Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the Promoter of FAT10 Gene in HCC Patients

FAT10, which is also known as diubiquitin, has been implicated to play important roles in immune regulation and tumorigenesis. Its expression is up-regulated in the tumors of Hepatocellular Carcinoma (HCC) and other cancer patients. High levels of FAT10 in cells have been shown to result in increased mitotic non-disjunction and chromosome instability, leading to tumorigenesis. To evaluate whether the aberrant up-regulation of the FAT10 gene in the tumors of HCC patients is due to mutations or the aberrant methylation of CG dinucleotides at the FAT10 promoter, sequencing and methylation-specific sequencing of the promoter of FAT10 was performed. No mutations were found that could explain the differential expression of FAT10 between the tumor and non-tumorous tissues of HCC patients. However, six single nucleotide polymorphisms (SNPs), including one that has not been previously reported, were identified at the promoter of the FAT10 gene. Different haplotypes of these SNPs were found to significantly mediate different FAT10 promoter activities. Consistent with the experimental observation, differential FAT10 expression in the tumors of HCC patients carrying haplotype 1 was generally higher than those carrying haplotype II. Notably, the methylation status of this promoter was found to correlate with FAT10 expression levels. Hence, the aberrant overexpression of the FAT10 gene in the tumors of HCC patients is likely due to aberrant methylation, rather than mutations at the FAT10 promoter.
Glutathione in Ovarian Cancer: A Double-Edged Sword

Glutathione (GSH) has several roles in a cell, such as a reactive oxygen species (ROS) scavenger, an intervenient in xenobiotics metabolism and a reservoir of cysteine. All of these activities are important in the maintenance of normal cells homeostasis but can also constitute an advantage for cancer cells, allowing disease progression and resistance to therapy. Ovarian cancer is the major cause of death from gynaecologic disease and the second most common gynaecologic malignancy worldwide. In over 50 years, the overall survival of patients diagnosed with epithelial ovarian cancer has not changed, regardless of the efforts concerning early detection, radical surgery and new therapeutic approaches. Late diagnosis and resistance to therapy are the main causes of this outcome, and GSH is profoundly associated with chemoresistance to platinum salts, which, together with taxane-based chemotherapy and surgery, are the main therapy strategies in ovarian cancer treatment. Herein, we present some insights into the role of GSH in the poor prognosis of ovarian cancer, and also point out how some strategies underlying the dependence of ovarian cancer cells on GSH can be further used to improve the effectiveness of therapy.
Spatial Coherence of Backscattered Signals in Multi-Line Transmit Ultrasound Imaging and Its Effect on Short-Lag Filtered-Delay Multiply and Sum Beamforming

In Multi-Line Transmission (MLT), high frame-rate ultrasound imaging is achieved by the simultaneous transmission of multiple focused beams along different directions, which unfortunately generates unwanted artifacts in the image due to inter-beam crosstalk. The Filtered-Delay Multiply and Sum (F-DMAS) beamformer, a non-linear spatial-coherence (SC)-based algorithm, was demonstrated to successfully reduce such artifacts, improving the spatial resolution at the same time. In this paper, we aim to provide further insights on the working principle and performance of F-DMAS beamforming in MLT imaging. First, we carry out an analytical study to analyze the behavior and trend of backscattered signals SC in MLT images, when the number of simultaneously transmitted beams and/or their angular spacing change. We then reconsider the F-DMAS algorithm proposing the “short-lag F-DMAS” formulation, in order to limit the maximum lag of signals used for the SC computation on which the beamformer is based. Therefore, we investigate in simulations how the performance of short-lag F-DMAS varies along with the maximum lag in the different MLT configurations considered. Finally, we establish a relation between the obtained results and the signals SC trend.
Cutting-Processed Single-Wall Carbon Nanotubes with Additional Edge Sites for Supercapacitor Electrodes

Carbon nanotubes are frequently selected for supercapacitors because of their major intrinsic properties of mechanical and chemical stability, in addition to their excellent electrical conductivity. However, electrodes using carbon nanotubes suffer from severe performance degradation by the phenomenon of re-stacking during fabrication, which hinders ion accessibility. In this study, short single-wall carbon nanotubes were further shortened by sonication-induced cutting to increase the proportion of edge sites. This longitudinally short structure preferentially exposes the active edge sites, leading to high capacitance during operation. Supercapacitors assembled using the shorter-cut nanotubes exhibit a 7-fold higher capacitance than those with pristine single-wall nanotubes while preserving other intrinsic properties of carbon nanotubes, including excellent cycle performance and rate capability. The unique structure suggests a design approach for achieving a high specific capacitance with those low-dimensional carbon materials that suffer from re-stacking during device fabrication.
Development of a Method to Monitor Gene Expression in Single Bacterial Cells During the Interaction With Plants and Use to Study the Expression of the Type III Secretion System in Single Cells of Dickeya dadantii in Potato

Dickeya dadantii is a bacterial plant pathogen that causes soft rot disease on a wide range of host plants. The type III secretion system (T3SS) is an important virulence factor in D. dadantii. Expression of the T3SS is induced in the plant apoplast or in hrp-inducing minimal medium (hrp-MM), and is repressed in nutrient-rich media. Despite the understanding of induction conditions, how individual cells in a clonal bacterial population respond to these conditions and modulate T3SS expression is not well understood. In our previous study, we reported that in a clonal population, only a small proportion of bacteria highly expressed T3SS genes while the majority of the population did not express T3SS genes under hrp-MM condition. In this study, we developed a method that enabled in situ observation and quantification of gene expression in single bacterial cells in planta. Using this technique, we observed that the expression of the T3SS genes hrpA and hrpN is restricted to a small proportion of D. dadantii cells during the infection of potato. We also report that the expression of T3SS genes is higher at early stages of infection compared to later stages. This expression modulation is achieved through adjusting the ratio of T3SS ON and T3SS OFF cells and the expression intensity of T3SS ON cells. Our findings not only shed light into how bacteria use a bi-stable gene expression manner to modulate an important virulence factor, but also provide a useful tool to study gene expression in individual bacterial cells in planta.
Synthesis, Immunosuppressive Properties, and Mechanism of Action of a New Isoxazole Derivative

This work describes the synthesis of a new series of isoxazole derivatives, their immunosuppressive properties, and the mechanism of action of a representative compound. A new series of N′-substituted derivatives of 5-amino-N,3-dimethyl-1,2-oxazole-4-carbohydrazide (MM1–MM10) was synthesized in reaction of 5-amino-N,3-dimethyl-1,2-oxazole-4-carbohydrazide with relevant carbonyl compounds. The isoxazole derivatives were tested in several in vitro models using human cells. The compounds inhibited phytohemagglutinin A (PHA)-induced proliferation of peripheral blood mononuclear cells (PBMCs) to various degrees. The toxicity of the compounds with regard to a reference A549 cell line was also differential. 5-amino-N′-(2,4-dihydroxyphenyl)methylidene-N,3-dimethyl-1,2-oxazole-4-carbohydrazide (MM3) compound was selected for further investigation because of its lack of toxicity and because it had the strongest antiproliferative activity. The compound was shown to inhibit lipopolysaccharide (LPS)-induced tumor necrosis factor (TNF α) production in human whole blood cell cultures. In the model of Jurkat cells, MM3 elicited strong increases in the expression of caspases, Fas, and NF-κB1, indicating that a proapoptotic action may account for its immunosuppressive action in the studied models.
Employee Attrition Prediction

We aim to predict whether an employee of a company will leave or not, using the k-Nearest Neighbors algorithm. We use evaluation of employee performance, average monthly hours at work and number of years spent in the company, among others, as our features. Other approaches to this problem include the use of ANNs, decision trees and logistic regression. The dataset was split, using 70% for training the algorithm and 30% for testing it, achieving an accuracy of 94.32%.
Speckle Reduction for Ultrasonic Imaging Using Frequency Compounding and Despeckling Filters along with Coded Excitation and Pulse Compression

A method for improving the contrast-to-noise ratio (CNR) while maintaining the −6 dB axial resolution of ultrasonic B-mode images is proposed. The technique proposed is known as eREC-FC, which enhances a recently developed REC-FC technique. REC-FC is a combination of the coded excitation technique known as resolution enhancement compression (REC) and the speckle-reduction technique frequency compounding (FC). In REC-FC, image CNR is improved but at the expense of a reduction in axial resolution. However, by compounding various REC-FC images made from various subband widths, the tradeoff between axial resolution and CNR enhancement can be extended. Further improvements in CNR can be obtained by applying postprocessing despeckling filters to the eREC-FC B-mode images. The despeckling filters evaluated were the following: median, Lee, homogeneous mask area, geometric, and speckle-reducing anisotropic diffusion (SRAD). Simulations and experimental measurements were conducted with a single-element transducer (f/2.66) having a center frequency of 2.25 MHz and a −3 dB bandwidth of 50%. In simulations and experiments, the eREC-FC technique resulted in the same axial resolution that would be typically observed with conventional excitation with a pulse. Moreover, increases in CNR of 348% were obtained in experiments when comparing eREC-FC with a Lee filter to conventional pulsing methods.
Fundamental Limits in Detecting Whether a Signal Has Been Quantized

It is often important to know whether a received signal was sent directly by a friend, or was recorded by an adversary and then replayed. In this paper, we use a characteristic of the recording, namely the quantization, to study if the replayed (quantized) signal can be detected. In particular, we consider the requirements on the quantizer to keep the quantization from being detected in additive Gaussian noise. If a signal with length $m$ is sent and a uniform quantizer with $b$ quantization bits is employed for recording, we prove that $2^{b} = \omega (\sqrt {m})$ and a quantizer span of $\omega (\sqrt {\ln m})$ are sufficient for the adversary to avoid detection; that is, the probability of error $P_{e}$ of the observer is bounded as $P_{e} \geq \displaystyle \frac {1}{2} -\epsilon $ for any $\epsilon > 0$. Conversely, having $2^{b} =\mathrm {O}(\sqrt {m})$ or a quantizer span of $o(\sqrt {\ln m})$ results in detection by the observer with high probability as $m\rightarrow \infty . $
Determination of bubbles in foods by X-ray microtomography and image analysis

Introduction. Bubbles play a key role in many types of food products including bakery products, dairy foams, confectionary, breakfast cereals, snacks and ice cream. Bubbles create an aerated structure resulting in novel textures, enhanced taste perception and attractive appearance. They are cheap ingredients and will add no calories. Soft foams such as whipped cream, aerated desserts and mousses contain separate gas bubbles in medium viscosity liquids or semi solids. However many food products are like sponges, in which nearly all bubbles are interconnected to give a porous network with a continuous gas phase. Examples are bread, cake and biscuits. Bubbles can be formed by a large variety of methods which may be specific to one or more food types, e.g. whipping, mixing, fermentation, chemical agents, freeze drying, puffing, extrusion, frying and gas injection. The microstructure will not only influence sensory properties but also the stability, shelf-life and preparation time of the products. A detailed understanding is needed of the relation between microstructure, and product properties. This paper describes a study that uses X-ray microtomography (μCT) for the characterisation and visualisation of the 3D microstructure of aerated desserts, ice cream, chocolate bars, dried vegetables, puffed rice and bread. 3D image analysis (IA) methods were used to obtain quantitative information about the cellular matrix.
Quantitative risk analysis using vulnerability indicators to assess food insecurity in the Niayes agricultural region of West Senegal

There is an increasing need to develop indicators of vulnerability and adaptive capacity to determine the robustness of response strategies over time and better understand the underlying processes. This study aimed to determine levels of risk of food insecurity using defined vulnerability indicators. For the purpose of this study, factors influencing food insecurity and different vulnerable indicators were examined using quantitative and qualitative research methods. Observations made on the physical environment (using tools for spatial analysis) and socio-economic surveys conducted with local populations have quantified vulnerability indicators in the Niayes agricultural region. Application of the Classification and Regression Tree (CART) model has enabled us to quantify the level of vulnerability of the zone. The results show that the decrease in agricultural surface areas is the most discriminant one in this study. The speed of reduction of the agricultural areas has specially increased between 2009 and 2014, with a loss of 65% of these areas. Therefore, a decision-making system, centred on the need for reinforcing the resilience of local populations, by preserving the agricultural vocation of the Niayes region and even in the Sahelian regions requires support and extension services for the farmers in order to promote sustainable agricultural practices.
Evidence of increased humoral endocrine organ-specific autoimmunity in severe and classic X-chromosome aneuploidies in comparison with 46,XY control subjects

Abstract Objective: In literature, the importance of X-linked gene dosage as a contributing factor for autoimmune diseases is generally assumed. However, little information is available on the frequency of humoral endocrine organ-specific autoimmunity in X-chromosome aneuploidies. In our preliminary study, we investigated the endocrine organ-specific humoral autoimmunity relative to four different organ-specific autoimmune diseases in a group of adult 47,XXY KS patients and in adults 46,XY control males (type 1 diabetes, T1DM; Addison’s disease, AD; Hashimoto thyroiditis, HT; autoimmune chronic atrophic gastritis, AG). The aim of the present study is to evaluate the frequency of autoantibodies (Abs) specific for T1DM, AD, HT, and AG in rarer higher grade X-chromosome aneuploidies (HGA) and in 47,XXY children. Design and methods: Samples from 192 Caucasian patients with an X-chromosome aneuploidy (176 patients (55 children, 121 adults) with 47,XXY karyotype (KS patients) and 16 HGA patients (eight children, eight adults)) recruited from Sapienza, University of Rome (2007–2017) were tested for Abs specific for T1DM (insulin-Abs, GAD-Abs, IA-2-Abs, Znt8-Abs), HT (TPO-Abs), AD (21-OH-Abs), and AG (APC-Abs). The results were compared to those found in 213 46,XY control subjects (96 children, 117 adults). Results: Altogether humoral organ-specific immunoreactivity was found in 13% of KS and HGA patients, with a significantly higher frequency than in the controls (p=.008). Almost 19% of HGA patients were positive for at least one of the organ-specific Abs investigated compared to 12.5% of KS patients. The frequency of the overall immunoreactivity was higher in KS children than in KS adults. The frequency of diabetes-specific Abs was significantly higher in the patient cohort than in controls (p=.005). Thyroid- and gastric-specific autoimmunity was also found in KS and HGA patients, while adrenal-specific immunoreactivity was rare. Conclusions: These results suggest for the first time that the risk of endocrine organ-specific humoral autoimmunity progressively increases with the severity of X-chromosome polisomy. The screening for diabetes-, thyroid-, and gastric-specific autoimmunity should be considered in clinical practice for identifying rare and classic X-chromosome aneuploid patients at risk of developing organ-specific autoimmune diseases.
Various Approaches of VANET Routing and Attack Detection

: VANET basically is the part of MANET that provides feasible communication to the vehicles.The RSU‘s in the phenomena help the vehicles to easily communicate and hence provide collisions. This paper briefly explains about the attack that occurs in the VANET scenario. In this various routing protocols, attack detection approaches used in VANET have been described. In this network safety message delivery without any delay has to be essential to avoid any collision in the network. On the basis of study of different approaches in VANET best approach can be extracted that can be used for VANET network in real world applications.
Selective Regulation of Cytoskeletal Dynamics and Filopodia Formation by Teleost Leukocyte Immune-Type Receptors Differentially Contributes to Target Capture During the Phagocytic Process

Phagocytosis evolved from a fundamental nutrient acquisition mechanism in primitive unicellular amoeboids, into a dynamic and complex component of innate immunity in multicellular organisms. To better understand the cellular mechanisms contributing to phagocytic processes across vertebrates, our research has focused on characterizing the involvement of innate immune proteins originally identified in channel catfish (Ictalurus punctatus) called leukocyte immune-type receptors (IpLITRs). These unique teleost proteins share basic structural as well as distant phylogenetic relationships with several immunoregulatory proteins within the mammalian immunoglobulin superfamily. In the present study, we use a combination of live-cell confocal imaging and high-resolution scanning electron microscopy to further examine the classical immunoreceptor tyrosine-based activation motif (ITAM)-dependent phagocytic pathway mediated by the chimeric construct IpLITR 2.6b/IpFcRγ-L and the functionally diverse immunoreceptor tyrosine-based inhibitory motif-containing receptor IpLITR 1.1b. Results demonstrate that IpLITR 1.1b-expressing cells can uniquely generate actin-dense filopodia-like protrusions during the early stages of extracellular target interactions. In addition, we observed that these structures retract after contacting extracellular targets to secure captured microspheres on the cell surface. This activity was often followed by the generation of robust secondary waves of actin polymerization leading to the formation of stabilized phagocytic cups. At depressed temperatures of 27°C, IpLITR 2.6b/IpFcRγ-L-mediated phagocytosis was completely blocked, whereas IpLITR 1.1b-expressing cells continued to generate dynamic actin-dense filopodia at this lower temperature. Overall, these results provide new support for the hypothesis that IpLITR 1.1b, but not IpLITR 2.6b/IpFcRγ-L, directly triggers filopodia formation when expressed in representative myeloid cells. This also offers new information regarding the directed ability of immunoregulatory receptor-types to initiate dynamic membrane structures and provides insights into an alternative ITAM-independent target capture pathway that is functionally distinct from the classical phagocytic pathways.
Multidrug-resistant bacteria isolated from cell phones in five intensive care units: Exploratory dispersion analysis.

Introduction Cell phones are susceptible to bacterial contamination. The aim of this study was to characterize the bacterial isolates and to explore their dispersion in five Intensive Care Units (ICUs) over the time. Methods We performed a secondary analysis of non-fermenting Gram-negative bacteria and Gram-positive cocci isolated from a 5-month observational cohort study developed among health care workers' cell phones in five ICUs. Cell phones were sampled using a swab every 15 days. Antimicrobial resistance was determined by the minimum inhibitory concentration method. We constructed resistance phenotypes to group the isolates according to species and antimicrobial resistance pattern to explore dispersion through time. Results A total of 35 P. aeruginosa, 16 Acinetobacter spp. , 30 S. aureus and 26 Enterococcus spp. were isolated from 491 phone samples. Multidrug resistance was 2.9% for P. aeruginosa, 31.3% for Acinetobacter spp. , 46.7% for S. aureus and 80.8% for Enterococcus spp. The resistance to methicillin in S. aureus and to vancomycin in Enterococcus spp. was 26.7% and 42.3%, respectively. We did not observe distribution patterns or clusters over the time for P. aeruginosa, Acinetobacter spp. and Enterococcus spp. isolates. All the S. aureus isolates grouped into eight phenotypes. Interestingly, we observed S. aureus isolates with the same phenotype in consecutive and separate sampling dates in the same cell phone. Conclusion Cell phones are contaminated with highly harmful bacteria and potentially can maintain them for prolonged periods of time. These devices could be considered as a potential source of nosocomial infections in ICUs.
Online EEG artifact removal for BCI applications by adaptive spatial filtering

Objective. The performance of brain–computer interfaces (BCIs) based on electroencephalography (EEG) data strongly depends on the effective attenuation of artifacts that are mixed in the recordings. To address this problem, we have developed a novel online EEG artifact removal method for BCI applications, which combines blind source separation (BSS) and regression (REG) analysis. Approach. The BSS-REG method relies on the availability of a calibration dataset of limited duration for the initialization of a spatial filter using BSS. Online artifact removal is implemented by dynamically adjusting the spatial filter in the actual experiment, based on a linear regression technique. Main results. Our results showed that the BSS-REG method is capable of attenuating different kinds of artifacts, including ocular and muscular, while preserving true neural activity. Thanks to its low computational requirements, BSS-REG can be applied to low-density as well as high-density EEG data. Significance. We argue that BSS-REG may enable the development of novel BCI applications requiring high-density recordings, such as source-based neurofeedback and closed-loop neuromodulation.