Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific

Hendra virus (HeV) and Nipah virus (NiV) are among a group of emerging bat-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in human beings. Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation in different hosts is lacking. A study of codon usage patterns in henipaviruses may provide some fruitful insight into their evolutionary processes of synonymous codon usage and host-adapted evolution. Here, we performed a systematic evolutionary and codon usage bias analysis of henipaviruses. We found a low codon usage bias in the coding sequences of henipaviruses and that natural selection, mutation pressure, and nucleotide compositions shapes the codon usage patterns of henipaviruses, with natural selection being more important than the others. Also, henipaviruses showed the highest level of adaptation to bats of the genus Pteropus in the codon adaptation index (CAI), relative to the codon de-optimization index (RCDI), and similarity index (SiD) analyses. Furthermore, a comparison to recently identified henipa-like viruses indicated a high tRNA adaptation index of henipaviruses for human beings, mainly due to F, G and L proteins. Consequently, the study concedes the substantial emergence of henipaviruses in human beings, particularly when paired with frequent exposure to direct/indirect bat excretions.
An immunohistochemical study of the diagnostic value of TREM-1 as marker for fatal sepsis cases

ABSTRACT Triggering receptor expressed on myeloid cells-1 (TREM-1) is produced and up-regulated by exposure of myeloid cells to lipopolysaccharides or other components of either bacterial or fungal origin, which causes it to be strongly expressed on phagocytes that accumulate in inflamed areas. Because TREM-1 participates in septic shock and in amplifying the inflammatory response to bacterial and fungal infections, we believe it could be an immunohistochemical marker for postmortem diagnosis of sepsis. We tested the anti-TREM-1 antibody in 28 cases of death by septic shock and divided them into two groups. The diagnosis was made according to the criteria of the Surviving Sepsis Campaign. In all cases, blood cultures were positive. The first group was comprised subjects that presented high ante-mortem serum procalcitonin and the soluble form of TREM-1 (s-TREM-1) values. The second group comprised subjects in which s-TREM-1 was not measured ante-mortem. We used samples of brain, heart, lung, liver and kidney for each case to test the anti-TREM-1 antibody. A semiquantitative evaluation of the immunohistochemical findings was made. In lung samples, we found immunostaining in the cells of the monocyte line in 24 of 28 cases, which suggests that TREM-1 is produced principally by cells of the monocyte line. In liver tissue, we found low TREM-staining in the hepatocyte cytoplasm, duct epithelium, the portal-biliary space and blood vessel. In kidney tissue samples, we found the TREM-1 antibody immunostaining in glomeruli and renal tubules. We also found TREM-1 staining in the lumen of blood vessels. Immunohistochemical staining using the anti-TREM-1 antibody can be useful for postmortem diagnosis of sepsis.
Plasma Derived Exosomal Biomarkers of Exposure to Ionizing Radiation in Nonhuman Primates

Exposure to ionizing radiation induces a cascade of molecular events that ultimately impact endogenous metabolism. Qualitative and quantitative characterization of metabolomic profiles is a pragmatic approach to studying the risks of radiation exposure since it provides a phenotypic readout. Studies were conducted in irradiated nonhuman primates (NHP) to investigate metabolic changes in plasma and plasma-derived exosomes. Specifically, rhesus macaques (Macaca mulatta) were exposed to cobalt-60 gamma-radiation and plasma samples were collected prior to and after exposure to 5.8 Gy or 6.5 Gy radiation. Exosomes were isolated using ultracentrifugation and analyzed by untargeted profiling via ultra-performance liquid chromatography mass spectrometry (UPLC-MS) based metabolomic and lipidomic analyses, with the goal of identifying a molecular signature of irradiation. The enrichment of an exosomal fraction was confirmed using quantitative ELISA. Plasma profiling showed markers of dyslipidemia, inflammation and oxidative stress post-irradiation. Exosomal profiling, on the other hand, enabled detection and identification of low abundance metabolites that comprise exosomal cargo which would otherwise get obscured with plasma profiling. We discovered enrichment of different classes of metabolites including N-acyl-amino acids, Fatty Acid ester of Hydroxyl Fatty Acids (FAHFA’s), glycolipids and triglycerides as compared to the plasma metabolome composition with implications in mediation of systemic response to radiation induced stress signaling.
Genital Wart Recurrence Among Men Residing in Brazil, Mexico, and the United States

BACKGROUND Genital wart (GW) incidence is high among men. The percentage and rate at which subsequent GW events occur are understudied. The purpose of this study was to describe the rate of subsequent GWs, associated human papillomavirus (HPV) types, and time to subsequent GW event among unvaccinated men. METHODS The study was nested within a multinational prospective HPV natural history study of men aged 18-70 years in the United States, Mexico, and Brazil, examined every 6 months for a median follow-up of 50.4 months. Subsequent GW events were defined as GWs detected after ≥16 weeks of the prior event. RESULTS Forty-four percent of men experienced ≥1 GW following the initial episode. Men with ≥2 subsequent events were at highest risk of continued GW experiences, with as high as 10 postinitial GW events. The incidence rate of each subsequent GW increased with increasing events (incidence of first subsequent event was 13.1 vs 36.6/1000 person-months for the fourth event). The proportion of GWs among HPV-6 and/or -11-positive patients remained constant across events. Approximately 63%-69% were positive for ≥1 of the 9-valent HPV vaccine types. CONCLUSIONS These data highlight the high burden of GWs among men across the lifespan and the need for vaccination to prevent multiple GW episodes.
Inhibition of microRNA suppression of Dishevelled results in Wnt pathway-associated developmental defects in sea urchin

ABSTRACT MicroRNAs (miRNAs) are highly conserved, small non-coding RNAs that regulate gene expressions by binding to the 3′ untranslated region of target mRNAs thereby silencing translation. Some miRNAs are key regulators of the Wnt signaling pathways, which impact developmental processes. This study investigates miRNA regulation of different isoforms of Dishevelled (Dvl/Dsh), which encode a key component in the Wnt signaling pathway. The sea urchin Dvl mRNA isoforms have similar spatial distribution in early development, but one isoform is distinctively expressed in the larval ciliary band. We demonstrated that Dvl isoforms are directly suppressed by miRNAs. By blocking miRNA suppression of Dvl isoforms, we observed dose-dependent defects in spicule length, patterning of the primary mesenchyme cells, gut morphology, and cilia. These defects likely result from increased Dvl protein levels, leading to perturbation of Wnt-dependent signaling pathways and additional Dvl-mediated processes. We further demonstrated that overexpression of Dvl isoforms recapitulated some of the Dvl miRNATP-induced phenotypes. Overall, our results indicate that miRNA suppression of Dvl isoforms plays an important role in ensuring proper development and function of primary mesenchyme cells and cilia. Summary: Blockade of microRNA-mediated suppression of Dishevelled isoforms during sea urchin development induces defects in the gut, spiculogenesis and ciliogenesis.
PRESERVICE MIDDLE SCHOOL MATHEMATICS TEACHERS’ KNOWLEDGE ABOUT STUDENTS’ MATHEMATICAL THINKING RELATED TO PERIMETER AND AREA

The purpose of the current study is to examine preservice middle school mathematics teachers’ knowledge about students’ mathematical thinking related to perimeter and area and determine the consistency between this knowledge and students’ actual mathematical thinking. Case study, one of the qualitative research designs, was used to gain an in-depth understanding of the situation. The study was conducted with four senior preservice middle school mathematics teachers who enrolled in the program of elementary mathematics education at a public university. The data obtained through video recordings from the process of planning, teaching and reflecting on two lessons towards perimeter and area. The videos from teaching were used to identify students’ mathematical thinking, difficulties, mistakes and misconceptions whereas the videos from planning and reflecting were used to describe preservice teachers’ knowledge of students’ mathematical thinking. The data were analyzed through content analysis method. The findings showed that students had lack of knowledge about the meanings of the concepts of perimeter and area, made mistakes related to calculation and use of measurement units. In addition to this, preservice teachers’ predictions and expectations about students’ mathematical thinking were very limited. Finally, it was observed that there were important differences between students’ thinking ways, difficulties, misconceptions and possible mistakes and preservice teachers’ expectations and predictions about these issues.
Class Setting and Children’s Non-Cognitive Outcomes

Setting is one form of ability grouping which is widely adopted in English schools; it involves dividing pupils from the same cohort into classes according to ability in a specific subject. The effect of setting has long been debated; while the existing evidence identifies a negative effect on cognitive outcomes, especially for the low ability, little research has been undertaken to understand the impact of setting on non-cognitive outcomes. This paper provides the first evidence of setting on non-cognitive outcomes when adopting a nationally representative sample of primary aged pupils. Using Millennium Cohort Study data, Fixed Effects (FE) and Instrumental Variables (IV) methodologies are adopted to overcome potential unobserved heterogeneity and endogeneity. For boys, setting in maths negatively impacts non-cognitive outcomes, as measured by the Strengths and Difficulties Questionnaire. This effect is driven by a worsening of internalising behaviours. Little evidence is found for a significant impact of lowest set placement on non-cognitive outcomes.
Icaritin inhibits glioblastoma cell viability and glycolysis by blocking the IL‐6/Stat3 pathway

Glioblastoma (GBM) is a common and aggressive brain tumor that is associated with significant increase in glycolysis for energy production. Icaritin is a natural compound and exhibits anticancer activity in GBM. However, the effect of icaritin on glycolysis in GBM cells remains unclear. The aim of the current study was to investigate the effect of icaritin on glycolysis in GBM cells. The human GBM cell lines U87 and T98G were treated with icaritin or the inhibitor of Stat3 (S3I‐201) in the presence or absence of recombinant human interleukin (IL)‐6. Cell viability was measured using the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5 diphenyltetrazolium bromide (MTT) assay. The glycolysis was analyzed by detecting the glucose consumption and lactate production. The Western blot analysis was conducted to detect the expressions of hexokinase 2 (HK2), signal transducer and activator of transcription 3 (Stat3), p‐Stat3, and B lymphoma Mo‐MLV insertion region 1 (Bmi‐1). Results showed that icaritin inhibited the viability of U87 and T98G cells in a dose‐dependent manner. The decreased glucose consumption and lactate production, accompanied by reduced expressions of HK2, were found in both U87 and T98G cells. Icaritin inhibited the IL‐6/Stat3 pathway, which is evidenced by the decreased expressions of p‐Stat3 and Bmi‐1. IL‐6 treatment induced the phosphorylation of Stat3 and Bmi‐1 expression, increased cell viability, as well as elevated glucose consumption, lactate production, and HK2 expression; however, the effects of IL‐6 were attenuated by icaritin or S3I‐201 treatment. In conclusion, icaritin exerted inhibitory effects on cell viability and glycolysis in GBM cells, which was mediated by the IL‐6/Stat3 pathway.
Cohort Profile: the EPI-CT study: A European pooled epidemiological study to quantify the risk of radiation-induced cancer from paediatric CT.

Cohort Profile: the EPI-CT study: a European pooled epidemiological study to quantify the risk of radiation-induced cancer from paediatric CT Marie-Odile Bernier,* Hélène Baysson, Mark S Pearce, Monika Moissonnier, Elisabeth Cardis, Michael Hauptmann, Lara Struelens, Jeremie Dabin, Christoffer Johansen, Neige Journy, Dominique Laurier, Maria Blettner, Lucian Le Cornet, Roman Pokora, Patrycja Gradowska, Johanna M Meulepas, Kristina Kjaerheim, Tore Istad, Hilde Olerud, Aste Sovik, Magda Bosch de Basea, Isabelle Thierry-Chef, Magnus Kaijser, Arvid Nordenskjöld, Amy Berrington de Gonzalez, Richard W Harbron and Ausrele Kesminiene Laboratory of Epidemiology, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France, Institute of Health & Society, NIHR Health Protection Research Unit in Chemical and Radiation Threats and Hazards, Newcastle University, Newcastle upon Tyne, UK, Section of Environment and Radiation, IARC, Lyon, France, Barcelona Institute for Global Health ISGlobal, ISGlobal, Barcelona, Spain, Radiation Programme, Universitat Pompeu Fabra (UPF), Barcelona, Spain, CIBER Epidemiologı́a y Salud Pública (CIBERESP), Madrid, Spain, Department of Epidemiology and Statistics, Netherlands Cancer Institute, Amsterdam, The Netherlands, Radiation Protection Dosimetry and Calibration Department, Belgian Nuclear Research Centre SCK-CEN, Mol, Belgium, Late Effect Unit, Oncology Clinic, Finsen Center, Copenhagen, Denmark, Institute for Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany, Department of Research, Cancer Registry of Norway, Oslo, Norway, Norwegian Radiation Protection Authority, Østerås, Norway, Department of Physics, University in Oslo, Oslo, Norway, Department of Neuroradiology, Karolinska University Hospital, Stockholm, Sweden, Clinical Epidemiological Unit, Solna, Karolinska Institutet, Stockholm, Sweden and Division of Cancer Epidemiology & Genetics, National Cancer Institute, Rockville, MD, USA
Vehiculation of Active Principles as a Way to Create Smart and Biofunctional Textiles

In some specific fields of application (e.g., cosmetics, pharmacy), textile substrates need to incorporate sensible molecules (active principles) that can be affected if they are sprayed freely on the surface of fabrics. The effect is not controlled and sometimes this application is consequently neglected. Microencapsulation and functionalization using biocompatible vehicles and polymers has recently been demonstrated as an interesting way to avoid these problems. The use of defined structures (polymers) that protect the active principle allows controlled drug delivery and regulation of the dosing in every specific case. Many authors have studied the use of three different methodologies to incorporate active principles into textile substrates, and assessed their quantitative behavior. Citronella oil, as a natural insect repellent, has been vehicularized with two different protective substances; cyclodextrine (CD), which forms complexes with it, and microcapsules of gelatin-arabic gum. The retention capability of the complexes and microcapsules has been assessed using an in vitro experiment. Structural characteristics have been evaluated using thermogravimetric methods and microscopy. The results show very interesting long-term capability of dosing and promising applications for home use and on clothes in environmental conditions with the need to fight against insects. Ethyl hexyl methoxycinnamate (EHMC) and gallic acid (GA) have both been vehicularized using two liposomic-based structures: Internal wool lipids (IWL) and phosphatidylcholine (PC). They were applied on polyamide and cotton substrates and the delivery assessed. The amount of active principle in the different layers of skin was determined in vitro using a Franz-cell diffusion chamber. The results show many new possibilities for application in skin therapeutics. Biofunctional devices with controlled functionality can be built using textile substrates and vehicles. As has been demonstrated, their behavior can be assessed using in vitro methods that make extrapolation to their final applications possible.
Astrocytes in the mouse visual cortex reliably respond to visual stimulation

Astrocytes are known to contact with a great number of synapses and may integrate sensory inputs. In the ferret primary visual cortex, astrocytes respond to a visual stimulus with a delay of several seconds with respect to the surrounding neurons. However, in the mouse visual cortex, it remains unclear whether astrocytes respond to visual stimulations. In this study, using dual-color simultaneous in vivo two-photon Ca2+ imaging of neurons and astrocytes in the awake mouse visual cortex, we examined the visual responsiveness of astrocytes and their precise response timing relative to the surrounding neurons. Neurons reliably responded to visual stimulations, whereas astrocytes often showed neuromodulator-mediated global activities, which largely masked small periodic activities. Administration of the selective α1-adrenergic receptor antagonist prazosin substantially reduced such global astrocytic activities without affecting the neuronal visual responses. In the presence of prazosin, astrocytes showed weak but consistent visual responses mostly at their somata. Cross-correlation analysis estimated that the astrocytic visual responses were delayed by approximately 5 s relative to the surrounding neuronal responses. In conclusion, our research demonstrated that astrocytes in the primary visual cortex of awake mice responded to visual stimuli with a delay of several seconds relative to the surrounding neurons, which may indicate the existence of a common mechanism of neuron–astrocyte communication across species. Highlights We performed dual-color in vivo two-photon Ca2+ imaging of neurons and astrocytes. α1-adrenoblocker prazosin substantially reduced global astrocytic activities. Astrocytes showed weak but reliable visual responses in the awake mouse visual cortex. Astrocytic visual responses were delayed by 5 s relative to the neuronal ones.
Modeling driver cells in developing neuronal networks

Spontaneous emergence of synchronized population activity is a characteristic feature of developing brain circuits. Recent experiments in the developing neo-cortex showed the existence of driver cells able to impact the synchronization dynamics when single-handedly stimulated. We have developed a spiking network model capable to reproduce the experimental results, thus identifying two classes of driver cells: functional hubs and low functionally connected (LC) neurons. The functional hubs arranged in a clique orchestrated the synchronization build-up, while the LC drivers were lately or not at all recruited in the synchronization process. Notwithstanding, they were able to alter the network state when stimulated by modifying the temporal activation of the functional clique or even its composition. LC drivers can lead either to higher population synchrony or even to the arrest of population dynamics, upon stimulation. Noticeably, some LC driver can display both effects depending on the received stimulus. We show that in the model the presence of inhibitory neurons together with the assumption that younger cells are more excitable and less connected is crucial for the emergence of LC drivers. These results provide a further understanding of the structural-functional mechanisms underlying synchronized firings in developing circuits possibly related to the coordinated activity of cell assemblies in the adult brain. Author Summary There is timely interest on the impact of peculiar neurons (driver cells) and of small neuronal sub-networks (cliques) on operational brain dynamics. We first provide experimental data concerning the effect of stimulated driver cells on the bursting activity observable in the developing entorhinal cortex. Secondly, we develop a network model able to fully reproduce the experimental observations. Analogously to the experiments two types of driver cells can be identified: functional hubs and low functionally connected (LC) drivers. We explain the role of hub neurons, arranged in a clique, for the orchestration of the bursting activity in control conditions. Furthermore, we report a new mechanism, which can explain why and how LC drivers emerge in the structural-functional organization of the enthorinal cortex.
The Influence of Practicum-Based Outdoor Inquiry Model on Science Process Skills in Learning Physics

The main purpose of this study is to find out the influence of practicum-based outdoor inquiry model on science process skills. Quasi-experiment design was employed as the research method by Matching Only Post-test Control Group. The research sample was taken using a cluster sampling technique. The samples consisted of experimental class (XI MIA 1) in a total of 25 students treated with practicum-based outdoor inquiry model. The control class (XI MIA 3) consisted of 29 students treated with direct instruction model. In collecting the data, essay test was used in the form of worksheets containing the aspect of science process skills of formulating hypotheses, designing experiment, interpreting data into tables, and drawing a conclusion (inferring). The study results demonstrate that practicum-based outdoor inquiry model was effective in improving the science process skills. It was shown in p-value (significant) of 0.00. The implication of this study is the need to design a practicum-based outdoor inquiry model by noticing what skills are going to improve by means of more varied outdoor activities.
Validation of Questionnaire Methods to Quantify Recreational Water Ingestion

Swimming pool water ingestion volumes are necessary for assessing infection risk from swimming. Pool water ingestion volumes can be estimated by questionnaire or measuring a chemical tracer in swimmer urine. Questionnaires are often preferred to the chemical tracer method because surveys are less time consuming, but no research exists validating questionnaires accurately quantify pool water ingestion volumes. The objective of this study was to explore if questionnaires are a reliable tool for collecting pool water ingestion volumes. A questionnaire was issued at four pool sites in Tucson, Arizona to 46 swimmers who also submitted a urine sample for analyzing cyanuric acid, a chemical tracer. Perceived ingestion volumes reported on the questionnaire were compared with pool water ingestion volumes, quantified by analyzing cyanuric acid in swimmer urine. Swimmers were asked if they swallowed (1) no water or only a few drops, (2) one to two mouthfuls, (3) three to five mouthfuls, or (4) six to eight mouthfuls. One mouthful is the equivalent of 27 mL of water. The majority (81%) of swimmers ingested <27 mL of pool water but reported ingesting >27 mL (“one mouthful”) on the questionnaire. More than half (52%) of swimmers overestimated their ingestion volume. These findings suggest swimmers are over-estimating pool water ingestion because they perceive one mouthful is <27 mL. The questionnaire did not reliably collect pool water ingestion volumes and should be improved for future exposure assessment studies. Images of the ingestion volume categories should be included on the questionnaire to help swimmers visualize the response options.