Miracle-dz/UniFAR-FTUs huggingface dataset:
Study Protocol of the PreFiPS Study: Prevention of Postoperative Pancreatic Fistula by Somatostatin Compared With Octreotide, a Prospective Randomized Controlled Trial

Background: Pancreatic fistula (PF), i. e. , a failure of the pancreatic anastomosis or closure of the remnant pancreas after distal pancreatectomy, is one of the most feared complications after pancreatic surgery. PF is also one of the most common complications after pancreatic surgery, occurring in about 30% of patients. Prevention of a PF is still a major challenge for surgeons, and various technical and pharmacological interventions have been investigated, with conflicting results. Pancreatic exocrine secretion has been proposed as one of the mechanisms by which PF occurs. Pharmacological prevention using somatostatin or its analogs to inhibit pancreatic exocrine secretion has shown promising results. We can hypothesize that continuous intravenous infusion of somatostatin-14, the natural peptide hormone, associated with 10–50 times stronger affinity with all somatostatin receptor compared with somatostatin analogs, will be associated with an improved PF prevention. Methods: A French comparative randomized open multicentric study comparing somatostatin vs. octreotide in adult patients undergoing pancreaticoduodenectomy (PD) or distal pancreatectomy with or without splenectomy. Patients with neoadjuvant radiation therapy and/or neoadjuvant chemotherapy within 4 weeks before surgery are excluded from the study. The main objective of this study is to compare 90-day grade B or C postoperative PF as defined by the last ISGPF (International Study Group on Pancreatic Fistula) classification between patients who receive perioperative somatostatin and octreotide. In addition, we analyze overall length of stay, readmission rate, cost-effectiveness, and postoperative quality of life after pancreatic surgery in patients undergoing PD. Conclusion: The PreFiPS study aims to evaluate somatostatin vs. octreotide for the prevention of postoperative PF.
Genome-Wide Profiling of Diadegma semiclausum Ichnovirus Integration in Parasitized Plutella xylostella Hemocytes Identifies Host Integration Motifs and Insertion Sites

Polydnaviruses (PDVs), classified into two genera, bracoviruses (BVs) and ichnoviruses (IVs), are large, double-stranded DNA viruses, which are beneficial symbionts of parasitoid wasps. PDVs do not replicate in their infected lepidopteran hosts. BV circles have been demonstrated to be integrated into host genomic DNA after natural parasitization. However, the integrations of IV circles in vivo remain largely unknown. Here, we analyzed the integration of Diadegma semiclausum ichnovirus (DsIV) in the genomic DNA of parasitized Plutella xylostella hemocytes. We found that DsIV circles are present in host hemocytes with non-integrated and integrated forms. Moreover, DsIV integrates its DNA circles into the host genome by two distinct strategies, conservatively, and randomly. We also found that four conserved-broken circles share similar motifs containing two reverse complementary repeats at their breaking sites, which were host integration motifs (HIMs). We also predicted HIMs of eight circles from other ichnoviruses, indicating that a HIM-mediated specific mechanism was conserved in IV integrations. Investigation of DsIV circle insertion sites of the host genome revealed the enrichment of microhomologies between the host genome and the DsIV circles at integration breakpoints. These findings will deepen our understanding of the infections of PDVs, especially IVs.
Modeling Inflammation in Zebrafish for the Development of Anti-inflammatory Drugs

Dysregulation of the inflammatory response in humans can lead to various inflammatory diseases, like asthma and rheumatoid arthritis. The innate branch of the immune system, including macrophage and neutrophil functions, plays a critical role in all inflammatory diseases. This part of the immune system is well-conserved between humans and the zebrafish, which has emerged as a powerful animal model for inflammation, because it offers the possibility to image and study inflammatory responses in vivo at the early life stages. This review focuses on different inflammation models established in zebrafish, and how they are being used for the development of novel anti-inflammatory drugs. The most commonly used model is the tail fin amputation model, in which part of the tail fin of a zebrafish larva is clipped. This model has been used to study fundamental aspects of the inflammatory response, like the role of specific signaling pathways, the migration of leukocytes, and the interaction between different immune cells, and has also been used to screen libraries of natural compounds, approved drugs, and well-characterized pathway inhibitors. In other models the inflammation is induced by chemical treatment, such as lipopolysaccharide (LPS), leukotriene B4 (LTB4), and copper, and some chemical-induced models, such as treatment with trinitrobenzene sulfonic acid (TNBS), specifically model inflammation in the gastro-intestinal tract. Two mutant zebrafish lines, carrying a mutation in the hepatocyte growth factor activator inhibitor 1a gene (hai1a) and the cdp-diacylglycerolinositol 3-phosphatidyltransferase (cdipt) gene, show an inflammatory phenotype, and they provide interesting model systems for studying inflammation. These zebrafish inflammation models are often used to study the anti-inflammatory effects of glucocorticoids, to increase our understanding of the mechanism of action of this class of drugs and to develop novel glucocorticoid drugs. In this review, an overview is provided of the available inflammation models in zebrafish, and how they are used to unravel molecular mechanisms underlying the inflammatory response and to screen for novel anti-inflammatory drugs.
A Case Study on the Use of Contexts and Socio-Scientific Issues-Based Science Education by Pre-service Junior High School Science Teachers in Indonesia During Their Final Year Teaching Internship

This paper presents a case study looking at the use of daily life contexts and socio-scientific issues by pre-service science teachers (PSTs) in Indonesia during their final year teaching internship. The study is based on a questionnaire distributed to 42 PSTs at a State University in East-Java after they took part in a teaching internship program. The questionnaire focuses on the contexts the PSTs used in their teaching and how the contexts were used. Additionally, eight of the PSTs who taught a unit on environmental pollution were interviewed to more deeply explore how deeply they referred to real-world contexts in their teaching practice and whether or not they presented the topics as socio-scientific issues (SSIs). Most of the PSTs stated that they had used daily life contexts quite often when teaching. The most frequent contexts the PSTs used were daily life objects and questions related to society and the environment. The contexts were mostly introduced at the beginning of the lesson, before the science content was taught. They suggested that the function of contexts was generally for motivational purposes and for student engagement with science concepts. The contexts were rarely used to provoke societal discussions, even though the PSTs acknowledged that many contexts can be used in the sense of socio-scientific issues and were considered to potentially provoke discussions beyond science.
Prognostic Significance of End-Stage Liver Diseases, Respiratory Tract Infection, and Chronic Kidney Diseases in Symptomatic Acute Hepatitis E

Symptomatic hepatitis E virus (HEV) infection is sporadic, and usually occurs in a limited number of infected patients, which hinders the investigation of risk factors for clinical outcomes in patients with acute HEV infection. A retrospective cohort study enrolling 1913 patients with symptomatic acute hepatitis E in Beijing 302 Hospital from January 1, 2001 to December 31, 2018 was conducted. The baseline characteristics, clinical features and laboratory data of these HEV infection cases were analyzed. Albumin (ALB), platelet (PLT), alanine aminotransferase (ALT), total bilirubin (T-BiL), international normalized ratio (INR) and serum creatinine (SCR) levels, along with the model for end-stage liver disease (MELD) score, hospitalization days, co-morbidity number and mortality were taken as major parameters for comparing the clinical manifestations in our study. We found that not all pre-existing chronic liver diseases exacerbate clinical manifestations of acute hepatitis E. Alcoholic hepatitis, fatty liver hepatitis, hepatic cyst, drug-induced hepatitis and hepatocellular carcinoma were not significantly associated with mortality of HEV patients. Among all of the comorbidities, end-stage liver diseases (ESLDs, including ascites, cirrhosis, hepatic coma and hepatorenal syndrome), respiratory tract infection and chronic kidney diseases (CKDs, including renal insufficiency and renal failure) were found to remarkably increase the mortality of patients with symptomatic HEV infection. Furthermore, the severity evaluation indexes (SEI), such as MELD score, duration of hospital stay, and co-morbidity number in HEV patients with underlying comorbidities were much worse than that of their counterparts without relevant comorbidities.
Tropomodulin1 Expression Increases Upon Maturation in Dendritic Cells and Promotes Their Maturation and Immune Functions

Dendritic cells (DCs) are the most potent antigen-presenting cells. Upon maturation, DCs express costimulatory molecules and migrate to the lymph nodes to present antigens to T cells. The actin cytoskeleton plays key roles in multiple aspects of DC functions. However, little is known about the mechanisms and identities of actin-binding proteins that control DC maturation and maturation-associated functional changes. Tropomodulin1 (Tmod1), an actin-capping protein, controls actin depolymerization and nucleation. We found that Tmod1 was expressed in bone marrow-derived immature DCs and was significantly upregulated upon lipopolysaccharide (LPS)-induced DC maturation. By characterizing LPS-induced mature DCs (mDCs) from Tmod1 knockout mice, we found that compared with Tmod1+/+ mDCs, Tmod1-deficient mDCs exhibited lower surface expression of costimulatory molecules and chemokine receptors and reduced secretion of inflammatory cytokines, suggesting that Tmod1 deficiency retarded DC maturation. Tmod1-deficient mDCs also showed impaired random and chemotactic migration, deteriorated T-cell stimulatory ability, and reduced F-actin content and cell stiffness. Furthermore, Tmod1-deficient mDCs secreted high levels of IFN-β and IL-10 and induced immune tolerance in an experimental autoimmune encephalomyelitis (EAE) mouse model. Mechanistically, Tmod1 deficiency affected TLR4 signaling transduction, resulting in the decreased activity of MyD88-dependent NFκB and MAPK pathways but the increased activity of the TRIF/IRF3 pathway. Rescue with exogenous Tmod1 reversed the effect of Tmod1 deficiency on TLR4 signaling. Therefore, Tmod1 is critical in regulating DC maturation and immune functions by regulating TLR4 signaling and the actin cytoskeleton. Tmod1 may be a potential target for modulating DC functions, a strategy that would be beneficial for immunotherapy for several diseases.
DNA Methylation Is Responsive to the Environment and Regulates the Expression of Biosynthetic Gene Clusters, Metabolite Production, and Virulence in Fusarium graminearum

Histone modifications play a significant role in the regulation of biosynthetic gene clusters (BGCs) in the phytopathogen Fusarium graminearum, by contrast, epigenetic regulation by DNA methyltransferases (DNMTs) is less documented. In this study, we characterized two DNMTs (FgDIM-2 and FgRID) in F. graminearum, with homologies to “Deficient in methylation” (DIM-2) and “Repeat-induced point (RIP) deficient” (RID) from Neurospora. The loss of DNMTs resulted in not only a decrease in average methylation density in the nutrient-poor, compared to nutrient-rich conditions, but also differences in the genes expressed between the WT and the DNMT mutant strains, implicating the external environment as an important trigger in altering DNA methylation patterns. Consequently, we observed significant changes in the regulation of multiple BGCs and alterations in the pathogenicity of the fungus.
The Effects of Gum Acacia on the Composition of the Gut Microbiome and Plasma Levels of Short-Chain Fatty Acids in a Rat Model of Chronic Kidney Disease

Chronic kidney disease (CKD) may be fatal for its victims and is an important long-term public health problem. The complicated medical procedures and diet restrictions to which patients with CKD are subjected alter the gut microbiome in an adverse manner, favoring over-accumulation of proteolytic bacteria that produce ammonia and other toxic substances. The present study aimed to investigate the effect of GA on 1) the composition of the gut microbiome and 2) on plasma levels of short-chain fatty acids. Male Wister rats were divided into four groups (six each) and treated for 4 weeks based on the following: control, dietary adenine (0.75%, w/w) to induce CKD, GA in the drinking water (15%, w/v), and both adenine and GA. At the end of the treatment period, plasma, urine, and fecal samples were collected for determination of several biochemical indicators of renal function and plasma levels of short-chain fatty acids (SCFAs) as well as characterization of the gut microbiome. Dietary adenine induced the typical signs of CKD, i.e., loss of body weight and impairment of renal function, while GA alleviated these effects. The intestine of the rats with CKD contained an elevated abundance of pathogenic Proteobacteria, Actinobacteria, and Verrucomicrobia but lowered proportions of Lactobacillaceae belonging to the Firmicutes phylum. Plasma levels of propionate and butyrate were lowered by dietary adenine and restored by GA. A negative association (Spearman’s p-value ≤ 0.01, r ≤ 0.5) was observed between Firmicutes and plasma creatinine, urea, urine N-acetyl-beta-D-glucosaminidase (NAG) and albumin. Phylum Proteobacteria on the other hand was positively associated with these markers while Phylum Bacteroidetes was positively associated with plasma SCFAs. In conclusion, the adverse changes in the composition of the gut microbiome, plasma levels of SCFAs, and biochemical indicators of renal function observed in the rats with CKD induced by dietary adenine were mitigated by GA. These findings are indicative of a link between uremia and the composition of the microbiome in connection with this disease. Dietary administration of GA to patients with CKD may improve their renal function via modulating the composition of their microbiome—a finding that certainly warrants further investigation.
Afro-Indigenous Cosmographies of Mobility: Fishes, Viruses and Others Amazonian Lives at the Confluence With the Sars-CoV-19

The article aims to demonstrate the susceptibility to death that certain Amazonian peoples are facing, as a consequence of their particular migratory demography, which instead of being curbed, have been exponentially intensified by the outbreak of Sars-CoV-19. The article offers an account of the “pendular migrations” and “return migrations” that the indigenous and black rural populations of that region carry out as a result of daily labor displacements, in the search for medical-hospital assistance and the consolidation of political and legal visibility within the cities. In a second effort, directly related to the previous one, we articulate the interference of the viral threat not on the contingency of population flow, but on the dangerous intensification of people circulation between the territorial nuclei of the “first habitation” and the average Amazonian cities, where, as a rule, these peoples maintain “second residences” and to where they regularly transmigrate. To illustrate this phenomenon, three accounts of different Brazilian Amazonian realities are reported: on the rural black population of the banks of the Turiaçu River, Maranhão state, the indigenous people of the savannah Lavrado, of the northeast of Roraima state, and the Mura people, who live in the southeast region of Amazonas state. On these realities, the cosmographies of the mobility of their populations are challenged by the changes and strategic conditions imposed by the pandemic.
Significant Differences in Host-Pathogen Interactions Between Murine and Human Whole Blood

Murine infection models are widely used to study systemic candidiasis caused by C. albicans. Whole-blood models can help to elucidate host-pathogens interactions and have been used for several Candida species in human blood. We adapted the human whole-blood model to murine blood. Unlike human blood, murine blood was unable to reduce fungal burden and more substantial filamentation of C. albicans was observed. This coincided with less fungal association with leukocytes, especially neutrophils. The lower neutrophil number in murine blood only partially explains insufficient infection and filamentation control, as spiking with murine neutrophils had only limited effects on fungal killing. Furthermore, increased fungal survival is not mediated by enhanced filamentation, as a filament-deficient mutant was likewise not eliminated. We also observed host-dependent differences for interaction of platelets with C. albicans, showing enhanced platelet aggregation, adhesion and activation in murine blood. For human blood, opsonization was shown to decrease platelet interaction suggesting that complement factors interfere with fungus-to-platelet binding. Our results reveal substantial differences between murine and human whole-blood models infected with C. albicans and thereby demonstrate limitations in the translatability of this ex vivo model between hosts.
Role of Endothelial and Mesenchymal Cell Transitions in Heart Failure and Recovery Thereafter

Background: Mechanisms of myocardial recovery are not well elucidated. Methods: 3-month-old C57/BL6 mice were treated with Angiotensin-II infusion and N (w)-nitro-L-arginine methyl ester in drinking water to induce HF at 5 weeks. These agents were discontinued, and animals studied with echocardiographic, histological and genetic assessment every 2 weeks until week 19. mRNA was extracted from these samples and human pre-post LVAD samples. Results: Histologic and echo characteristics showed progressive worsening of cardiac function by week 5 and normalization by week 19 accompanied by normalization of the transcriptional profile. Expression of 1,350 genes were upregulated and 3,050 genes down regulated in HF compared to controls; during recovery, this altered gene expression was largely reversed. We focused on genes whose expression was altered during HF but reverted to control levels by Week 19. A gene ontology (GO) analysis of this cohort of genes implicated pathways involved in EndoMT and MEndoT. The cohort of genes that were differentially regulated in heart failure recovery in the murine model, were similarly regulated in human myocardial samples obtained pre- and post-placement of a left ventricular assist device (LVAD). Human end stage HF myocardial samples showed cells with dual expressed VE-Cadherin and FSP-1 consistent with cell fate transition. Furthermore, we observed a reduction in fibrosis, and an increase in endothelial cell density, in myocardial samples pre- and post-LVAD. Conclusions: Cell fate transitions between endothelial and mesenchymal types contribute to the pathophysiology of heart failure followed by recovery.
Kinetics versus thermodynamics in materials modeling: The case of the di-vacancy in iron

Monte Carlo models are widely used for the study of microstructural and microchemical evolution of materials under irradiation. However, they often link explicitly the relevant activation energies to the energy difference between local equilibrium states. We provide a simple example (di-vacancy migration in iron) in which a rigorous activation energy calculation, by means of both empirical interatomic potentials and density functional theory methods, clearly shows that such a link is not granted, revealing a migration mechanism that a thermodynamics-linked activation energy model cannot predict. Such a mechanism is, however, fully consistent with thermodynamics. This example emphasizes the importance of basing Monte Carlo methods on models where the activation energies are rigorously calculated, rather than deduced from widespread heuristic equations.
Responsive Vagus Nerve Stimulation for Drug Resistant Epilepsy: A Review of New Features and Practical Guidance for Advanced Practice Providers

Vagus nerve stimulation (VNS) is a safe and effective therapy that has been available for over 20 years for adults and children with drug resistant epilepsy (DRE). Since U.S. Food and Drug Administration approval in 1997, VNS has been implanted in over 100,000 patients including over 30,000 children as an adjunctive therapy in reducing the frequency of seizures in patients 4 years of age and older with focal seizures that are refractory to antiseizure medications. VNS Therapy® has evolved over time and currently offers closed-loop, responsive stimulation as well as advanced features that streamline dosing and patient management. Advanced Practice Providers (APPs) such as nurse practitioners, physician assistants and clinical nurse specialists are integral in a comprehensive healthcare team, and dedicated VNS clinics have formed at comprehensive epilepsy centers across the world that are often managed by APPs. This approach improves access, education, and continuity of care for those with VNS or those considering VNS. Here we provide a review for APPs on the VNS Therapy® system focused on new features, dosing, and troubleshooting strategies with the goal to provide guidance to those managing VNS patients.
Design and Development of a Virtual Reality-Based Mobility Training Game for People With Parkinson's Disease

People with Parkinson's disease (PD) commonly have gait impairments that reduce their ability to walk safely in the community. These impairments are characterized, in part, by a compromised ability to turn and negotiate both predictable and unpredictable environments. Here, we describe the development and usability assessment of a virtual reality training application, Wordplay VR, that allows people with PD to practice skills such as turning, obstacle avoidance, and problem-solving during over-ground walking in a game-based setting. Nine people with PD completed three sessions with Wordplay VR, and each session was directed by their personal physical therapist. Our outcome measures included perceived sense of presence measured using the International Test Commission–Sense of Presence Inventory (ITC-SOPI), levels of motivation using the Intrinsic Motivation Inventory (IMI), overall system usability using the System Usability Scale (SUS), and setup time by the physical therapists. Both the people with PD and the physical therapists rated their sense of presence in the training system positively. The system received high ratings on the interest and value subscales of the IMI, and the system was also rated highly on usability, from the perspective of both the patient during gameplay and the therapist while controlling the experience. These preliminary results suggest that the application and task design yielded an experience that was motivating and user-friendly for both groups. Lastly, with repeated practice over multiple sessions, therapists were able to reduce the time required to help their patients don the headset and sensors and begin the training experience.