Miracle-dz/UniFAR-FTUs huggingface dataset:
Microproteomic sample preparation

Multiple applications of proteomics in life and health science, pathology and pharmacology, require handling size‐limited cell and tissue samples. During proteomic sample preparation, analyte loss in these samples arises when standard procedures are used. Thus, specific considerations have to be taken into account for processing, that are summarised under the term microproteomics (μPs). Microproteomic workflows include: sampling (e.g., flow cytometry, laser capture microdissection), sample preparation (possible disruption of cells or tissue pieces via lysis, protein extraction, digestion in bottom‐up approaches, and sample clean‐up) and analysis (chromatographic or electrophoretic separation, mass spectrometric measurements and statistical/bioinformatic evaluation). All these steps must be optimised to reach wide protein dynamic ranges and high numbers of identifications. Under optimal conditions, sampling is adapted to the studied sample types and nature, sample preparation isolates and enriches the whole protein content, clean‐up removes salts and other interferences such as detergents or chaotropes, and analysis identifies as many analytes as the instrumental throughput and sensitivity allow. In the suggested review, we present and discuss the current state in μP applications for processing of small number of cells (cell μPs) and microscopic tissue regions (tissue μPs).
Extracellular Vesicles in Allergic Rhinitis and Asthma and Laboratory Possibilities for Their Assessment

Currently, extracellular vesicles (EVs) have been implicated in the etiopathogenesis of many diseases, including lung disorders, with the possibility of diagnostic and therapeutic applications. The analysis of EV in respiratory tract diseases faces many obstacles, including material collection from airways, standardization of isolation techniques, detection methods, the analysis of their content, etc. This review focuses on the role of extracellular vesicles in the pathogenesis of atopic respiratory diseases, especially asthma, with a special focus on their clinical applicability as a diagnostic tool. We also summarize available laboratory techniques that enable the detection of EVs in various biological materials, with particular emphasis on flow cytometry. The opportunities and limitations of detecting EV in bronchoalveolar lavage fluid (BALF) were also described.
Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

The first reference to the “C-value paradox” reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.
Improved Dissolution Rate and Intestinal Absorption of Fexofenadine Hydrochloride by the Preparation of Solid Dispersions: In Vitro and In Situ Evaluation

The objective of this study was to enhance dissolution and permeation of a low soluble, absorbable fexofenadine hydrochloride (FFH) by preparing solid dispersions using polyethylene glycol 20,000 (PEG 20,000) and poloxamer 188 as carriers. The phase solubility measurement for the supplied FFH revealed a linear increase in the solubility of fexofenadine with increasing carrier concentration in water (1.45 mg/mL to 11.78 mg/mL with 0% w/v to 30% w/v PEG 20,000; 1.45 mg/mL to 12.27 mg/mL with 0% w/v to 30% w/v poloxamer 188). To select the appropriate drug carrier concentration, a series of solid dispersions were prepared in the drug carrier weight ratios of 1:1, 1:2 and 1:4 by fusion method. The solid dispersions composed of drug carrier at 1:4 weight ratio showed highest dissolution with the time required for the release of 50% of the drug <15 min compared to the supplied FFH (>120 min). The intestinal absorption study presented a significant improvement in the absorption of drug from the solid dispersions composed of poloxamer 188 than PEG 20,000. In summary, the solid dispersions of FFH prepared using PEG 20,000 and poloxamer 188 demonstrated improved dissolution and absorption than supplied FFH and could be used to improve the oral bioavailability of fexofenadine.
Current status of antigen-specific T-cell immunotherapy for advanced renal-cell carcinoma

ABSTRACT In renal-cell carcinoma (RCC), tumor-reactive T-cell responses can occur spontaneously or in response to systemic immunotherapy with cytokines and immune checkpoint inhibitors. Cancer vaccines and engineered T-cell therapies are designed to selectively augment tumor antigen-specific CD8+ T-cell responses with the goal to elicit tumor regression and avoid toxicities associated with nonspecific immunotherapies. In this review, we provide an overview of the central role of T-cell immunity in the treatment of advanced RCC. Clinical outcomes for antigen-targeted vaccines or other T-cell-engaging therapies for RCC are summarized and evaluated, and emerging new strategies to enhance the effectiveness of antigen-specific therapy for RCC are discussed.
Nanostructured TiO2 Films with Controlled Morphology Synthesized in a Single Step Process: Performance of Dye-Sensitized Solar Cells and Photo Watersplitting

Nanostructured titanium dioxide (TiO2) films were synthesized with controlled morphology and thickness in an ambient pressure single-step flame aerosol reactor (FLAR) for use in water splitting photocells and dye-sensitized solar cells. Two different morphologies were studied: a granular morphology and a highly crystalline columnar morphology. The granular morphology consisted of nanoparticles, approximately 10 nm in diameter, aggregated into fractal structures on the substrate. The granular morphology contained a large number of grain boundaries and other interfacial defects. The columnar morphology consisted of single-crystal structures, approximately 85 nm in width, oriented normal to the substrate. The well controlled deposition process was used to deposit films with thicknesses in the range from 98 nm to 12 μm to establish the relationship to water splitting and dye-sensitized solar cell performance. It was found that for watersplitting there was an optimum thickness (∼1.5 μm), which was a tradeoff .
A Scoping Review of Neuromodulation Techniques in Neurodegenerative Diseases: A Useful Tool for Clinical Practice?

Background and Objectives: Neurodegenerative diseases that typically affect the elderly such as Alzheimer’s disease, Parkinson’s disease and frontotemporal dementia are typically characterised by significant cognitive impairment that worsens significantly over time. To date, viable pharmacological options for the cognitive symptoms in these clinical conditions are lacking. In recent years, various studies have employed neuromodulation techniques to try and contrast patients’ decay. Materials and Methods: We conducted an in-depth literature review of the state-of-the-art of the contribution of these techniques across these neurodegenerative diseases. Results: The present review reports that neuromodulation techniques targeting cognitive impairment do not allow to draw yet any definitive conclusion about their clinical efficacy although preliminary evidence is very encouraging. Conclusions: Further and more robust studies should evaluate the potentialities and limitations of the application of these promising therapeutic tools to neurodegenerative diseases.
Detection Line Spectrum of Ship Radiated Noise Based on a New 3D Chaotic System

Abstracts This paper proposes a new detection model of a weak signal based on a third-order chaotic system. Using a dynamic analysis tool, such as the Lyapunov exponent and the bifurcation diagram, variations of dynamic behavior can be observed, and the weak signal underwater can be picked up. In order to improve the observability of detection signals in the time domain and frequency domain, the spectral entropy complexity algorithm (SE) and C0 complexity algorithms are used to analyze and extract the weak signal. The experimental results show that the spectrum extraction based on the complexity algorithm can accurately reflect the dynamic characteristics of the detected signal. It provides the theoretical direction and experimental data support for the application of the chaotic system in the field of acoustic detection.
Medical and Nonmedical Information during Multidisciplinary Team Meetings in Cancer Care

Background: Multidisciplinary team (MDT) meetings provide treatment recommendations based on available information and collective decision-making in teams with complementary professions, disciplines and skills. We aimed to map ancillary medical and nonmedical patient information during case presentations and case discussions in MDT meetings in cancer care. Methods: Through a nonparticipant, observational approach, we mapped verbal information on medical, nonmedical and patient-related characteristics and classified these based on content. Data were collected from 336 case discussions in three MDTs for neuro-oncology, sarcoma and hepato-biliary cancer. Results: Information on physical status was presented in 48.2% of the case discussions, psychological status in 8.9% and comorbidity in 48.5% of the cases. Nonmedical factors, such as family relations, occupation, country of origin and abode were referred to in 3.6–7.7% of the cases, and patient preferences were reported in 4.2%. Conclusions: Provision of information on comorbidities in half of the cases and on patient characteristics and treatment preferences in <10% of case discussions suggest a need to define data elements and develop reporting standards to support robust MDT decision-making.
Identification of Enzymatic Bottlenecks for the Aerobic Production of Malate from Glycerol by the Systematic Gene Overexpression of Anaplerotic Enzymes in Escherichia coli

The biotechnological production of dicarboxylic acids (C4) from renewable carbon sources represents an attractive approach for the provision of these valuable compounds by green chemistry means. Glycerol has become a waste product of the biodiesel industry that serves as a highly reduced carbon source for some microorganisms. Escherichia coli is capable of consuming glycerol to produce succinate under anaerobic fermentation, but with the deletion of some tricarboxylic acid (TCA) cycle genes, it is also able to produce succinate and malate in aerobiosis. In this study, we investigate possible rate-limiting enzymes by overexpressing the C-feeding anaplerotic enzymes Ppc, MaeA, MaeB, and Pck in a mutant that lacks the succinate dehydrogenase (Sdh) enzyme. The overexpression of the TCA enzyme Mdh and the activation of the glyoxylate shunt was also examined. Using this unbiased approach, we found that phosphoenol pyruvate carboxylase (Ppc) overexpression enhances an oxidative pathway that leads to increasing succinate, while phosphoenol pyruvate carboxykinase (Pck) favors a more efficient reductive branch that produces mainly malate, at 57.5% of the theoretical maximum molar yield. The optimization of the culture medium revealed the importance of bicarbonate and pH in the production of malate. An additional mutation of the ppc gene highlights its central role in growth and C4 production.
Blocking Aerobic Glycolysis by Targeting Pyruvate Dehydrogenase Kinase in Combination with EGFR TKI and Ionizing Radiation Increases Therapeutic Effect in Non-Small Cell Lung Cancer Cells

Simple Summary Non-small cell lung cancer (NSCLC) patients harboring oncogenic mutations in the epidermal growth factor receptor (EGFR) inevitably develop resistance to targeted EGFR tyrosine kinase inhibitors (TKI) therapy. To support malignant features associated with cancer development and therapy resistance, the cancer cells adapt their metabolic rate and pathways. As an example, aerobic glycolysis, where the cells use glycolysis in the presence of oxygen, is frequently seen. Here we show that targeting aerobic glycolysis represents a promising strategy in cancer therapeutics. Abstract Increased glycolytic activity is a hallmark of cancer initiation and progression and is often observed in non-small cell lung cancer (NSCLC). Pyruvate dehydrogenase (PDH) complex acts as a gatekeeper between glycolysis and oxidative phosphorylation, and activation of PDH is known to inhibit glycolytic activity. As part of a standard therapeutic regimen, patients with NSCLC harboring oncogenic mutations in the epidermal growth factor receptor (EGFR) are treated with EGFR tyrosine kinase inhibitors (EGFR TKIs). Independent of good initial response, development of resistance to this therapy is inevitable. In the presented work, we propose that inhibition of glycolysis will add to the therapeutic effects and possibly prevent development of resistance against both EGFR TKIs and ionizing radiation in NSCLC. Analysis of transcriptome data from two independent NSCLC patient cohorts identified increased expression of pyruvate dehydrogenase kinase 1 (PDHK1) as well as upregulated expression of genes involved in glucose metabolism in tumors compared to normal tissue. We established in vitro models of development of resistance to EGFR TKIs to study metabolism and determine if targeting PDHK would prevent development of resistance to EGFR TKIs in NSCLC cells. The PDHK1 inhibitor dichloroacetate (DCA) in combination with EGFR TKIs and/or ionizing radiation was shown to increase the therapeutic effect in our NSCLC cell models. This mechanism was associated with redirected metabolism towards pyruvate oxidation and reduced lactate production, both in EGFR TKI sensitive and resistant NSCLC cells. Using DCA, the intracellular pool of pyruvate available for lactic fermentation becomes limited. Consequently, pyruvate is redirected to the mitochondria, and reinforces mitochondrial activity. Addition of DCA to cell culture deacidifies the extracellular microenvironment as less lactate is produced and excreted. In our study, we find that this redirection of metabolism adds to the therapeutic effect of EGFR TKI and ionizing radiation in NSCLC.
Responses of Vaginal Microbiota to Dietary Supplementation with Lysozyme and its Relationship with Rectal Microbiota and Sow Performance from Late Gestation to Early Lactation

Simple Summary The vaginal microbiota has a crucial role for the health of the sow and the newborn piglet. The purpose of this study was to investigate the effect of dietary supplementation with lysozyme in the vaginal microbiota and evaluate its relationship with the fecal microbiota of the rectum and the reproductive performance of the sow. The results suggest that, lysozyme supplementation changed vaginal microbiota composition at different taxonomic levels, the changed vaginal microbiota was associated with variations in fecal microbiota, and these changes correlated with some reproductive performance of the sow. Abstract This study was conducted to evaluate the effects of dietary lysozyme (LZM) supplementation on the vaginal microbiota, as well as the relationship between vaginal microbiota and the fecal microbiota of rectum and the reproductive performance of the sow. A total of 60 Yorkshire × Landrace sows (3–6 of parity) were arranged from day 85 of gestation to the end of lactation in a completely randomized design with three treatments (control diet, control diet + lysozyme 150 mg/kg, control diet + lysozyme 300 mg/kg). The results showed that sows fed with lysozyme increased serum interleukin-10 (IL-10, p < 0.05) on day 7 of lactation. The vaginal microbiota varied at different taxonomic levels with LZM supplementation by 16S rRNA gene sequencing. The most representative changes included a decrease in Tenericutes, Streptococcus, Bacillus and increase in Bacteroidetes, Actinobacteria, Enterococcus, and Lactobacillus (p < 0.05). There were 777 OTUs existing in both, vaginal and fecal microbiota. The addition of LZM also decreased the abundance of Tenericutes (p < 0.05) in the vagina and feces. The changes in the microbiota were correlated in some cases positively with the performance of the sow, for example, Bacillus in feces was positively correlated with the neonatal weight (p < 0.05). These results indicate that the addition of lysozyme to the diet of sow during perinatal period promote the change of vaginal bacterial community after farrowing. The variations in vaginal microbiota are also associated with the changes in the fecal microbiology of the rectum and the reproductive performance of the sow. Therefore, it is concluded that dietary supplementation with lysozyme in sows in late gestation stage until early lactation, is beneficial to establish vaginal microbiota that seems to promote maternal health and reproductive performance.
Bio-Impedance Measurement Optimization for High-Resolution Carotid Pulse Sensing

Continuous hemodynamic monitoring is important for long-term cardiovascular healthcare, especially in hypertension. The impedance plethysmography (IPG) based carotid pulse sensing is a non-invasive diagnosis technique for measuring pulse signals and further evaluating the arterial conditions of the patient such as continuous blood pressure (BP) monitoring. To reach the high-resolution IPG-based carotid pulse detection for cardiovascular applications, this study provides an optimized measurement parameter in response to obvious pulsation from the carotid artery. The influence of the frequency of excitation current, electrode cross-sectional area, electrode arrangements, and physiological site of carotid arteries on IPG measurement resolution was thoroughly investigated for optimized parameters. In this study, the IPG system was implemented and installed on the subject’s neck above the carotid artery to evaluate the measurement parameters. The measurement results within 6 subjects obtained the arterial impedance variation of 2137 mΩ using the optimized measurement conditions, including excitation frequency of 50 kHz, a smaller area of 2 cm2, electrode spacing of 4 cm and 1.7 cm for excitation and sensing functions, and location on the left side of the neck. The significance of this study demonstrates an optimized measurement methodology of IPG-based carotid pulse sensing that greatly improves the measurement quality in cardiovascular monitoring.
Extracorporeal Gas Exchange for Acute Respiratory Distress Syndrome: Open Questions, Controversies and Future Directions

Veno-venous extracorporeal membrane oxygenation (V-V ECMO) in acute respiratory distress syndrome (ARDS) improves gas exchange and allows lung rest, thus minimizing ventilation-induced lung injury. In the last forty years, a major technological and clinical improvement allowed to dramatically improve the outcome of patients treated with V-V ECMO. However, many aspects of the care of patients on V-V ECMO remain debated. In this review, we will focus on main issues and controversies on caring of ARDS patients on V-V ECMO support. Particularly, the indications to V-V ECMO and the feasibility of a less invasive extracorporeal carbon dioxide removal will be discussed. Moreover, the controversies on management of mechanical ventilation, prone position and sedation will be explored. In conclusion, we will discuss evidences on transfusions and management of anticoagulation, also focusing on patients who undergo simultaneous treatment with ECMO and renal replacement therapy. This review aims to discuss all these clinical aspects with an eye on future directions and perspectives.
Optimizing Calcium Detection Methods in Animal Systems: A Sandbox for Synthetic Biology

Since the 1970s, the emergence and expansion of novel methods for calcium ion (Ca2+) detection have found diverse applications in vitro and in vivo across a series of model animal systems. Matched with advances in fluorescence imaging techniques, the improvements in the functional range and stability of various calcium indicators have significantly enhanced more accurate study of intracellular Ca2+ dynamics and its effects on cell signaling, growth, differentiation, and regulation. Nonetheless, the current limitations broadly presented by organic calcium dyes, genetically encoded calcium indicators, and calcium-responsive nanoparticles suggest a potential path toward more rapid optimization by taking advantage of a synthetic biology approach. This engineering-oriented discipline applies principles of modularity and standardization to redesign and interrogate endogenous biological systems. This review will elucidate how novel synthetic biology technologies constructed for eukaryotic systems can offer a promising toolkit for interfacing with calcium signaling and overcoming barriers in order to accelerate the process of Ca2+ detection optimization.
High Frequency of Enterocytozoon bieneusi Genotype WL12 Occurrence among Immunocompromised Patients with Intestinal Microsporidiosis

Microsporidiosis is an emerging opportunistic infection causing severe digestive disorders in immunocompromised patients. The aim of this study was to investigate the prevalence of intestinal microsporidia carriage among immunocompromised patients hospitalized at a major hospital complex in the Tunis capital area, Tunisia (North Africa), and perform molecular epidemiology and population structure analyses of Enterocytozoon bieneusi, which is an emerging fungal pathogen. We screened 250 stool samples for the presence of intestinal microsporidia from 171 patients, including 81 organ transplant recipients, 73 Human Immunodeficiency Virus (HIV)-positive patients, and 17 patients with unspecified immunodeficiency. Using a nested PCR-based diagnostic approach for the detection of E. bieneusi and Encephalitozoon spp. , we identified 18 microsporidia-positive patients out of 171 (10.5%), among which 17 were infected with E. bieneusi. Microsporidia-positive cases displayed chronic diarrhea (17 out of 18), which was associated more with HIV rather than with immunosuppression other than HIV (12 out of 73 versus 6 out of 98, respectively, p = 0.02) and correlated with extended hospital stays compared to microsporidia-negative cases (60 versus 19 days on average, respectively; p = 0.001). Strikingly, internal transcribed spacer (ITS)-based genotyping of E. bieneusi strains revealed high-frequency occurrence of ITS sequences that were identical (n = 10) or similar (with one single polymorphic site, n = 3) to rare genotype WL12. Minimum-spanning tree analyses segregated the 17 E. bieneusi infection cases into four distinct genotypic clusters and confirmed the high prevalence of genotype WL12 in our patient population. Phylogenetic analyses allowed the mapping of all 17 E. bieneusi strains to zoonotic group 1 (subgroups 1a and 1b/1c), indicating loose host specificity and raising public health concern. Our study suggests a probable common source of E. bieneusi genotype WL12 transmission and prompts the implementation of a wider epidemiological investigation.