Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of Shewanella Phage Thanatos Infecting and Lysing Shewanella oneidensis and Promoting Nascent Biofilm Formation

Species of the genus Shewanella are widespread in nature in various habitats, however, little is known about phages affecting Shewanella sp. Here, we report the isolation of phages from diverse freshwater environments that infect and lyse strains of Shewanella oneidensis and other Shewanella sp. Sequence analysis and microscopic imaging strongly indicate that these phages form a so far unclassified genus, now named Shewanella phage Thanatos, which can be positioned within the subfamily of Tevenvirinae (Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tevenvirinae). We characterized one member of this group in more detail using S. oneidensis MR-1 as a host. Shewanella phage Thanatos-1 possesses a prolate icosahedral capsule of about 110 nm in height and 70 nm in width and a tail of about 95 nm in length. The dsDNA genome exhibits a GC content of about 34.5%, has a size of 160.6 kbp and encodes about 206 proteins (92 with an annotated putative function) and two tRNAs. Out of those 206, MS analyses identified about 155 phage proteins in PEG-precipitated samples of infected cells. Phage attachment likely requires the outer lipopolysaccharide of S. oneidensis, narrowing the phage’s host range. Under the applied conditions, about 20 novel phage particles per cell were produced after a latent period of approximately 40 min, which are stable at a pH range from 4 to 12 and resist temperatures up to 55°C for at least 24 h. Addition of Thanatos to S. oneidensis results in partial dissolution of established biofilms, however, early exposure of planktonic cells to Thanatos significantly enhances biofilm formation. Taken together, we identified a novel genus of Myophages affecting S. oneidensis communities in different ways.
Toward an “Ancient” Virtual World: Improvement Methods on X-ray CT Data Processing and Virtual Reconstruction of Fossil Skulls

This article focuses on new virtual advances to solve technical problems usually encountered by paleontologists when using X-ray computed tomography (XCT), such as (i) the limited scanning envelope (i.e., field of view of CT systems/machines) to acquire data on large structures; (ii) the use in the same study of biological objects acquired with different types of computed tomography systems (medical and laboratory XCTs and laboratory high-resolution XμCT) and therefore different resolutions; and (iii) matrix removal within the fossil (e.g., cranial cavities, intratrabecular cavities, among other cavities). All these problems are very common in paleontology, and therefore, solving them is important to save effort and the time invested in data processing. In this article, we propose various solutions to tackle these issues, based on new technical advances focused on improving and processing the images obtained from XCT. Other aspects include image filtering and histogram calibration to remove background noise and artifacts. Such artifacts can result from dense mineral inclusion occurring during the fossilization process or derived from anthropogenic restoration of the sample. Accordingly, here, we provide a protocol to acquire data on samples with size that exceed the scanning envelope of the X-ray tomography machine, joining the parts with enough accuracy, and we propose the use of the interpolation “bicubic” method. Moreover, using this method, it is possible to use medical/laboratory XCT data together with XμCT data and therefore opening new ways to manipulate the acquired data within the image stack. Another advantage is the use of plugins for quantitative analysis, which require data with isometric voxels, such as the plugin BoneJ of the software ImageJ. We also deal with the problem of removing the exogenous material that usually fills the internal cavities of fossils by means of using filters based on edge detection by gradient. Applying this method, it is possible to segment the non-bony matrix parts more quickly and efficiently. All of this is exemplified using five fossil skulls belonging to the cave bear group (Ursus spelaeus sensu lato), an iconic fossil species from the Pleistocene of Eurasia.
Concentration of the Phytoalexin Resveratrol in Wine

Resveratrol is a phytoalexin found in grapes. Recent research had shown that orally administered resveratrol lowered lipid levels in the liver of rats. Wine had been shown to lower serum lipid levels in humans. The concentration of resveratrol was measured in selected wines using HPLC and spectrophotometry. Geographical origin, variety, growing methods, and winemaking procedures all seemed to affect resveratrol concentration. Analysis of wines indicated that resveratrol may be the active ingredient in wines causing reduction of serum lipids.
Inhibition of Hepatitis B Virus DNA Polymerase by Thymidine Triphosphate Analogues in vitro

A series of thymidine triphosphate analogues was tested for effect inhibitory on DNA polymerase activity in isolated hepatitis B virus (HBV) particles. The most efficient compounds were 2′,3′-dideoxy-3′-fluoro-5-vinyluridine triphosphate [50% inhibititory dose (ID50) = 0.25 μm], 2′,3′-dideoxy-3′-fluoro-5-bromovinyluridine triphosphate (ID50 = 0.80 μm), 2′,3′-dideoxy-3′-fluoro-4-thiothymidine triphosphate (ID50 = 0.80 μm) and 2′,3′-dideoxy-3′-fluoro-5-bromouridine triphosphate (ID50 = 1.00 μm). The inhibitors only moderately influenced the cellular DNA polymerase α (ID50 ranging from 10 μm to 140 μm) but had a noteworthy effect on DNA polymerase β (ID50 ranging from 0.8 μm to 7.0 μm), which could be associated with toxicity and mutagenicity in human cells. Kinetic analysis revealed a competitive type of inhibition for the most efficient compound, fluoro-5-vinyluridine triphosphate. The inhibition constant (Ki) was estimated to be 0.25 μm compared with a Michaelis constant (Km) value of about 0.4 μm for the substrate.
Transcriptome-Based Network Analysis Unveils Eight Immune-Related Genes as Molecular Signatures in the Immunomodulatory Subtype of Triple-Negative Breast Cancer

Objective: Triple-negative breast cancer (TNBC) is a high heterogeneity cancer. The identification of genomic aberrations that drive each of the TNBC subtypes may predict the prognosis of patients with TNBC and provide novel therapeutic strategies in clinical practice. This study focuses on the transcriptome-based gene expression of TNBC and aims to generate comprehensive gene co-expression networks correlated with the immune-related subtype of TNBC. Methods: The transcriptome profiles of 107 female patients with TNBC were analyzed. Weighted gene co-expression network analysis (WGCNA) was applied to construct related networks and to sort hub-genes associated with the survival of TNBC patients. The data of the transcriptional expression, genomic alteration, survival status, and tumor immune microenvironment, which associated with hub-genes, were extracted, retrieved, and analyzed from Oncomine, UALCAN, TCGA, starBase, Kaplan–Meier Plotter, cBioPortal, and TIMER databases. Results: Immune-related hub-genes, including BIRC3, BTN3A1, CSF2RB, GIMAP7, GZMB, HCLS1, LCP2, and SELL, were found to be associated with clinical features of TNBC evaluated by WGCNA. These hub-genes belonged to the immunomodulatory subtype of TNBC and were upregulated in the TNBC cells. The protein expression of eight immune-related hub-genes was further confirmed to be upregulated in TNBC/CD8+ tissues detected by immunohistochemical staining. Survival analysis revealed that overexpression of eight immune-related hub-genes was in favor of the survival of patients with TNBC. Moreover, a positive correlation between eight immune-related hub-genes and immune cell infiltration was observed in TNBC patients. Furthermore, checkpoint inhibitor genes such as PD-L1, PD-1, and CTLA4 were more enrichment in the immunomodulatory subtype of TNBC and the expression of PD-L1, PD-1, and CTLA4 was positively correlated with eight immune-related hub-genes in the breast cancer dataset of TCGA. Conclusions: Eight immune-related hub-genes were identified to be molecular signatures in the immunomodulatory subtype of TNBC, which may provide therapeutic targets for the treatment of patients with breast cancer.
MicroRNAs of Human Herpesvirus 6A and 6B in Serum and Cerebrospinal Fluid of Multiple Sclerosis Patients

Human herpesvirus-6A (HHV-6A) and −6B (HHV-6B) might be involved in the etiopathogenesis of multiple sclerosis (MS), especially the HHV-6A. We aim at assessing, for the first time in the scientific literature, the HHV-6A/B microRNAs in MS patients. We analyzed the miRNAs of HHV-6A: miR-U86, and −6B: hhv6b-miR-Ro6-1, −2, −3-3p, −3-5p, and −4 in paired samples of serum and CSF of 42 untreated MS patients and 23 patients with other neurological diseases (OND), using Taqman MicroRNA Assays. Intrathecal HHV-6A/B antibody production and anti-HHV-6A/B IgG/IgM levels in serum were measured. MS clinical data were available. We detected the following miRNAs: hhv6b-miR-Ro6-2 (serum: MS:97.7%, OND:95.7%; CSF: MS:81%, OND:86.4%), 3-3p (serum: MS:4.8%, OND:0%; CSF: MS:2.4%, OND:4.5%), −3-5p (serum: MS:95.2%, OND:91.3%; CSF: MS:50%, OND:54.5%), and miR-U86 (serum: MS:54.8%, OND:47.8%; CSF: MS:11.9%, OND:9.1%). In the serum of the whole population (MS and OND patients) we found a significant correlation between the levels of hhv6b-miR-Ro6-2 and −3-5p (Spearman r = 0.839, pcorr = 3E-13), −2 and miR-U86 (Spearman r = 0.578, pcorr = 0.001) and −3-5p and miR-U86 (Spearman r = 0.698, pcorr = 1.34E-5); also in the CSF, between hhv6b-miR-Ro6-2 and −3-5p (Spearman r = 0.626, pcorr = 8.52E-4). These correlations remained statistically significant when both populations were considered separately. The anti-HHV-6A/B IgG levels in CSF and the intrathecal antibody production in positive MS patients for hhv6b-miR-Ro6-3-5p were statistically significant higher than in the negative ones (pcorr = 0.006 and pcorr = 0.036). The prevalence of miR-U86 (30.8%) in the CSF of individuals without gadolinium-enhancing lesions was higher (p = 0.035) than in the ones with these lesions (0%); however, the difference did not withstand Bonferroni correction (pcorr = 0.105). We propose a role of HHV-6A/B miRNAs in the maintenance of the viral latency state. Further investigations are warranted to validate these results and clarify the function of these viral miRNAs.
Where the Wild Things Are: Transposable Elements as Drivers of Structural and Functional Variations in the Wheat Genome

Transposable elements (TEs) are major contributors to genome plasticity and thus are likely to have a dramatic impact on genetic diversity and speciation. Recent technological developments facilitated the sequencing and assembly of the wheat genome, opening the gate for whole genome analysis of TEs in wheat, which occupy over 80% of the genome. Questions that have been long unanswered regarding TE dynamics throughout the evolution of wheat, are now being addressed more easily, while new questions are rising. In this review, we discuss recent advances in the field of TE dynamics in wheat and possible future directions.
Case Report: Safety and Efficacy of Denosumab in Four Children With Noonan Syndrome With Multiple Giant Cell Lesions of the Jaw

Noonan syndrome is a genetic disorder caused by mutations in the RAS/MAPK pathway. Multiple giant cell lesions are a rare sequelae of disruptions in this pathway, termed Noonan-like multiple giant cell lesions (NL/MGCLs). Medical management of these tumors rather than surgical intervention is preferential as the lesions are benign but locally destructive and recurring. This case series describes four male pediatric patients with Noonan syndrome and multiple giant cell lesions of the jaw treated with denosumab, a monoclonal antibody to receptor activator of nuclear factor kappa B ligand (RANKL), which has been approved for the treatment of malignant giant cell tumors in adults but not evaluated for safety or efficacy in children. All four pediatric patients responded clinically and radiographically to the treatment. Adverse events occurred in a predictable pattern and included hypocalcemia and joint pain during the initiation of treatment and symptomatic hypercalcemia after the cessation of treatment. Growth was not significantly impaired in these skeletally immature patients. This case series demonstrates how a weight-adjusted denosumab dose can effectively treat NL/MGCLs and provides laboratory data for consideration of the timing of monitoring for known side effects.
Culture and Green Advertising Preference: A Comparative and Critical Discursive Analysis

As environmental concerns began to emerge, companies started to target toward the growing ‘green market’ to launch their green products. Companies’ green advertising played an important role in facilitating corporate green marketing and fuelling the desire for environmental-friendly commodities. Applying a Critical Discursive Perspective, this study focuses on corporate environmental advertising in order to illuminate their discursive strategies and the process through which corporate green advertising generates and symbolically structures the necessity of green consumption. The comparison of constructive characteristics and constructed meanings of green advertisings identified embody distinction in Western and Chinese cognitive style and process.
Identification of late-stage phyllosoma larvae of the scyllarid and palinurid lobsters in the japanese waters

Based on zooplankton samples collected in the Kumano-and Enshu-nada seas north of the Kuroshio Current, phyllosoma larvae were examined, with the result that those of eleven species, belonging to five genera Ibacus, Parribacus, Scyllarides and Scyllarus (Scyllaridae) and Panulirus (Palinuridae), are identified. Among these larvae, five species of Scyllarus and two species of Panutirus are described herein. Further, keys to the genus and species of late stages of scyllarid and palinurid phyllosoma larvae in the Japanese waters are represented.
Feasibility Study of a Modified XELOX Adjuvant Chemotherapy for High-Recurrence Risk Patients With Operated Stage III Colon Cancer

Background Our previous study reported the favorable efficacy and good tolerance associated with a modified XELOX adjuvant chemotherapy with eight cycles of capecitabine and six cycles of oxaliplatin for operated stage III colon cancer. The current study aimed to confirm the feasibility of modified XELOX chemotherapy for treating specific high-risk (T4, N2, or both) stage III colon cancer. Methods We selected 142 consecutive patients with high-risk stage III colon cancer who received colon tumor resection followed by modified XELOX or standard full-cycle XELOX chemotherapy from November 2007 to June 2016 at Sun Yat-sen University Cancer Center. Disease-free survival (DFS), overall survival (OS), and adverse events of patients treated with the two chemotherapy regimens were compared. Results Seventy-four (52.1%) patients received standard XELOX chemotherapy, and 68 (47.8%) received modified XELOX chemotherapy. Neurotoxicity was the most common adverse event in 99 (69.7%) patients. Grade 2-3 neurotoxicity, grade 2–4 thrombocytopenia and grade 3–4 leucopenia were the major severe adverse events related to the decision to treat patients with modified XELOX chemotherapy. After a median follow-up of 69 months, the modified XELOX group presented a comparable 5-year DFS rate (79.0 vs. 80.3%, P = 0.891) and 5-year OS rate (93.8 vs. 87.8%, P = 0.446) as those in the standard XELOX group. Univariate survival analysis indicated that poor tumor differentiation (HR: 2.381, 95% CI: 1.141–4.968, P = 0.021) was the only significant risk factor for DFS, but no significant prognostic factor was identified for OS. Conclusions The modified XELOX adjuvant chemotherapy presented a comparable oncologic efficacy as standard XELOX chemotherapy for high-risk stage III colon cancer. The modified XELOX adjuvant chemotherapy could be an alternative treatment for patients suffering severe adverse events, especially severe neurotoxicity.
Systemic Reprogramming of Monocytes in Cancer

Monocytes influence multiple aspects of tumor progression, including antitumor immunity, angiogenesis, and metastasis, primarily by infiltrating tumors, and differentiating into tumor-associated macrophages. Emerging evidence suggests that the tumor-induced systemic environment influences the development and phenotype of monocytes before their arrival to the tumor site. As a result, circulating monocytes show functional alterations in cancer, such as the acquisition of immunosuppressive activity and reduced responsiveness to inflammatory stimuli. In this review, we summarize available evidence about cancer-induced changes in monopoiesis and its impact on the abundance and function of monocytes in the periphery. In addition, we describe the phenotypical alterations observed in tumor-educated peripheral blood monocytes and highlight crucial gaps in our knowledge about additional cellular functions that may be affected based on transcriptomic studies. We also highlight emerging therapeutic strategies that aim to reverse cancer-induced changes in monopoiesis and peripheral monocytes to inhibit tumor progression and improve therapy responses. Overall, we suggest that an in-depth understanding of systemic monocyte reprogramming will have implications for cancer immunotherapy and the development of clinical biomarkers.
Dynamics of the Sphere Model of Consciousness: Silence, Space, and Self

The Sphere Model of Consciousness (SMC) delineates a sphere-shaped matrix that aims to describe subjective experiences using geometric coordinates, in accordance with a neurophenomenological perspective. According to the SMC, an experience of overcoming the habitual self and the conditioning of memories could be placed at the center of the matrix, which can then be called the Place of Pre-Existence (PPE). The PPE is causally associated with self-determination. In this context, we suggest that silence could be considered an intentional inner environment enabling self-perception to focus on the “here and now,” which in turn improves perception of one’s own body in space. To investigate the hypotheses grounded in the model, the current preliminary study examined the Place of Pre-Existence Technique (PPEt), in which practitioners are guided to focus on a self-defined aim, reach a state of detachment from the habitual self, and envision the future. Four-hundred eighty-one volunteer PPEt practitioners completed self-report questionnaires before and after an intensive 3-day meditative training. We analyzed potential relationships between subjective experiences related to physical, emotional, mental, temporal, and spatial components, as well as self-determination and silence, before and after training. The results indicated a transition from a prevailing influence of mental dimension on the other aspects of experience, to a prevailing influence of the spatial dimension. Silence was reported more often following the training and was predominantly related to mental and emotional experiences. The results are discussed in the framework of the SMC, as compared to other models, and in relation to the shift from Narrative to Minimal Self and to increased balance among the considered dimensions.
Transmission of Chromosomal MDR DNA Fragment Encoding Ciprofloxacin Resistance by a Conjugative Helper Plasmid in Salmonella

Resistance to ciprofloxacin, a treatment choice for Salmonella infections, has increased dramatically in recent years in particular in serotype Salmonella Derby with most of strains carrying chromosome-encoded multiple plasmid-mediated quinolone resistance (PMQR) genes. In this work, we discovered a conjugative plasmid, pSa64-96kb, in a Salmonella Derby isolate, namely Sa64, which could extract and fuse to a multiple drug resistance (MDR) DNA fragment containing two PMQR genes, aac(6’)-Ib-cr, and qnrS2 located on the chromosome of the Salmonella strain. This process led to the formation of a new 188 kb fusion plasmid, which could be then subsequently transmitted to recipient strain Escherichia coli J53. The chromosomal MDR DNA fragment was shown to be flanked by one copy of IS26 element at each end and could be excised from the chromosome to form circular intermediate, which was then fused to pSa64-96kb and form a single plasmid through IS26 mediated homologous recombination. The role of IS26 on enhancing the efficacy of fusion and transmission of this chromosomal MDR DNA fragment was further proven in other Salmonella strains. These findings showed that dynamic interaction between specific chromosomal fragment and plasmids may significantly enhance resistance development and transferability of mobile resistance-encoding elements among bacterial pathogens.
Fecal Microbiota Transplantation for the Treatment of Inflammatory Bowel Disease: An Update

Fecal microbiota transplantation (FMT) has successfully been applied for the treatment of recurrent Clostridioides difficile infection (CDI), which has led to studies on its application to other gastrointestinal diseases and extraintestinal diseases associated with gut microbiota dysbiosis. Recently, the results of FMT for patients with inflammatory bowel disease (IBD) have been encouraging. However, studies have not fully clarified the clinical application of this emerging therapy. Here, we aimed to review the current knowledge in this fast-growing field and characterize the effectiveness, safety and mechanisms of FMT for the treatment of IBD patients.
Why Most Research Findings About Psi Are False: The Replicability Crisis, the Psi Paradox and the Myth of Sisyphus

The replicability crisis in psychology has been influenced by the results of nine experiments conducted by Bem (2011) and presented as supporting the existence of precognition. In this paper, we hope to show how the debate concerning these experiments could be an opportunity to develop original thinking about psychology and replicability. After a few preliminary remarks about psi and scientific epistemology, we examine how psi results lead to a paradox which questions how appropriate the scientific method is to psi research. This paradox highlights a problem in the way experiments are conducted in psi research and its potential consequence on mainstream research in psychology. Two classical experiments – the Ganzfeld protocol and the Bem studies – are then analyzed in order to illustrate this paradox and its consequences. Mainstream research is also addressed in the broader context of the replication crisis, decline effect and questionable research practices. Several perspectives for future research are proposed in conclusion and underline the heuristic value of psi studies for psychology.