Miracle-dz/UniFAR-FTUs huggingface dataset:
University of Birmingham High speed imaging of biofilm removal from a dental implant model using ultrasonic cavitation

Objectives: Current instruments cannot clean in between dental implant threads and effectively remove biofilm from the rough implant surface without damaging it. Cavitation bubbles have the potential to disrupt biofilms. The aim of this study was to see how biofilms can be disrupted using non-contact cavitation from an ultrasonic scaler, imaged inside a restricted implant pocket model using high speed imaging. Methods : Streptococcus sanguinis biofilm was grown for 7 days on dental implants. The implants were placed inside a custom made restricted pocket model and immersed inside a water tank. An ultrasonic scaler tip was placed 0.5 mm away from the implant surface and operated at medium power or high power for 2s. The biofilm removal process was imaged using a high speed camera operating at 500 fps. Image analysis was used to calculate the amount of biofilm removed from the high speed images. Scanning electron microscopy was done to visualise the implant surface after cleaning. Results: Cavitation was able to remove biofilm from dental implants. More biofilm was removed at high power. Scanning electron microscopy showed that the implant surface was clean at the points where the cavitation was most intense. High speed imaging showed biofilm removal underneath implant threads, in areas next to the ultrasonic scaler tip. Significance: A high speed imaging protocol has been developed to visualise and quantify biofilm removal from dental implants in vitro . Cavitation bubbles from dental ultrasonic scalers are able to successfully disrupt biofilm in between implant threads.
Draft Genome Sequence of Gordonia sp. Strain YY1, Isolated from an Explosive-Contaminated Environment

We report the whole-genome sequence of Gordonia sp. strain YY1, which was isolated from the surface soil in an explosive-contaminated site in Israel and cultivated with hexahydro-1,3,5-trinitro-1,3,5-triazine, i.e., royal demolition explosive (RDX), as a nitrogen source. This genome sequence will improve our understanding of the genes for RDX degradation. In addition, this research will reveal metabolic pathways in order to develop new bioremediation methods for polluted soil and groundwater. ABSTRACT We report the whole-genome sequence of Gordonia sp. strain YY1, which was isolated from the surface soil in an explosive-contaminated site in Israel and cultivated with hexahydro-1,3,5-trinitro-1,3,5-triazine, i.e., royal demolition explosive (RDX), as a nitrogen source. This genome sequence will improve our understanding of the genes for RDX degradation. In addition, this research will reveal metabolic pathways in order to develop new bioremediation methods for polluted soil and groundwater.
Bats reveal the true power of influenza A virus adaptability

Influenza A viruses (IAVs) circulate among a wide variety of different hosts. They can cross species barriers and establish new virus lineages in avian and mammalian species. As a consequence, IAVs are exposed to recurrent selective pressures, leading to a range of virus variants that are able to cope with the new host environment [1]. Bats were not considered to be part of this IAV habitat until recently, when two phylogenetically distinct IAV lineages, designated H17N10 and H18N11, were identified in the New World bats Sturnira lilium and Artibeus spp, respectively [2–4]. Likewise, Old World bats can harbor influenza viruses, as exemplified by the genetically distinct H9N2 virus found in Egyptian fruit bats (Rousettus aegyptiacus) [5]. The discovery of influenza viruses in New and Old World bats did severely challenge our previous conception of IAV host range and phylogeny. It, moreover, provided unexpected insights into the remarkable adaptive potential of these viruses and their evolutionary origin.
A pedagogical approach to science outreach

Encouragement of students across all communities through scientific outreach programs is critical to engaging the next generation, exciting young minds to pursue careers in science and medicine. Herein, we present a uniquely structured and widely influential science outreach program. Founded in 2005, the Duke Chemistry Outreach (DCO) employs a pedagogical approach to outreach that aims to teach its audience a new scientific concept, while instilling a pure enjoyment of science. DCO has performed 583 events reaching over 70,000 participants throughout 2,270 hours, with the majority of events in Durham, the surrounding North Carolinian communities, and across 8 other states. The flexibility and diversity of this outreach program creates a framework amendable for others to adopt in both secondary and higher education settings.
ChemOS: An orchestration software to democratize autonomous discovery

The current Edisonian approach to discovery requires up to two decades of fundamental and applied research for materials technologies to reach the market. Such a slow and capital-intensive turnaround calls for disruptive strategies to expedite innovation. Self-driving laboratories have the potential to provide the means to revolutionize experimentation by empowering automation with artificial intelligence to enable autonomous discovery. However, the lack of adequate software solutions significantly impedes the development of self-driving laboratories. In this paper, we make progress towards addressing this challenge, and we propose and develop an implementation of ChemOS; a portable, modular and versatile software package which supplies the structured layers necessary for the deployment and operation of self-driving laboratories. ChemOS facilitates the integration of automated equipment, and it enables remote control of automated laboratories. ChemOS can operate at various degrees of autonomy; from fully unsupervised experimentation to actively including inputs and feedbacks from researchers into the experimentation loop. The flexibility of ChemOS provides a broad range of functionality as demonstrated on five applications, which were executed on different automated equipment, highlighting various aspects of the software package.
Low-energy nanoemulsions as carriers for red raspberry seed oil: Formulation approach based on Raman spectroscopy and textural analysis, physicochemical properties, stability and in vitro antioxidant/ biological activity

Considering a growing demand for medicinal/cosmetic products with natural actives, this study focuses on the low-energy nanoemulsions (LE-NEs) prepared via the Phase inversion composition (PIC) method at room temperature as potential carriers for natural oil. Four different red raspberry seed oils (ROs) were tested, as follows: cold-pressed vs. CO2-extracted, organic vs. non-organic, refined vs. unrefined. The oil phase was optimized with Tocopheryl acetate and Isostearyl isostearate, while water phase was adjusted with either glycerol or an antioxidant hydro-glycolic extract. This study has used a combined approach to formulation development, employing both conventional methods (pseudo-ternary phase diagram − PTPD, electrical conductivity, particle size measurements, microscopical analysis, and rheological measurements) and the methods novel to this area, such as textural analysis and Raman spectroscopy. Raman spectroscopy has detected fine differences in chemical composition among ROs, and it detected the interactions within nanoemulsions. It was shown that the cold-pressed, unrefined, organic grade oil (RO2) with 6.62% saturated fatty acids and 92.25% unsaturated fatty acids, was optimal for the LE-NEs. Textural analysis confirmed the existence of cubic gel-like phase as a crucial step in the formation of stable RO2-loaded LE-NEs, with droplets in the narrow nano-range (125 to 135 nm; PDI ≤ 0.1). The DPPH test in methanol and ABTS in aqueous medium have revealed a synergistic free radical scavenging effect between lipophilic and hydrophilic antioxidants in LE-NEs. The nanoemulsion carrier has improved the biological effect of raw materials on HeLa cervical adenocarcinoma cells, while exhibiting good safety profile, as confirmed on MRC-5 normal human lung fibroblasts. Overall, this study has shown that low-energy nanoemulsions present very promising carriers for topical delivery of natural bioactives. Raman spectroscopy and textural analysis have proven to be a useful addition to the arsenal of methods used in the formulation and characterization of nanoemulsion systems.
Body image disorders associated with lifestyle and body composition of female adolescents

Abstract Objective: To investigate the association between body image disorders and the lifestyle and body composition of female adolescents. Design: Cross-sectional study. Setting: The Body Shape Questionnaire (BSQ) and Silhouette Scale and Sociocultural Attitudes Towards Appearance Questionnaire-3 were used to evaluate the participants’ body image. Body composition was evaluated by a Dual-Energy X-ray Absorptiometry equipment, and lifestyles were identified by latent class analysis (LCA) using the poLCA package for R. Participants: Female adolescents aged 14–19 years old, in the city of Viçosa-MG, Brazil. Results: In total, 405 girls participated in the study. Almost half of the participants were dissatisfied with their current physical appearance (51·4 %), presented body perception distortions (52·9 %). 47·3 % of the adolescents were dissatisfied with their body according to the BSQ, and another 8 % severely so. Subjects with an ‘Inactive and Sedentary’ latent lifestyle were 1·71 times as likely to feel dissatisfied as those with active and sedentary or inactive and non-sedentary lifestyles (95 % CI 1·08, 2·90, P = 0·047). Body image disorders showed an association with decreased amounts of moderate and vigorous physical activity, high screen time, increased alcohol consumption and excess body fat. Conclusions: Particular patterns of lifestyle and body composition seem to be associated in female adolescents with dissatisfaction with, distortion of and excessive concern about appearance. Specifically, physical inactivity, sedentary behaviour, alcohol consumption and high body fat percentage may be strongly linked to body image disorders.
Unveiling dynamic metabolic signatures in human induced pluripotent and neural stem cells

Metabolism plays an essential role in cell fate decisions. However, the methods used for metabolic characterization and for finding potential metabolic regulators are still based on characterizing cellular metabolic steady-state which is dependent on the extracellular environment. In this work, we hypothesized that the response dynamics of intracellular metabolic pools to extracellular stimuli is controlled in a cell type-specific manner. We applied principles of process dynamics and control to human induced pluripotent stem cells (hiPSC) and human neural stem cells (hNSC) subjected to a sudden extracellular glutamine step. The fold-changes of steady-states and the transient profiles of metabolic pools revealed that dynamic responses were reproducible and cell type-specific. Importantly, many amino acids had conserved dynamics and readjusted their steady state concentration in response to the increased glutamine influx. Overall, we propose a novel methodology for systematic metabolic characterization and identification of potential metabolic regulators.
Lactation milk yield prediction in primiparous cows on a farm using the seasonal auto-regressive integrated moving average model, nonlinear autoregressive exogenous artificial neural networks and Wood’s model

Objective The aim of the present study was to compare the effectiveness of three approaches (the seasonal auto-regressive integrated moving average [SARIMA] model, the nonlinear autoregressive exogenous [NARX] artificial neural networks and Wood’s model) to the prediction of milk yield during lactation. Methods The dataset comprised monthly test-day records from 965 Polish Holstein-Friesian Black-and-White primiparous cows. The milk yields from cows in their first lactation (from 5 to 305 days in milk) were used. Each lactation was divided into ten lactation stages of approximately 30 days. Two age groups and four calving seasons were distinguished. The records collected between 2009 and 2015 were used for model fitting and those from 2016 for the verification of predictive performance. Results No significant differences between the predicted and the real values were found. The predictions generated by SARIMA were slightly more accurate, although they did not differ significantly from those produced by the NARX and Wood’s models. SARIMA had a slightly better performance, especially in the initial periods, whereas the NARX and Wood’s models in the later ones. Conclusion The use of SARIMA was more time-consuming than that of NARX and Wood’s model. The application of the SARIMA, NARX and Wood’s models (after their implementation in a user-friendly software) may allow farmers to estimate milk yield of cows that begin production for the first time.
Epidemiology of hospitalised paediatric community-acquired pneumonia and bacterial pneumonia following the introduction of 13-valent pneumococcal conjugate vaccine in the national immunisation programme in Japan

Abstract Studies on community-acquired pneumonia (CAP) and pneumococcal pneumonia (PP) related to the 13-valent pneumococcal conjugate vaccine (PCV13) introduction in Asia are scarce. This study aimed to investigate the epidemiological and microbiological determinants of hospitalised CAP and PP after PCV13 was introduced in Japan. This observational hospital-based surveillance study included children aged ⩽15 years, admitted to hospitals in and around Chiba City, Japan. Participants had bacterial pneumonia based on a positive blood or sputum culture for bacterial pathogens. Serotype and antibiotic-susceptibility testing of Streptococcus pneumoniae and Haemophilus influenzae isolates from patients with bacterial pneumonia were assessed. The CAP hospitalisation rate per 1000 child-years was 17.7, 14.3 and 9.7 in children aged <5 years and 1.18, 2.64 and 0.69 in children aged 5–15 years in 2008, 2012 and 2018, respectively. There was a 45% and 41% reduction in CAP hospitalisation rates, between the pre-PCV7 and PCV13 periods, respectively. Significant reductions occurred in the proportion of CAP due to PP and PCV13 serotypes. Conversely, no change occurred in the proportion of CAP caused by H. influenzae. The incidence of hospitalised CAP in children aged ⩽15 years was significantly reduced after the introduction of PCV13 in Japan. Continuous surveillance is necessary to detect emerging PP serotypes.
Draft Genome Sequence of the Oomycete Globisporangium splendens Strain rgcb-1

Globisporangium splendens (formerly Pythium splendens) is an oomycete pathogen of many economically important vegetable crops. Here, we present the first draft genome of P. splendens, which comprises 197 scaffolds with a total length of 53.3 Mb and 17,350 predicted protein-coding genes. ABSTRACT Globisporangium splendens (formerly Pythium splendens) is an oomycete pathogen of many economically important vegetable crops. Here, we present the first draft genome of P. splendens, which comprises 197 scaffolds with a total length of 53.3 Mb and 17,350 predicted protein-coding genes.
Effect of ketamine on voltage-gated potassium channels in rat primary sensory cortex pyramidal neurons

Ketamine is an intravenous anesthetic commonly used in clinical, which has sedative and analgesic effects. Potassium channels exert many physiological functions in excitable cells. Therefore, potassium channels may be one of the targets of ketamine. In this study, we used patch clamp to study the effects of ketamine on voltage-gated potassium channels in primary sensory cortex (S1) neurons. We recorded the outward potassium currents (IA) and delayed rectifier potassium currents (IK) separately. We found that ketamine both concentration-dependently inhibited IA currents and IK currents in S1 neurons. Ketamine (100 and 300 μM) induced a concentration-dependent hyperpolarizing shift in V1/2, without affecting the slope factor (κ) or inactivation of IA. Ketamine induced a concentration-dependent hyperpolarizing shift in V1/2 of IK, without affecting its κ. Ketamine (100 and 300 μM) did not alter the steady-state activation or its κ. Hence, ketamine inhibits IA and IK in a concentration-dependent manner in S1 pyramidal neurons. The inactivation of IA does not appear to be involved in the inhibitory effect of ketamine on IA. Ketamine inhibits IK mainly by speeding up the inactivation of IK in S1 pyramidal neurons.
Systematic Research and Evaluation Models of Nanomotors for Cancer Combined Therapy.

Limited tumor permeability of therapeutic agents is a great challenge faced by current cancer therapy methods. Herein, a novel near infrared (NIR)-driven nanomotors with autonomous movement, targeted ability, hierarchical porous structure, loaded multi-drugs for cancer chemo/photothermal therapy is designed, prepared and characterized. Further, a method for studying the interaction between nanomotors and cells, along with their tumor permeability mechanism was established, including 2D cellular models, 3D multicellular tumor spheroids model and in vivo model. Tumor elimination results in vivo verify that the movement behaviour of the nanomotors can greatly facilitate them to eliminate tumor through multiple therapeutic methods. This work pays attention to setting systematic research and evaluation models and elaborates a strategy to understand the relationship between motion behaviour and cell permeation efficiency of nanomotors in depth and to employ nanomotors to enhance tissue permeability of drugs for effective cancer therapy.
TRIHALOMETHANE AND HALOACETIC ACID FORMATION POTENTIAL OF TROPICAL PEAT WATER: EFFECT OF TIDAL AND SEASONAL VARIATIONS

The existence of humic substances in peat water impacts the presence of the dissolved organic matter (DOM) which is the precursor of trihalomethanes (THMs) and haloacetic acids (HAAs). However, information on DOM characteristics, THMs and HAAs Formation Potential (THMFP and HAAFP) in tropical peat water are still limited. This study aimed to determine the correlations between DOM, THMFP, and HAAFP during dry and rainy seasons in tropical peat water in Indonesia. Samples of peat water are taken from the water canal and tidally affected river on Sumatera’s peatland during the rainy season and dry season to determine the effects of the seasons and tides. DOM measured by dissolved organic carbon (DOC), specific ultraviolet absorbance and the ratio of E465/E665 while THMFP determined from a total of THMFP4 measurements and HAAFP determined from measurement of total HAAFP5. Compared to dry season, values of all organic parameters on rainy season were higher but fewer in river. Canal water has a higher DOC while river water has a higher chloride and bromide content. Increasing of DOC in the rainy season correlates with increasing of THMFP4 and HAAFP5. THMFP4 is dominated by chloroform on canal while brominated THMs predominate in river water which correlates with the presence of bromide. Chlorinated HAAs dominate HAAFP5 in canal water while brominated HAAs increases in the river. Seasons and tides affect the appearance of bromide contaminants in water that affects the form of THMFP and HAAFP.
Original Contribution Association Between Glucose Tolerance Level and Cancer Death in a General Japanese Population The Hisayama Study

The authors examined the associations of glucose tolerance status and fasting and 2-hour postload glucose levels with the risk of cancer death in a 19-year follow-up study of 2,438 Japanese subjects aged 40–79 years who underwent a 75-g oral glucose tolerance test (1988–2007). During follow-up, 229 subjects died of cancer. The risk of cancer death was significantly higher in subjects with fasting plasma glucose levels of ≥5.6 mmol/L or 2-hour postload glucose levels of ≥11.1 mmol/L than in those with the lowest fasting or 2-hour postload glucose levels, after adjustment for potentially confounding factors. According to glucose tolerance status, not only diabetes but also impaired fasting glycemia and impaired glucose tolerance were significant risk factors for cancer death (for impaired fasting glycemia, multivariable-adjusted hazard ratio (HR) = 1.49 (95% confidence interval (CI): 1.05, 2.11); for impaired glucose tolerance, HR = 1.52 (95% CI: 1.05, 2.22); and for diabetes, HR = 2.10 (95% CI: 1.41, 3.12)). With regard to site-specific cancers, elevated fasting or 2-hour postload glucose levels were associated with the risks of death from stomach, liver, and lung cancer. These findings suggest that both prediabetic hyperglycemia and diabetes are significant risk factors for cancer death in the general Japanese population.
The Energetics of Lifetime Reproductive Success in the Zebra Finch Taeniopygia guttata

Recent studies that have shown that variation in avian foraging behavior can produce changes in reproductive success and survival have raised the question of the role of energy budgets in determining reproductive behavior and other life-history traits of birds. The study reported here describes how the daily energy budgets of breeding populations of the zebra finch Taeniopygia guttata influenced the rate at which broods were produced, the size of broods that could be success-fully supported by their parents, and the subsequent survival of the parents. This was examined by experimentally altering the net rate of energy gain of four populations of randomly chosen zebra finches. The experimental design increased the amount of time spent searching for food without altering the amount of food available or consumed, which resulted in differences in the daily energy budget. Zebra finches with low rates of energy gain spent more time and energy foraging and had less energy available for reproduction than did finches with high rates of energy gain. A decrease in energy available for reproduction increased the time interval between successive broods while decreasing average brood size, juvenile survivorship, and adult survivorship.
The Future of Anti-Amyloid Trials

The termination of many clinical trials of amyloid-targeting therapies for the treatment of Alzheimer’s disease (AD) has had a major impact on the AD clinical research enterprise. However, positive signals in recent studies have reinvigorated support for the amyloid hypothesis and amyloid-targeting strategies. In December 2019, the EU-US Clinical Trials on Alzheimer’s Disease (CTAD) Task Force met to share learnings from these studies in order to inform future trials and promote the development of effective AD treatments. Critical factors that have emerged in studies of anti-amyloid monoclonal antibody therapies include developing a better understanding of the specific amyloid species targeted by different antibodies, advancing our insight into the mechanism by which those antibodies may reduce pathology, implementing more comprehensive repertoires of biomarkers into trials, and identifying appropriate doses. Studies suggest that Amyloid-Related Imaging Abnormalities — effusion type (ARIA-E) are a manageable safety concern and that caution should be exercised before terminating studies based on interim analyses. The Task Force concluded that opportunities for developing effective treatments include developing new biomarkers, intervening in early stages of disease, and use of combination therapies.