Miracle-dz/UniFAR-FTUs huggingface dataset:
PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations

Pupylation is a type of reversible post-translational modification of proteins, which plays a key role in the cellular function of microbial organisms. Several proteomics methods have been developed for the prediction and analysis of pupylated proteins and pupylation sites. However, the traditional experimental methods are laborious and time-consuming. Hence, computational algorithms are highly needed that can predict potential pupylation sites using sequence features. In this research, a new prediction model, PUP-Fuse, has been developed for pupylation site prediction by integrating multiple sequence representations. Meanwhile, we explored the five types of feature encoding approaches and three machine learning (ML) algorithms. In the final model, we integrated the successive ML scores using a linear regression model. The PUP-Fuse achieved a Mathew correlation value of 0.768 by a 10-fold cross-validation test. It also outperformed existing predictors in an independent test. The web server of the PUP-Fuse with curated datasets is freely available.
Advances and Perspectives in the Management of Varicella-Zoster Virus Infections

Varicella-zoster virus (VZV), a common and ubiquitous human-restricted pathogen, causes a primary infection (varicella or chickenpox) followed by establishment of latency in sensory ganglia. The virus can reactivate, causing herpes zoster (HZ, shingles) and leading to significant morbidity but rarely mortality, although in immunocompromised hosts, VZV can cause severe disseminated and occasionally fatal disease. We discuss VZV diseases and the decrease in their incidence due to the introduction of live-attenuated vaccines to prevent varicella or HZ. We also focus on acyclovir, valacyclovir, and famciclovir (FDA approved drugs to treat VZV infections), brivudine (used in some European countries) and amenamevir (a helicase-primase inhibitor, approved in Japan) that augur the beginning of a new era of anti-VZV therapy. Valnivudine hydrochloride (FV-100) and valomaciclovir stearate (in advanced stage of development) and several new molecules potentially good as anti-VZV candidates described during the last year are examined. We reflect on the role of antiviral agents in the treatment of VZV-associated diseases, as a large percentage of the at-risk population is not immunized, and on the limitations of currently FDA-approved anti-VZV drugs. Their low efficacy in controlling HZ pain and post-herpetic neuralgia development, and the need of multiple dosing regimens requiring daily dose adaptation for patients with renal failure urges the development of novel anti-VZV drugs.
Air Pollution Health Risk Assessment (AP-HRA), Principles and Applications

Air pollution is a major public health problem. A significant number of epidemiological studies have found a correlation between air quality and a wide variety of adverse health impacts emphasizing a considerable role of air pollution in the disease burden in the general population ranging from subclinical effects to premature death. Health risk assessment of air quality can play a key role at individual and global health promotion and disease prevention levels. The Air Pollution Health Risk Assessment (AP-HRA) forecasts the expected health effect of policies impacting air quality under the various policy, environmental and socio-economic circumstances, making it a key tool for guiding public policy decisions. This paper presents the concept of AP-HRA and offers an outline for the proper conducting of AP-HRA for different scenarios, explaining in broad terms how the health hazards of air emissions and their origins are measured and how air pollution-related impacts are quantified. In this paper, seven widely used AP-HRA tools will be deeply explored, taking into account their spatial resolution, technological factors, pollutants addressed, geographical scale, quantified health effects, method of classification, and operational characteristics. Finally, a comparative analysis of the proposed tools will be conducted, using the SWOT (strengths, weaknesses, opportunities, and threats) method.
Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields

In cells, intrinsic endogenous direct current (DC) electric fields (EFs) serve as morphogenetic cues and are necessary for several important cellular responses including activation of multiple signaling pathways, cell migration, tissue regeneration and wound healing. Endogenous DC EFs, generated spontaneously following injury in physiological conditions, directly correlate with wound healing rate, and different cell types respond to these EFs via directional orientation and migration. Application of external DC EFs results in electrode polarity and is known to activate intracellular signaling events in specific direction. In contrast, alternating current (AC) EFs are known to induce continuous bidirectional flow of charged particles without electrode polarity and also minimize electrode corrosion. In this context, the present study is designed to study effects of AC EFs on corneal epithelial cell gene and protein expression profiles in vitro. We performed gene and antibody arrays, analyzed the data to study specific influence of AC EFs, and report that AC EFs has no deleterious effect on epithelial cell function. Gene Ontology results, following gene and protein array data analysis, showed that AC EFs influence similar biological processes that are predominantly responsive to organic substance, chemical, or external stimuli. Both arrays activate cytokine–cytokine receptor interaction, MAPK and IL-17 signaling pathways. Further, in comparison to the gene array data, the protein array data show enrichment of diverse activated signaling pathways through several interconnecting networks.
Is Probiotic Supplementation Useful for the Management of Body Weight and Other Anthropometric Measures in Adults Affected by Overweight and Obesity with Metabolic Related Diseases? A Systematic Review and Meta-Analysis

The aim of this systematic review and meta-analysis is to assess the effectiveness of probiotics in inducing body weight loss in patients with overweight or obesity with related metabolic diseases. The research was carried out on PubMed and Scopus, focusing on studies reporting the effect on anthropometric measures (weight, body mass Index (BMI), waist circumference (WC), and hip circumference (HC) after administration of various probiotic strains compared to placebo. Twenty randomized controlled trials, that included 1411 patients, were considered. The meta-analyzed mean differences (MD) for random effects showed no significant decrease in body weight after probiotic supplementation (−0.26 kg [−075, 0.23], p = 0.30), while a significant BMI decrease was found (−0.73 kg/m2 [−1.31, −0.16], p = 0.01). For WC and HC, the meta-analyzed MD for random effects showed a significant decrease (WC: −0.71 cm [−1.24; −0.19], p = 0.008 and HC: −0.73 cm [−1.16; −0.30], p = 0.0008). The risk of bias was also evaluated considering a high risk and a low risk according to PRISMA criteria. In conclusion, the results of this meta-analysis highlight a positive trend of probiotics supplementation on the amelioration of anthropometric measures of overweight and obese patients with related metabolic diseases. However, further research is needed before recommending the use of probiotics as a therapeutic strategy for these patients. The focus of the future research should be to evaluate the efficacy of different probiotic strains, the quantities to be administered, and the duration of the intervention.
Genetic and Chemical Engineering of Phages for Controlling Multidrug-Resistant Bacteria

Along with the excessive use of antibiotics, the emergence and spread of multidrug-resistant bacteria has become a public health problem and a great challenge vis-à-vis the control and treatment of bacterial infections. As the natural predators of bacteria, phages have reattracted researchers’ attentions. Phage therapy is regarded as one of the most promising alternative strategies to fight pathogens in the post-antibiotic era. Recently, genetic and chemical engineering methods have been applied in phage modification. Among them, genetic engineering includes the expression of toxin proteins, modification of host recognition receptors, and interference of bacterial phage-resistant pathways. Chemical engineering, meanwhile, involves crosslinking phage coats with antibiotics, antimicrobial peptides, heavy metal ions, and photothermic matters. Those advances greatly expand the host range of phages and increase their bactericidal efficiency, which sheds light on the application of phage therapy in the control of multidrug-resistant pathogens. This review reports on engineered phages through genetic and chemical approaches. Further, we present the obstacles that this novel antimicrobial has incurred.
Monte Carlo Simulations of the Kinetics of Protein Adsorption

The past decade has been characterized by rapid progress in Monte Carlo simulations of protein folding in a solution. This review summarizes the main results obtained in the field, as a background to the major topic, namely corresponding advances in simulations of protein adsorption kinetics at solid–liquid interfaces. The latter occur via diffusion in the liquid towards the interface followed by actual adsorption, and subsequent irreversible conformational changes, resulting in more or less pronounced denaturation of the native protein structure. The conventional kinetic models describing these steps are based on the assumption that the denaturation transitions obey the first-order law with a single value of the denaturation rate constant kr. The validity of this assumption has been studied in recent lattice Monte Carlo simulations of denaturation of model protein-like molecules with different types of the monomer–monomer interactions. The results obtained indicate that, due to trapping in metastable states, (i) the transition of a molecule to the denatured state is usually nonexponential in time, i.e. it does not obey the first-order law, and (ii) the denaturation transitions of an ensemble of different molecules are characterized by different time scales, i.e. the denaturation process cannot be described by a single rate constant kr. One should, rather, introduce a distribution of values of this rate constant (physically, different values of kr reflect the fact that the transitions to the altered state occurs via different metastable states). The phenomenological kinetics of irreversible adsorption of proteins with and without a distribution of the denaturation rate constant values have been calculated in the limits where protein diffusion in the solution is, respectively, rapid or slow. In both cases, the adsorption kinetics with a distribution of kr are found to be close to those with a single–valued rate constant kr, provided that the average value of kr in the former case is equal to kr in the latter case. This conclusion holds even for wide distributions of kr. The consequences of this finding for the fitting of global experimental kinetics on the basis of phenomenological equations are briefly discussed.
Multi-Modality Imaging Approach in a Challenging Case of Surgically Corrected Partial Anomalous Pulmonary Venous Return and Atrial Tachycardia Treated With Radiofrequency Ablation

Pulmonary anomalous venous return (PAPVR) is defined as a congenital anomaly in which at least one but not all of the pulmonary veins abnormally drain into a systemic vein or directly into the right atrium. Signs and symptoms related to this condition are due to the hemodynamic abnormalities secondary to left-to-right shunt and the possible presence of other associated cardiac anomalies (e.g., sinus venous atrial septal defect). Therefore, depending on the extent of the shunt, the clinical presentation of PAPVR is variable, ranging from asymptomatic patients to patients affected by severe heart failure with right-sided volume overload. PAPVR with a clinically significant shunt should be referred for surgical correction with different techniques depending on the presence of associated cardiac anomalies. We are presenting a case of partial anomalous venous return (PAPVR) in a 66-year-old man who underwent surgery 26 years ago to correct an anomalous venous connection between the right superior pulmonary vein (RSPV) and the superior vena cava (SVC) through a veno-atrial baffle. The patient was admitted to the emergency department due to atrial tachycardia. Trans-thoracic echocardiography (TTE) showed a dilated right ventricle (RV) with mild RV systolic dysfunction and pulmonary hypertension. Cardiac magnetic resonance (CMR) further confirmed the findings described by TTE and also demonstrated areas of fibrosis replacement in the hinge points. Cardiac computed tomography (CCT) was able to accurately depict and evaluate the surgically created veno-atrial baffle and also showed an anomalous connection between the left superior pulmonary vein (LSPV) and the brachiocephalic vein (BCV) through a vertical vein. The patient was successfully treated with radiofrequency ablation for his arrhythmia.
Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.
Polymeric Materials with Antibacterial Activity: A Review

Infections caused by bacteria are one of the main causes of mortality in hospitals all over the world. Bacteria can grow on many different surfaces and when this occurs, and bacteria colonize a surface, biofilms are formed. In this context, one of the main concerns is biofilm formation on medical devices such as urinary catheters, cardiac valves, pacemakers or prothesis. The development of bacteria also occurs on materials used for food packaging, wearable electronics or the textile industry. In all these applications polymeric materials are usually present. Research and development of polymer-based antibacterial materials is crucial to avoid the proliferation of bacteria. In this paper, we present a review about polymeric materials with antibacterial materials. The main strategies to produce materials with antibacterial properties are presented, for instance, the incorporation of inorganic particles, micro or nanostructuration of the surfaces and antifouling strategies are considered. The antibacterial mechanism exerted in each case is discussed. Methods of materials preparation are examined, presenting the main advantages or disadvantages of each one based on their potential uses. Finally, a review of the main characterization techniques and methods used to study polymer based antibacterial materials is carried out, including the use of single force cell spectroscopy, contact angle measurements and surface roughness to evaluate the role of the physicochemical properties and the micro or nanostructure in antibacterial behavior of the materials.
Non-Destructive Corrosion Inspection of Reinforced Concrete Using Ground-Penetrating Radar: A Review

Reduced maintenance costs of concrete structures can be ensured by efficient and comprehensive condition assessment. Ground-penetrating radar (GPR) has been widely used in the condition assessment of reinforced concrete structures and it provides completely non-destructive results in real-time. It is mainly used for locating reinforcement and determining concrete cover thickness. More recently, research has focused on the possibility of using GPR for reinforcement corrosion assessment. In this paper, an overview of the application of GPR in corrosion assessment of concrete is presented. A literature search and study selection methodology were used to identify the relevant studies. First, the laboratory studies are shown. After that, the studies for the application on real structures are presented. The results have shown that the laboratory studies have not fully illuminated the influence of the corrosion process on the GPR signal. Also, no clear relationship was reported between the results of the laboratory studies and the on-site inspection. Although the GPR has a long history in the condition assessment of structures, it needs more laboratory investigations to clarify the influence of the corrosion process on the GPR signal.
Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response

Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.
Prognostic Role of Tumor Budding in Breast Cancer Patients Receiving Neo-Adjuvant Therapy

Background: Isolated tumor cells or small clusters of tumor cells observed in the vicinity of the main tumor mass in pathology sections, termed tumor budding, are common in cancers and have been associated with prognosis in some settings. This study examined the clinical associations and treatment efficacy implications of tumor budding in breast cancer patients receiving neo-adjuvant therapy. Methods: Breast cancer patients that received neo-adjuvant therapy before definitive surgical treatment in a single cancer center over a 7-year period were included, and their records were reviewed. Data extracted included patient demographics, tumor characteristics and pathologic response to treatment at surgery. The initial breast cancer biopsy before any therapy was reviewed by two pathologists, and a hot spot area was evaluated for tumor budding (defined as 1 to 5 cancer cells observed detached from the main tumor mass). Results: Seventy-five patients who received neo-adjuvant therapy (73 received chemotherapy and 2 received hormonal therapy) were included. Tumor budding was observed in two-thirds of the patients. There were no significant differences in patient (age and menopause status) and tumor (stage, histology and molecular sub-type equivalent) characteristics between the group that had tumor budding and the group that did not have tumor budding in the pre-treatment biopsy. Likewise, no statistically significant differences were observed in the frequency of complete or partial responses between the two groups. Conclusion: In this cohort of breast cancer patients receiving neo-adjuvant therapy, tumor budding was frequent, but it was not associated with tumor characteristics or pathologic responses to treatment. The value of tumor budding as a prognostic factor in the neo-adjuvant setting within the general breast cancer population could not be confirmed, but such a value in specific sub-groups deserves further investigation, given the pathophysiologic rationale and data from other settings.
Analysis of Nucleotide Sequence of Tax, miRNA and LTR of Bovine Leukemia Virus in Cattle with Different Levels of Persistent Lymphocytosis in Russia

Bovine Leukemia Virus (BLV) is the etiological agent of enzootic bovine leucosis (EBL), a lymphoproliferative disease of the bovine species. In BLV-infected cells, the long terminal repeat (LTR), the viral Tax protein and viral miRNAs promote viral and cell proliferation as well as tumorigenesis. Although their respective roles are decisive in BLV biology, little is known about the genetic sequence variation of these parts of the BLV genome and their impact on disease outcome. Therefore, the objective of this study was to assess the relationship between disease progression and sequence variation of the BLV Tax, miRNA and LTR regions in infected animals displaying either low or high levels of persistent lymphocytosis (PL). A statistically significant association was observed between the A(+187)C polymorphism in the downstream activator sequence (DAS) region in LTR (p-value = 0.00737) and high lymphocytosis. Our study also showed that the mutation A(−4)G in the CAP site occurred in 70% of isolates with low PL and was not found in the high PL group. Conversely, the mutations G(−133)A/C in CRE2 (46.7%), C(+160)T in DAS (30%) and A(310)del in BLV-mir-B4-5p, A(357)G in BLV-mir-B4-3p, A(462)G in BLV-mir-B5-5p, and GA(497–498)AG in BLV-mir-B5-3p (26.5%) were often seen in isolates with high PL and did not occur in the low PL group. In conclusion, we found several significant polymorphisms among BLV genomic sequences in Russia that would explain a progression towards higher or lower lymphoproliferation. The data presented in this article enabled the classification between two different genotypes; however, clear association between genotypes and the PL development was not found.