Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Glyph Based and Topographical Techniques to Visualize United States Congressional Earmarks.

ROGERS, GEOFFREY J. Combining Glyph Based and Topographical Techniques to Visualize United States Congressional Earmarks. (Under the direction of Christopher G. Healey, Ph.D.) Recent advances in computing technologies have created a vast quantity of unprocessed data, and visualizations assist in extracting knowledge from this ever increasing data repository. Current glyph based visualization techniques are effective at representing various multidimensional data sets; however, they abstract the data from their underlying context. Topographical map based techniques retain the underlying context of the data set, but are limited in how many attributes can be displayed at a given map location. This thesis presents a novel information visualization approach for displaying multidimensional data with underlying topographical context. The technique addresses three problem areas within visualization: 1) displaying multiple attributes for a region or location on a map, 2) allowing the viewer to make comparisons among neighboring data points, and 3) maintaining a relative encoding of data across regions that allows for direct comparison of data across multiple areas. The technique developed to meet these requirements involves a combination of glyph based and topographical visualization techniques. Starting with a topographical map of the United States as a foundation, glyphs are used to denote individual states and regions within states. The hue, saturation, luminance and height of the glyphs are varied to represent different attributes of the data set. Visualizations were generated which show U.S. congressional earmark requests in a single fiscal year as well as trends between fiscal years. This technique is not limited to U.S. political delineation, but can accommodate multidimensional data from any domain that has underlying geographical context. © Copyright 2011 by Geoffrey J. Rogers
Effects of Polycyclic Aromatic Hydrocarbons on the Composition of the Soil Bacterial Communities in the Tidal Flat Wetlands of the Yellow River Delta of China

Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants in coastal ecosystems, especially in tidal flat wetlands. However, the mechanisms through which PAHs impact the soil bacterial communities of wetlands featuring a simple vegetation structure in the Yellow River Delta (China) remain largely unclear. In this study, we examined soil samples from two sites featuring a single vegetation type (Suaeda salsa) in the Yellow River Delta. Specifically, we investigated the impacts of PAHs on the diversity and composition of soil bacteria communities through high-throughput 16 S rRNA sequencing. PAHs significantly increased the soil organic carbon content but decreased the total phosphorus content (p = 0.02). PAH contamination notably reduced soil bacterial community α diversity (Shannon index) and β diversity. Furthermore, PAHs significantly altered the relative abundance of bacterial phyla, classes, and genera (p < 0.05). Specifically, PAHs increased the relative abundance of the bacterial phyla Acidobacteriota and Gemmatimonadota (p < 0.05), while decreasing the relative abundance of Bacteroidota, Desulfobacterota, and Firmicutes compared to the control wetland (p < 0.05). Moreover, PAHs and certain soil properties [total nitrogen (TN), soil organic carbon (SOC), total phosphorus (TP), and total salt (TS)] were identified as key parameters affecting the community of soil bacteria, with the abundance of specific bacteria being both negatively and positively affected by PAHs, SOC, and TN. In summary, our findings could facilitate the identification of existing environmental problems and offer insights for improving the protection and management of tidal flat wetland ecosystems in the Yellow River Delta of China.
Preparation of Bio-Based Polyurethane Coating from Citrullus colocynthis Seed Oil: Characterization and Corrosion Performance

In this study, a new epoxidized oil from Citrullus colocynthis seed oil (CCSO) was obtained for a potential application in the formulation of polyurethane coatings. Initially, the fatty acid composition of CCSO was determined by gas chromatography–mass spectrometry (GC–MS). Subsequently, the epoxidation of CCSO was performed with in situ generated peracetic acid, which was formed with hydrogen peroxide (30 wt.%) and glacial acetic acid and catalyzed with sulfuric acid. The reaction was continued at a molar ratio of 1.50:1.0 of hydrogen peroxide to double bond (H2O2:DB) for 6 h at a controlled temperature of 60 °C. The resulting epoxidized oil was then used to produce a bio-based polyol by hydroxylation. The molar ratio of epoxy groups to methanol and distilled water was maintained at 1:11:2, and the reaction was carried out for 2 h at a controlled temperature of 65 °C. The major functional groups of the epoxidized oil and its polyol were validated by Fourier-transform infrared (FT-IR) and proton nuclear magnetic resonance (1H NMR) spectroscopies. A polyurethane (PU) coating was produced from the synthesized polyol and 3HDI isocyanurate, keeping the molar ratio of NCO:OH at 1:1. The resulting PU coating was then applied to glass and aluminum panels (Al 1001). After the film was cured, the properties of the PU coating were evaluated using various techniques including pencil hardness, pendulum hardness, adhesion, gloss, chemical resistance, and EIS tests. The results show that the PU coating obtained from CCSO is a promising new raw material for coating applications.
Parenteral Vaccination with a Live Brucella melitensis Mutant Protects against Wild-Type B. melitensis 16M Challenge

Susceptibility to brucellosis remains prevalent, even in herds vaccinated with conventional vaccines. Efforts are underway to develop an improved brucellosis vaccine, and possibly a universal vaccine, given that Brucella species are highly homologous. To this end, two B. melitensis mutants were developed, znBM-lacZ (znBMZ) and znBM-mCherry (znBM-mC), and were tested for their ability to confer systemic immunity against virulent B. melitensis challenge. To assess the extent of their attenuation, bone-marrow-derived macrophages and human TF-1 myeloid cells were infected with both mutants, and the inability to replicate within these cells was noted. Mice infected with varying doses of znBM-mC cleared the brucellae within 6–10 weeks. To test for efficacy against systemic disease, groups of mice were vaccinated once by the intraperitoneal route with either znBMZ or B. abortus S19 vaccine. Relative to the PBS-dosed mice, znBMZ vaccination greatly reduced splenic brucellae colonization by ~25,000-fold compared to 700-fold for S19-vaccinated mice. Not surprisingly, both znBMZ and S19 strains induced IFN-γ+ CD4+ T cells, yet only znBMZ induced IFN-γ+ CD8+ T cells. While both strains induced CD4+ effector memory T cells (Tems), only znBMZ induced CD8+ Tems. Thus, these results show that the described znBM mutants are safe, able to elicit CD4+ and CD8+ T cell immunity without a boost, and highly effective, rendering them promising vaccine candidates for livestock.
Toward New AQP4 Inhibitors: ORI-TRN-002

Cerebral edema is a life-threatening condition that can cause permanent brain damage or death if left untreated. Existing therapies aim at mitigating the associated elevated intracranial pressure, yet they primarily alleviate pressure rather than prevent edema formation. Prophylactic anti-edema therapy necessitates novel drugs targeting edema formation. Aquaporin 4 (AQP4), an abundantly expressed water pore in mammalian glia and ependymal cells, has been proposed to be involved in cerebral edema formation. A series of novel compounds have been tested for their potential inhibitory effects on AQP4. However, selectivity, toxicity, functional inhibition, sustained therapeutic concentration, and delivery into the central nervous system are major challenges. Employing extensive density-functional theory (DFT) calculations, we identified a previously unreported thermodynamically stable tautomer of the recently identified AQP4-specific inhibitor TGN-020 (2-(nicotinamide)-1,3,4-thiadiazol). This novel form, featuring a distinct hydrogen-bonding pattern, served as a template for a COSMOsim-3D-based virtual screen of proprietary compounds from Origenis™. The screening identified ORI-TRN-002, an electronic homologue of TGN-020, demonstrating high solubility and low protein binding. Evaluating ORI-TRN-002 on AQP4-expressing Xenopus laevis oocytes using a high-resolution volume recording system revealed an IC50 of 2.9 ± 0.6 µM, establishing it as a novel AQP4 inhibitor. ORI-TRN-002 exhibits superior solubility and overcomes free fraction limitations compared to other reported AQP4 inhibitors, suggesting its potential as a promising anti-edema therapy for treating cerebral edema in the future.
Advanced Cellular Models for Rare Disease Study: Exploring Neural, Muscle and Skeletal Organoids

Organoids are self-organized, three-dimensional structures derived from stem cells that can mimic the structure and physiology of human organs. Patient-specific induced pluripotent stem cells (iPSCs) and 3D organoid model systems allow cells to be analyzed in a controlled environment to simulate the characteristics of a given disease by modeling the underlying pathophysiology. The recent development of 3D cell models has offered the scientific community an exceptionally valuable tool in the study of rare diseases, overcoming the limited availability of biological samples and the limitations of animal models. This review provides an overview of iPSC models and genetic engineering techniques used to develop organoids. In particular, some of the models applied to the study of rare neuronal, muscular and skeletal diseases are described. Furthermore, the limitations and potential of developing new therapeutic approaches are discussed.
Potato Resistant Starch Type 1 Promotes Obesity Linked with Modified Gut Microbiota in High-Fat Diet-Fed Mice

Obesity has become a major disease that endangers human health. Studies have shown that dietary interventions can reduce the prevalence of obesity and diabetes. Resistant starch (RS) exerts anti-obesity effects, alleviates metabolic syndrome, and maintains intestinal health. However, different RS types have different physical and chemical properties. Current research on RS has focused mainly on RS types 2, 3, and 4, with few studies on RS1. Therefore, this study aimed to investigate the effect of RS1 on obesity and gut microbiota structure in mice. In this study, we investigated the effect of potato RS type 1 (PRS1) on obesity and inflammation. Mouse weights, as well as their food intake, blood glucose, and lipid indexes, were assessed, and inflammatory factors were measured in the blood and tissues of the mice. We also analyzed the expression levels of related genes using PCR, with 16S rRNA sequencing used to study intestinal microbiota changes in the mice. Finally, the level of short-chain fatty acids was determined. The results indicated that PRS1 promoted host obesity and weight gain and increased blood glucose and inflammatory cytokine levels by altering the gut microbiota structure.
Salvage Strategies for Local Recurrences of Squamous Cell Carcinoma of the Nasal Vestibule: A Single-Center Experience of 22 Years

Squamous cell carcinomas of the nasal vestibule are an extremely rare neoplastic disease. Although brachytherapy is gaining popularity for primary treatment, surgery remains the best option in case of recurrences. The aim of this paper is to outline our treatment experience of local recurrence of SCCNVs over the past 22 years. We retrospectively reviewed the clinical data of the patients who underwent surgical treatment for local recurrence of SCCNV: data regarding age, sex, primary tumor treatment, recurrence location and time of appearance, surgical resection, type of reconstruction, postoperative complication, surgical revision, and re-recurrence rate were analyzed. Twenty patients were included in the study. The median period for recurrence appearance was 17 months, and the prevalent location of recurrence was the nasal alae. Prevalent reconstructive procedures were the nasolabial flap and paramedian forehead flap. No postoperative complications were observed, and one case of re-recurrence was detected at 12-months of follow-up. Based on our experience, salvage surgical procedures for SCCNV recurrences must be individualized and carefully planned, taking into account the peculiar pattern of tumor spread and the presence of scar and heavily radiotherapy damaged tissue from previous treatment; delayed reconstruction should be considered for all the cases with skeletal involvement.
Incidence and Severity of COVID-19 in Relation to Anti-Receptor-Binding Domain IgG Antibody Level after COVID-19 Vaccination in Kidney Transplant Recipients

Kidney transplant recipients (KTRs) elicit an impaired immune response after COVID-19 vaccination; however, the exact clinical impact remains unclear. We therefore analyse the relationship between antibody levels after vaccination and the risk of COVID-19 in a large cohort of KTRs. All KTRs living in the Netherlands were invited to send a blood sample 28 days after their second COVID-19 vaccination for measurement of their IgG antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein (anti-RBD IgG). Information on COVID-19 was collected from the moment the blood sample was obtained until 6 months thereafter. Multivariable Cox and logistic regression analyses were performed to analyse which factors affected the occurrence and severity (i.e., hospitalization and/or death) of COVID-19. In total, 12,159 KTRs were approached, of whom 2885 were included in the analyses. Among those, 1578 (54.7%) became seropositive (i.e., anti-RBD IgG level >50 BAU/mL). Seropositivity was associated with a lower risk for COVID-19, also after adjusting for multiple confounders, including socio-economic status and adherence to COVID-19 restrictions (HR 0.37 (0.19–0.47), p = 0.005). When studied on a continuous scale, we observed a log-linear relationship between antibody level and the risk for COVID-19 (HR 0.52 (0.31–0.89), p = 0.02). Similar results were found for COVID-19 severity. In conclusion, antibody level after COVID-19 vaccination is associated in a log-linear manner with the occurrence and severity of COVID-19 in KTRs. This implies that if future vaccinations are indicated, the aim should be to reach for as high an antibody level as possible and not only seropositivity to protect this vulnerable patient group from disease.
The Impact of Cesarean Section Delivery on Intestinal Microbiota: Mechanisms, Consequences, and Perspectives—A Systematic Review

The relationship between cesarean section (CS) delivery and intestinal microbiota is increasingly studied. CS-born infants display distinct gut microbial compositions due to the absence of maternal birth canal microorganisms. These alterations potentially link to long-term health implications like immune-related disorders and allergies. This correlation underscores the intricate connection between birth mode and the establishment of diverse intestinal microbiota. A systematic literature review was conducted on the PubMed, Scopus, and Web of Science databases by analyzing the articles and examining the intricate interactions between CS delivery and the infant’s intestinal microbiota. The analysis, based on a wide-ranging selection of studies, elucidates the multifaceted dynamics involved in CS-associated shifts in the establishment of fetal microbiota. We also explore the potential ramifications of these microbial changes on neonatal health and development, providing a comprehensive overview for clinicians and researchers. By synthesizing current findings, this review contributes to a deeper understanding of the interplay between delivery mode and early microbial colonization, paving the way for informed clinical decisions and future investigations in the field of perinatal medicine.
β-1,3-Glucan recognition by Acanthamoeba castellanii as a putative mechanism of amoeba-fungal interactions

ABSTRACT In this study, we conducted an in-depth analysis to characterize potential Acanthamoeba castellanii (Ac) proteins capable of recognizing fungal β-1,3-glucans. Ac specifically anchors curdlan or laminarin, indicating the presence of surface β-1,3-glucan-binding molecules. Using optical tweezers, strong adhesion of laminarin- or curdlan-coated beads to Ac was observed, highlighting their adhesive properties compared to controls (characteristic time τ of 46.9 and 43.9 s, respectively). Furthermore, Histoplasma capsulatum (Hc) G217B, possessing a β-1,3-glucan outer layer, showed significant adhesion to Ac compared to a Hc G186 strain with an α-1,3-glucan outer layer (τ of 5.3 s vs τ 83.6 s). The addition of soluble β-1,3-glucan substantially inhibited this adhesion, indicating the involvement of β-1,3-glucan recognition. Biotinylated β-1,3-glucan-binding proteins from Ac exhibited higher binding to Hc G217B, suggesting distinct recognition mechanisms for laminarin and curdlan, akin to macrophages. These observations hinted at the β-1,3-glucan recognition pathway’s role in fungal entrance and survival within phagocytes, supported by decreased fungal viability upon laminarin or curdlan addition in both phagocytes. Proteomic analysis identified several Ac proteins capable of binding β-1,3-glucans, including those with lectin/glucanase superfamily domains, carbohydrate-binding domains, and glycosyl transferase and glycosyl hydrolase domains. Notably, some identified proteins were overexpressed upon curdlan/laminarin challenge and also demonstrated high affinity to β-1,3-glucans. These findings underscore the complexity of binding via β-1,3-glucan and suggest the existence of alternative fungal recognition pathways in Ac. IMPORTANCE Acanthamoeba castellanii (Ac) and macrophages both exhibit the remarkable ability to phagocytose various extracellular microorganisms in their respective environments. While substantial knowledge exists on this phenomenon for macrophages, the understanding of Ac’s phagocytic mechanisms remains elusive. Recently, our group identified mannose-binding receptors on the surface of Ac that exhibit the capacity to bind/recognize fungi. However, the process was not entirely inhibited by soluble mannose, suggesting the possibility of other interactions. Herein, we describe the mechanism of β-1,3-glucan binding by A. castellanii and its role in fungal phagocytosis and survival within trophozoites, also using macrophages as a model for comparison, as they possess a well-established mechanism involving the Dectin-1 receptor for β-1,3-glucan recognition. These shed light on a potential parallel evolution of pathways involved in the recognition of fungal surface polysaccharides.
Exploring Biomarkers in Breast Cancer: Hallmarks of Diagnosis, Treatment, and Follow-Up in Clinical Practice

Breast cancer is a prevalent malignancy in the present day, particularly affecting women as one of the most common forms of cancer. A significant portion of patients initially present with localized disease, for which curative treatments are pursued. Conversely, another substantial segment is diagnosed with metastatic disease, which has a worse prognosis. Recent years have witnessed a profound transformation in the prognosis for this latter group, primarily due to the discovery of various biomarkers and the emergence of targeted therapies. These biomarkers, encompassing serological, histological, and genetic indicators, have demonstrated their value across multiple aspects of breast cancer management. They play crucial roles in initial diagnosis, aiding in the detection of relapses during follow-up, guiding the application of targeted treatments, and offering valuable insights for prognostic stratification, especially for highly aggressive tumor types. Molecular markers have now become the keystone of metastatic breast cancer diagnosis, given the diverse array of chemotherapy options and treatment modalities available. These markers signify a transformative shift in the arsenal of therapeutic options against breast cancer. Their diagnostic precision enables the categorization of tumors with elevated risks of recurrence, increased aggressiveness, and heightened mortality. Furthermore, the existence of therapies tailored to target specific molecular anomalies triggers a cascade of changes in tumor behavior. Therefore, the primary objective of this article is to offer a comprehensive review of the clinical, diagnostic, prognostic, and therapeutic utility of the principal biomarkers currently in use, as well as of their clinical impact on metastatic breast cancer. In doing so, our goal is to contribute to a more profound comprehension of this complex disease and, ultimately, to enhance patient outcomes through more precise and effective treatment strategies.
Whole Genome Sequences, De Novo Assembly, and Annotation of Antibiotic Resistant Campylobacter jejuni Strains S27, S33, and S36 Newly Isolated from Chicken Meat

Campylobacter is a leading bacterial cause of gastrointestinal infections in humans and has imposed substantial medical and public health burdens worldwide. Among a total of 39 species in the Campylobacter genus, C. jejuni is the most important species responsible for approx. 90% of human Campylobacter illness. Most cases of the infection were acquired by ingesting undercooked poultry meat due to the high prevalence of Campylobacter in the products. Here, we reported the dataset of raw sequences, de novo assembled and annotated genomes of C. jejuni strains S27, S33, and S36 recently isolated from retail chicken by using PacBio highly accurate long-read sequencing technology combined with bioinformatics tools. Our data revealed several virulence and antibiotic resistance genes in each of the chromosomes, a type IV secretion system in the plasmid (pCjS33) of C. jejuni S33, and a type VI secretion system and a phage in the plasmid (pCjS36) of C. jejuni S36. This study not only provides new sequence data but also extends the knowledge pertaining to the genomic and functional aspects of this important foodborne pathogen, including the genetic determinants of virulence and antibiotic resistance.
Tissue Culture via Protocorm-like Bodies in an Orchids Hybrids Paphiopedilum SCBG Huihuang90

This study successfully established an efficient in vitro propagation system for Paphiopedilum SCBG Huihuang90 via protocorm-like body (PLB) formation from seed-derived calluses, PLB proliferation and differentiation, root induction and greenhouse acclimatization. Furthermore, 1/2 Murashige and Skoog (MS) + 0.025 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D) was suitable for the proliferation of PLBs, and 1/2MS + 10% coconut water (CW, v/v) + 0.5 g/L activated carbon (AC) was suitable for PLB differentiation. PLBs at different developmental stages required different kinds of sugars. This study provided a reference for research on the propagation techniques of other Paphiopedilum.