as IFNG and CXCL9. 16S rRNA sequencing of proximal colon digesta samples revealed that inulin supplementation reduced the abundance of bacterial phyla linked to inflammation, such as Proteobacteria and Firmicutes, and simultaneously increased Actinobacteria and Bacteroidetes. Interestingly, pigs treated with both inulin and T. suis displayed the highest Bacteroidetes: Firmicutes ratio and the lowest gut pH, suggesting an interaction of diet and helminth infection that stimulates the growth of beneficial bacterial species. Overall, our data demonstrate that T. suis infection and inulin co-operatively enhance anti-inflammatory immune responses, which is potentially mediated by changes in microbiota composition. Our results highlight the intricate interactions between diet, immune function and microbiota composition in a porcine helminth infection model. This porcine model should facilitate further investigations into the use of bioactive diets as immunomodulatory mediators against inflammatory conditions, and how diet and parasites may influence gut health.
In vitro Assessment of the Probiotic Properties and Bacteriocinogenic Potential of Pediococcus pentosaceus MZF16 Isolated From Artisanal Tunisian Meat “Dried Ossban”

Pediococcus pentosaceus MZF16 has been isolated from artisanal Tunisian meat so called “Dried Ossban,” an original ecological niche, and identified by MALDI-TOF mass spectrometry and 16S rDNA sequencing. This bacterium showed a high tolerance to gastric stress conditions, and toward bile salts. P. pentosaceus MZF16 also demonstrated a hydrophobic surface profile (high adhesion to xylene), autoaggregation, and adhesive abilities to the human intestinal Caco-2/TC7 cell line. These properties may help the bacterium colonizing the gut. Furthermore, MZF16 was found to be resistant to gentamycin and chloramphenicol but did not harbor any transferable resistance determinants and/or virulence genes. The data also demonstrated absence of cytotoxicity of this strain. Conversely, P. pentosaceus MZF16 can slightly stimulate the immune system and enhance the intestinal epithelial barrier function. Moreover, this bacterium has been shown to be highly active against Listeria spp. due to bacteriocin production. Characterization of the bacteriocin by PCR amplification, sequencing and bioinformatic analyses revealed that MZF16 produces a bacteriocin 100% identical to coagulin, a pediocin-like inhibitory substance produced by Bacillus coagulans. To our knowledge, this is the first report that highlights the production of a pediocin 100% identical to coagulin in a Pediococcus strain. As coagulin, pediocin MZF16 has the consensus sequence YYGNGVXCXXXXCXVXXXXA (X denotes any amino acid), which confirms its belonging to class IIa bacteriocins, and its suitability to preserve foods from Listeria monocytogenes development. According to these results, P. pentosaceus MZF16 can be proposed as a probiotic and bioprotective agent for fermented foods, including Tunisian dry meat and sausages. Further investigations will aim to study the behavior of this strain in meat products as a component of functional food.
Reduction of Acquisition time using Partition of the sIgnal Decay in Spectroscopic Imaging technique (RAPID-SI)

To overcome long acquisition times of Chemical Shift Imaging (CSI), a new Magnetic Resonance Spectroscopic Imaging (MRSI) technique called Reduction of Acquisition time by Partition of the sIgnal Decay in Spectroscopic Imaging (RAPID-SI) using blipped phase encoding gradients inserted during signal acquisition was developed. To validate the results using RAPID-SI and to demonstrate its usefulness in terms of acquisition time and data quantification; simulations, phantom and in vivo studies were conducted, and the results were compared to standard CSI. The method was based upon the partition of a magnetic resonance spectroscopy (MRS) signal into sequential sub-signals encoded using blipped phase encoding gradients inserted during signal acquisition at a constant time interval. The RAPID-SI technique was implemented on a clinical 3 T Siemens scanner to demonstrate its clinical utility. Acceleration of data collection was performed by inserting R (R = acceleration factor) blipped gradients along a given spatial direction during data acquisition. Compared to CSI, RAPID-SI reduced acquisition time by the acceleration factor R. For example, a 2D 16x16 data set acquired in about 17 min with CSI, was reduced to approximately 2 min with the RAPID-SI (R = 8). While the SNR of the acquired RAPID-SI signal was lower compared to CSI by approximately the factor √R, it can be improved after data pre-processing and reconstruction. Compared to CSI, RAPID-SI reduces acquisition time, while preserving metabolites information. Furthermore, the method is flexible and could be combined with other acceleration methods such as Parallel Imaging.
Positive sentinel node in luminal A-like breast cancer patients - implications for adjuvant chemotherapy?

Abstract Background: In luminal A-like breast cancer, the indication for adjuvant chemotherapy still is largely based on lymph nodestatus. Sentinel node (SN) positive patients who are no longer recommended an axillary lymph node dissection (ALND) risk undertreatment, especially if they have ≥4 lymph node metastases (LNMs). Aim: To quantify the group of SN positive luminal A-like patients with ≥4 LNMs and to investigate if the ratio between positive SNs and examined SNs (SN ratio) can provide information of the axillary tumor burden. Material and methods: Nearly 370 patients between 2014-2016 in Western Sweden with a clinically node-negative invasive breast cancer treated with both SNB and subsequent ALND were included. SNB findings were compared to ALND findings and the ability of the SN ratio to describe the axillary tumor burden was evaluated using multivariable analysis. Results: In total,17.6% of patients with luminal A-like tumors had ≥4 LNMs. The SN ratio was statistically significant for predicting ≥4 LNMs among luminal A-like patients (p = .013, OR 1.89 (95% CI 1.14–3.12) per 0.1 increment in SN ratio). Conclusions: One sixth of patients with SN positive luminal A-like tumors risk undertreatment. The SN ratio may aid in identifying many of these patients.
Tracking Analysis and Improvement of Broadband Kalman Filter Using the Two-Echo-Path Model as a Rapid Tunnel

A time-domain Kalman filter, namely the broadband Kalman filter, was proposed for acoustic system identification to bridge between the exact Kalman filter and normalized least-mean-square algorithm. The broadband Kalman filter was found to exhibit both fast convergence and robustness to noise disturbance. However, its tracking capability is degraded especially when the observation noise variance is approximated by the error variance. We present the theoretical analysis of the tracking capability of the broadband Kalman filter by resorting to its steady-state predicted system distance and corresponding step size. In addition, a two-echo-path approach is employed to improve the tracking. Simulation results agree with the theoretical prediction and demonstrated that the algorithm's reconvergence ability is significantly improved with the two-echo-path model using speech as input.
CS-FCDA: A Compressed Sensing-Based on Fault-Tolerant Data Aggregation in Sensor Networks

When the nodes in the network are deployed in the target area with an appropriate density, the effective aggregation and transmission of the data gathered in the monitoring area remain to be solved. The existing Compressed Sensing (CS) based on data aggregation schemes are accomplished in a centralized manner and the Sink node achieves the task of data aggregation. However, these existing schemes may suffer from load imbalance and coverage void issues. In order to address these problems, we propose a Compressed Sensing based on Fault-tolerant Correcting Data Aggregation (CS-FCDA) scheme to accurately reconstruct the compressed data. Therefore, the network communication overhead can be greatly reduced while maintaining the quality of the reconstructed data. Meanwhile, we adopt the node clustering mechanism to optimize and balance the network load. It is shown via simulation results, compared with other data aggregation schemes, that the proposed scheme shows obvious improvement in terms of the Fault-tolerant correcting capability and the network energy efficiency of the data reconstruction.
Operational and Financial Considerations of Using Drones for Medical Support of Mass Events in Poland

ABSTRACT Objective The implementation of drones in the medical security system requires a proper planning of the cooperation of different services, dividing the area into sectors, assessing potential risks, and other factors. This study refers to the cost analysis of using drones in the medical support of mass events. The aim of this research is to analyze the costs of unmanned aerial vehicle (UAV) implementation in the mass event medical support system. Methods The description includes purchase and maintenance costs of UAVs. The analysis also involves ways of raising funds for projects related to the UAV sector. Apart from the financial aspect, staff and drone operator training issues are the subjects of this analysis as well. Results This study is based on a specialist research involving drones and referring to reports on the current situation in Poland and in the world. Conclusions The presented funds required for such projects and the way of raising these funds illustrate the range of the project and its requirements. (Disaster Med Public Health Preparedness. 2019;13:527-532)
High body mass index in children with sickle cell disease: a retrospective single-centre audit

Objective To assess the prevalence of high body mass index (BMI) in children with sickle cell disease and assess correlation between BMI and disease severity. Design Retrospective chart review followed by statistical analysis. Setting A single tertiary paediatric clinic in inner city London. Patients All patients with sickle cell disease, including homozygous haemoglobin (HbSS) and compound heterozygous Hb (HbSC), age 2–18 years receiving clinical care at the centre, were included in the study. Interventions Height and weight measurements, steady-state laboratory blood tests, hospital admission rates, adjunct therapy such as hydroxycarbamide or blood transfusions and obstructive sleep apnoea (OSA) data were obtained from the hospital electronic patient records. Main outcome measures To study the prevalence of high BMI and to identify any correlation between BMI and disease severity. Results 385 patients were included. 64 children (17%) were overweight or obese, of which a significantly higher number of children with HbSC were obese or overweight (23 out of 91, 25%) compared with those with HbSS (36 out of 273, 13%), p≤0.001. No correlation was found between high BMI and presence of OSA, and markers of disease severity such as admission rates, fetal haemoglobin or lactate dehydrogenase levels. Conclusions High BMI did not correlate with disease severity in this cohort of patients with sickle cell disease. Obesity was more prevalent in females and those with HbSC. Further prospective studies are needed to determine long-term effects of BMI in disease severity and outcome.
Advances and challenges in understanding the role of the lipid raft proteome in human health

ABSTRACT Introduction: Phase separation as a biophysical principle drives the formation of liquid-ordered ‘lipid raft’ membrane microdomains in cellular membranes, including organelles. Given the critical role of cellular membranes in both compartmentalization and signaling, clarifying the roles of membrane microdomains and their mutual regulation of/by membrane proteins is important in understanding the fundamentals of biology, and has implications for health. Areas covered: This article will consider the evidence for lateral membrane phase separation in model membranes and organellar membranes, critically evaluate the current methods for lipid raft proteomics and discuss the biomedical implications of lipid rafts. Expert commentary: Lipid raft homeostasis is perturbed in numerous chronic conditions; hence, understanding the precise roles and regulation of the lipid raft proteome is important for health and medicine. The current technical challenges in performing lipid raft proteomics can be overcome through well-controlled experimental design and careful interpretation. Together with technical developments in mass spectrometry and microscopy, our understanding of lipid raft biology and function will improve through recognition of the similarity between organelle and plasma membrane lipid rafts and considered integration of published lipid raft proteomics data.
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

Abstract The Integrated Microbial Genome/Virus (IMG/VR) system v.2. 0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. Since the last report published in the 2016, NAR Database Issue, the data has tripled in size and currently contains genomes of 8389 cultivated reference viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, and 735 112 viral genomic fragments computationally predicted from assembled shotgun metagenomes. Nearly 60% of the viral genomes and genome fragments are clustered into 110 384 viral Operational Taxonomic Units (vOTUs) with two or more members. To improve data quality and predictions of host specificity, IMG/VR v.2. 0 now separates prokaryotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and provides viral genome quality scores based on the estimated genome completeness. New features also include enhanced BLAST search capabilities for external queries. Finally, geographic map visualization to locate user-selected viral genomes or genome fragments has been implemented and download options have been extended. All of these features make IMG/VR v.2. 0 a key resource for the study of viruses.
Lessons From Tesla for Plasma Medicine

It can be argued that plasma medicine originated with Nikola Tesla in the late 19th century when he showed that one could pass large quantities of high frequency currents through a human body with no apparent damage. Tesla’s work inspired much more extensive investigations over a period of several decades by numerous other researchers, on both the physics and biomedical effects of these currents. These early pioneers had a surprisingly modern view of some aspects of the therapeutic mechanisms of high frequency currents that clearly overlap with recent results. The perspective of this community was that the most important physiological effects are associated with the high frequency currents rather than the gas phase plasma per se. Some early work, such as the analgesic effects of dielectric barrier air plasma on tissue, is not well known today. The range of afflictions that early practitioners treated successfully is remarkable. This body of work, in some cases almost 130 years old, might have important lessons for current investigations into plasma medicine. Observations from Tesla and other early practitioners suggests that high frequency currents are potentially important and plasma medicine researchers should probably pay more attention to them.
Repetitive Motion Estimation Network: Recover cardiac and respiratory signal from thoracic imaging

Tracking organ motion is important in image-guided interventions, but motion annotations are not always easily available. Thus, we propose Repetitive Motion Estimation Network (RMEN) to recover cardiac and respiratory signals. It learns the spatio-temporal repetition patterns, embedding high dimensional motion manifolds to 1D vectors with partial motion phase boundary annotations. Compared with the best alternative models, our proposed RMEN significantly decreased the QRS peaks detection offsets by 59.3%. Results showed that RMEN could handle the irregular cardiac and respiratory motion cases. Repetitive motion patterns learned by RMEN were visualized and indicated in the feature maps.
Imaging Mass Spectrometry Reveals Crosstalk between the Fallopian Tube and the Ovary that Drives Primary Metastasis of Ovarian Cancer

High grade serous ovarian cancer (HGSOC) is the fifth leading cause of cancer deaths among women. New evidence suggests that HGSOC arises in the fallopian tube and then colonizes the ovary before spreading into the peritoneal space. Therefore, due to the proximity of this metastasis, an experimental design was optimized using imaging mass spectrometry to capture the spatial composition of small molecules uniquely expressed when fallopian-tube-derived tumor cells were grown in the microenvironment of the ovary as a model of primary metastasis. The observed mass-to-charge ratios (m/z’s) that were induced specifically in coculture represent small molecules that may contribute to the metastasis of HGSOC selectively to the ovary. Human fallopian tube epithelial HGSOC and tumorigenic murine oviductal epithelial cells, but not normal cell types, repeatedly induced a signal from the ovary at m/z 170. This signal was identified as norepinephrine, which was confirmed to stimulate invasion of ovarian cancer cells lacking wild-type p53. These molecules may reveal pathways that contribute to metastasis and biological targets for therapeutic intervention to block ovarian metastasis of fallopian-tube-derived HGSOC. The developed mass spectrometry method can be adapted to other mammalian-based model systems for investigation of untargeted metabolomics that facilitate metastasis.
Understanding the Users Personal Attributes Selection Tendency across Social Networks

Today, we are using social media services for virtual interaction with friends and colleagues. With each passing decade, several new and interactive social networks are coming into the existence to serve the people. Each established social network emulates the trait of new media and add the new features to survive in the versatile market. To enjoy the services of newly introduced social media, people migrate from one social network to the other by sharing her personal identities in a variety of formats. To understand the users' migration pattern from one social media to another, here we propose a hybrid personal information retrieval model consisting of two sub- methods, namely; cross-link based personal attributes matching and cross-platform based common friend relationship. Both the methods are effective for finding the similarities among the profile attributes across Twitter and LinkedIn. Further, both the techniques uses Levenshtein distance to match the user's personal attributes across the social media. The result shows that accuracy of name similarity using the first method is 66%, while the username and name similarity is 20%. Second method shows that 11.2% users contain the same or similar username and name on both the sites. It is found that the accuracy of the cross linked based approach is better than the friend relationship based approach.
Musical-Noise-Free Speech Enhancement with Low Speech Distortion by Biased Harmonic Regeneration Technique

Many noise reduction techniques generate two frequently occurring problems: speech distortion and musical noise. A number of methods have been proposed to solve these problems. One, which addresses the former problem, is harmonic regeneration noise reduction (HRNR). Using restored signals, HRNR regenerates the harmonics that were eliminated. Another, which addresses the latter problem, is a musical-noise-free noise reduction method based on the minimum mean-square error short-time spectral amplitude estimator. The method can suppress noisy speech without generating musical noise. This paper describes a new noise reduction technique we propose that combines these two methods. The technique is shown to be effective in suppressing both speech distortion and musical noise generation.
Object Tracking Under Occlusion Using LGEM-Trained SSVM

Adaptive tracking-by-detection methods are widely used in computer vision for object tracking. Struck tracking is known as avoiding unclear intermediate labeling steps, and utilizing both the SMO and the budgeting mechanism for updating. However, the fixed budget is inflexible and heuristic, and the optimization-loop easily leads SVMs to overfitting, and the fixed combination of three kernels with specified features weakens extension capabilities. Furthermore, the quick update causes wrong learning under occlusion, considering previous “negative” samples as the current “positive” samples and drifting the tracker to that “neg-ative” samples. In this paper, we present a framework based on both the one-kernel Struck and the Localized Generalization Error Model (LGEM). By comparing the $Q$ values of Structured output SVM (SSVM) with different structures and con-troling the updating loops, a tradeoff the Optimality and Generalization is realized. Moreover, via measuring the fluctuation on $Q$ value, suitable new samples are selected for updating, tracking is simplified into using a single Gaussian kernel for further potential extension. As a result, a more generalized, occlusion-overcoming tracker is constructed. Experimentally, our algorithm is shown to be able to outperform state-of-the-art trackers on occlusion handle on various benchmark videos.
CAAD 2018: Iterative Ensemble Adversarial Attack

Deep Neural Networks (DNNs) have recently led to significant improvements in many fields. However, DNNs are vulnerable to adversarial examples which are samples with imperceptible perturbations while dramatically misleading the DNNs. Adversarial attacks can be used to evaluate the robustness of deep learning models before they are deployed. Unfortunately, most of existing adversarial attacks can only fool a black-box model with a low success rate. To improve the success rates for black-box adversarial attacks, we proposed an iterated adversarial attack against an ensemble of image classifiers. With this method, we won the 5th place in CAAD 2018 Targeted Adversarial Attack competition.