julilili42/papers huggingface dataset:
Optimal pH set point for simultaneous production and pertraction of n‐caproic acid: an experimental and simulation study
2020-05-18

Abstract BACKGROUND The high rate production of n ‐caproic acid (C6) through chain elongation can be achieved with the use of pertraction systems for the continuous and selective extraction of C6. However, although the biological conversion processes are enhanced at a neutral pH, high extraction efficiency depends on acidic conditions. Understanding of these divergent pH effects is fundamental for a reliable operation and scale‐up of these C6‐producing systems. RESULTS A bench‐scale anaerobic filter (12.8 L) fed with fermented sugarcane at organic loading rates of ≈7.2 g of chemical oxygen demand (COD) L −1 day −1 achieved C6 production rates of 2.1 and 3.8 g COD L −1 day −1 , without and with in‐line extraction, respectively. Compared to previous studies, a high average extraction rate of 24.7 g COD m −2 day −1 was observed due to a high reactor volume‐to‐membrane‐area ratio. The novel model described here with biological and pertraction processes for continuously operated systems indicates that an optimal operative pH can simultaneously maximize C6 production and extraction. The hydraulic retention time was another key parameter for balancing inhibition by undissociated C6 and losses due to nonextracted C6. CONCLUSIONS Sugarcane biorefineries can produce C6, which has a market value that is &gt;10‐fold higher than ethanol. Simulations of chain elongation processes require the implementation of hydrogenotrophic methanogens to allow for a comprehensive description of ethanol consumption together with the C6 formation, in‐line C6 extraction processes, and formation of gaseous by‐products. Although these simulations were possible using parameter sets from the literature, further studies are needed for parameter identification, especially under inhibition at low pH. © 2020 Society of Chemical Industry
Impact of implementing a non-restrictive antibiotic stewardship program in an emergency department: a four-year quasi-experimental prospective study
2020-05-18

Abstract Antibiotic resistance is increasing worldwide. The implementation of antibiotic stewardship programmes (ASPs) is of utmost importance to optimize antibiotic use in order to prevent resistance development without harming patients. The emergency department (ED), cornerstone between hospital and community, represents a crucial setting for addressing ASP implementation; however, evidence data on ASP in ED are poor. In this study, a 4-year, non-restrictive, multi-faceted ASP was implemented in a general ED with the aim to evaluate its impact on antibiotic use and costs. Secondly, the study focused on assessing the impact on length of hospital stay (LOS), Clostridioides difficile infection (CDI) incidence rate, and mortality in the patients’ group admitted from ED to medical wards. The ASP implementation was associated with a reduction of antibiotic use and costs. A mild but sustained LOS decrease in all medical wards and a significant downward trend of CDI incidence rate were observed, while mortality did not significantly change. In conclusion, the implementation of our ED-based ASP has demonstrated to be feasible and safe and might clinically benefit the hospital admitted patients’ group. Further research is needed to identify the most suitable ASP design for ED and the key outcome measures to reliably assess its effectiveness.
Curious Containers: A framework for computational reproducibility in life sciences with support for Deep Learning applications
2020-05-18

In clinical scenarios, there is an increasing interest in complex computational experiments, as for example the training of Deep Learning models. Reproducibility is an essential property of such experiments, especially if the result contributes to a patient's treatment. This paper introduces Curious Containers, a software framework for computational reproducibility that treats data, software and runtime environment as decentralized network resources. All experiment resources are described in a single file, using a new format that is compatible with a subset of the Common Workflow Language. Docker is used to deploy the experiment software in a container image, including arbitrary data transmission programs to connect with existing storage solutions. The framework supports Deep Learning applications, that have a high demand in storage and processing capabilities. Large datasets can be mounted inside containers via network filesystems like SSHFS based on the filesystem in user-space technology. The Nvidia-Container-Toolkit enables GPU usage. Curious Containers has been tested in two biomedical scenarios. The first use case is a Deep Learning application for tumor classification in images that requires a large dataset and a GPU. In this context, a prototypical integration of the framework with the existing Data Version Control system for exploratory Deep Learning modeling has been developed. The second use case extends an existing container image, including a scientific workflow for detection and comparison of human protein in mass spectrography data. The container image was originally developed for an archiving platform and could be extended to be compatible with both Curious Containers and cwltool, the Common Workflow Language reference implementation. The presented solution allows for consistent description and execution of computational experiments, while trying to be both flexible and interoperable with existing software and standards. Support for Deep Learning experiments is gaining importance as such systems are increasingly validated as medical decision support systems.
An Examination of the #NGSSchat Storify Database
2020-05-18

Teachers frequently use Twitter to engage in professional learning activities. A prominent example of teachers’ use of Twitter for such purposes is evident within the #NGSSchat community, which encouraged synchronous (at the same time) conversations between teachers and other educational stakeholders regarding the Next Generation Science Standards (NGSS) curriculum reform in the United States. Notably, #NGSSchat moderators archived the chats via the Storify platform, which has subsequently been used by researchers to understand science teachers’ professional learning activities on Twitter. However, what has not been established is the representativeness of this archive of #NGSSchat tweets. In other words, whether those who archived #NGSSchat content selected only a (potentially biased) selection of tweets is as yet unknown. Thus, in this study, we examined the Storify #NGSSchat database and compared it with raw data requests using the Twitter API. We found that the synchronous chats most data was adequately achieved. Contrarily (but as anticipated given what distinguishes the #NGSSchat community-synchronous conversations), the Storify #NGSSchat database did not capture most data outside these synchronous chat sessions. Importantly, we did not find an indication of systematic content- or user-driven tweet exclusion within the synchronous NGSS chat sessions on Storify, suggesting that the #NGSSchat archive via Storify (and potentially others like it) may be used by researchers for most research-related purposes.
A Comparative Study on Adolescents’ Health Literacy in Europe: Findings from the HBSC Study
2020-05-19

(1) Background: There is a need for studies on population-level health literacy (HL) to identify the current state of HL within and between countries. We report comparative findings from 10 European countries (Austria, Belgium (Fl), Czechia, England, Estonia, Finland, Germany, Macedonia, Poland, and Slovakia) on adolescents’ HL and its associations with gender, family affluence (FAS), and self-rated health (SRH). (2) Methods: Representative data (N = 14,590; age 15) were drawn from the HBSC (Health Behavior in School-Aged Children) study. The associations between HL, gender, FAS, and SRH were examined via path models. (3) Results: The countries exhibited differences in HL means and in the range of scores within countries. Positive associations were found between FAS and HL, and between HL and SRH in each country. Gender was associated with differences in HL in only three countries. HL acted as a mediator between gender and SRH in four countries, and between FAS and SRH in each country. (4) Conclusions: The findings confirm that there are differences in HL levels within and between European countries, and that HL does contribute to differences in SRH. HL should be taken into account when devising evidence-informed policies and interventions to promote the health of adolescents.
Low-Impedance 3D PEDOT:PSS Ultramicroelectrodes
2020-05-19

The technology for producing microelectrode arrays (MEAs) has been developing since the 1970s and extracellular electrophysiological recordings have become well established in neuroscience, drug screening and cardiology. MEAs allow monitoring of long-term spiking activity of large ensembles of excitable cells noninvasively with high temporal resolution and mapping its spatial features. However, their inability to register subthreshold potentials, such as intrinsic membrane oscillations and synaptic potentials, has inspired a number of laboratories to search for alternatives to bypass the restrictions and/or increase the sensitivity of microelectrodes. In this study, we present the fabrication and <i>in vitro</i> experimental validation of arrays of PEDOT:PSS-coated 3D ultramicroelectrodes, with the best-reported combination of small size and low electrochemical impedance. We observed that this type of microelectrode does not alter neuronal network biological properties, improves the signal quality of extracellular recordings and exhibits higher selectivity toward single unit recordings. With fabrication processes simpler than those reported in the literature for similar electrodes, our technology is a promising tool for study of neuronal networks.
Epidemiology of Schistosomiasis and Soil-Transmitted Helminth Coinfections among Schoolchildren Living in Lambaréné, Gabon
2020-05-19

Schistosomiasis is a parasitic infection highly prevalent in Central Africa where it is co-endemic with many other parasitic infections, including soil-transmitted helminths (STHs). For its optimal control, there is a need of descriptive epidemiological data for each endemic region. The objective of the present study was to determine the epidemiological situation around schistosomiasis in Lambaréné, Gabon. A cross-sectional study was conducted among schoolchildren. One urine sample per day was collected on three consecutive days for the diagnosis of schistosomiasis using a urine filtration technique. One stool sample was collected for the detection of <i>Schistosoma</i> spp. and STH spp. eggs using the Kato-Katz technique, and for larvae, using the coproculture technique. A total of 614 schoolchildren were included in the analysis. The overall prevalence of schistosomiasis and STH infections was 26% (159/614) and 15% (70/473), respectively. Human-freshwater contact was the main risk factor for schistosomiasis in the area (relative risk (RR) = 2.96 [2.20-4.00], <i>P</i> < 0.001). Hematuria (RR = 5.53 [4.30-7.10], <i>P</i> < 0.001) and proteinuria (RR = 2.12 [1.63-2.75], <i>P</i> < 0.001) as well as infection with <i>Trichuris trichiura</i> (RR = 1.86 [1.33-2.61], <i>P</i> = 0.002) and <i>Ascaris lumbricoides</i> (RR = 1.96 [1.19-3.21], <i>P</i> = 0.039) were associated with an increased risk of schistosomiasis. <i>Trichuris trichiura</i> was the highest prevalent STH species in the area. Our study reports a moderate prevalence for schistosomiasis with human-water contact as the main risk factor, whereas the prevalence of STH infections appears to be low. Our results stress the need for the implementation of WHO recommendations for schistosomiasis control.
Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
2020-05-19

Abstract The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
Confirmation of TACO1 as a Leigh Syndrome Disease Gene in Two Additional Families
2020-05-19

The identification of two Turkish families with similar characteristic clinical presentation and an additional homozygous nonsense mutation confirms that TACO1 is a human mitochondrial disease gene. Although most patients with this clinical presentation undergo next generation sequencing analysis, screening for selected founder mutations in the Turkish population based on the precise clinical presentation may reduce time and cost of finding the genetic diagnosis even in the era of massively parallel sequencing.
An Intramolecular Hydrogen‐Shift in a Peroxy Radical at Cryogenic Temperatures: The Reaction of 2‐Hydroxyphenyl Radical with O2
2020-05-19

Abstract Peroxy radical hydrogen‐shifts are pivotal elementary reaction steps in the oxidation of small hydrocarbons in autoignition and the lower atmosphere. Although these reactions are typically associated with a substantial barrier, we demonstrate that the [1,5]H‐shift in the peroxy species derived from the 2‐hydroxyphenyl radical 1 is so facile that it even proceeds rapidly in an argon matrix at 35 K through a proton‐coupled electron transfer mechanism. Hydrogen‐bound complexes of o ‐benzoquinone are identified as the main reaction products by infrared spectroscopy although their formation through O−O bond scission is hampered by a barrier of 11.9 kcal mol −1 at the ROCCSD(T)/cc‐pVTZ/UB3LYP/6–311G(d,p) level of theory.
Equivocal evidence for a change in balance between selfing and pollinator‐mediated reproduction in annual Brassicaceae growing along a rainfall gradient
2020-05-19

Abstract Because many plants ensure their reproductive success using some level of self‐fertilization, it is predicted that the balance between pollinator‐mediated pollen transfer and autonomous selfing will be correlated with habitat harshness and pollinator activity. To study these correlations, we used three annual species that differ in their self‐incompatibility and compared their reproductive success in the form of fruit production and seed viability, with and without pollinators, along a rainfall gradient and in relation to pollinator activity. We found that pollinator activity decreased with increasing aridity. Although the reproductive success in the absence of pollinators fitted the species’ level of self‐incompatibility, no clear trend was detected between pollinator visits or site harshness and relative reproductive success. Only one of the species, Sinapis alba , showed a consistent increase in autonomous selfing with both increased aridity and decreased pollinator visits, a finding that was supported by an increase in the viability of seeds produced in the absence of pollinators. Nevertheless, unlike our prediction, the absolute number of seeds produced per S. alba flower increased with aridity. Our overall findings suggest that despite decreasing pollinator abundance and diversity with increasing aridity, the reproductive success of annual species, even of those with high self‐incompatibility, remains relatively high. Although there may be several mechanisms governing these results, the overall constant seed production despite environmental uncertainties may be part of the mechanism by which plants in arid ecosystems buffer environmental variations.
Detecting the Emergent or Re-Emergent COVID-19 Pandemic in a Country: Modelling Study of Combined Primary Care and Hospital Surveillance
2020-05-19

Aims: We aimed to determine the effectiveness of surveillance using testing for SARS-CoV-2 to identify an outbreak arising from a single case of border control failure at a country level. Methods: A stochastic version of the SEIR model CovidSIM v1.1 designed specifically for COVID-19 was utilised. It was seeded with New Zealand (NZ) population data and relevant parameters sourced from the NZ and international literature. Results: For what we regard as the most plausible scenario with an effective reproduction number of 2.0, the results suggest that 95% of outbreaks from a single imported case would be detected in the period up to day 33 after introduction. At the time point of detection, there would be a median number of 6 infected cases in the community (95%UI: 1-68). To achieve this level of detection, an on-going programme of 7,800 tests per million people per week for the NZ population would be required. The vast majority of this testing (96%) would be of symptomatic cases in primary care settings and the rest in hospitals. Despite the large number of tests required, there are plausible strategies to enhance testing yield and cost-effectiveness eg, (i) adjusting the eligibility criteria via symptom profiles; (ii) and pooling of test samples. Conclusions: This model-based analysis suggests that a surveillance system with a very high level of routine testing is probably required to detect an emerging or re-emerging SARS-CoV-2 outbreak within one month of a border control failure in a nation.
Explorative study of emerging blood biomarkers in progressive multiple sclerosis (EmBioProMS): Design of a prospective observational multicentre pilot study
2020-05-19

This longitudinal multicentre study will reveal to what extent the prediction of disease progression in patients with PMS will be improved by the analysis of serum biomarkers in conjunction with routine clinical data and neuroimaging measures.
Hidden Husbandry: Disentangling a Disturbed Profile at Beckery Chapel, a Medieval Ecclesiastical Site Near Glastonbury (UK)
2020-05-19

Beckery Chapel, near Glastonbury, is the site which has the earliest scientific dating evidence for monastic life in the UK, and later in the medieval period became a Chapel that played a significant role as a destination for pilgrims, as part of the Glastonbury Abbey estate. The site was previously excavated in the 1880s and the 1960s, and in 2016 the South West Heritage Trust excavated a building, that proved to be an outbuilding used when the medieval chapel was in operation. Soil micromorphological analysis was conducted first to understand the sediments within the profile from this building, which appeared fairly homogenous and bioturbated in the field. It untangled the bioturbation processes and revealed a rare northern European, geoarchaeological example of a livestock enclosure from a dryland context in this temperate environment. The results of our innovative multi-proxy approach highlight the potential and methodological considerations for future studies to integrate micromorphology, palaeoparasitology and mycology to examine animal management on dryland archaeological sites. They increase the knowledge of the economic activities of the ecclesiastical occupation at Beckery, contributing to an enhanced understanding of the Chapel site, its wider landscape and its role as part of the Glastonbury Abbey estate.
A Methodological Rejoinder to
2020-05-19

There is a presumption that when an individual's comparison of his with the incomes of others in his comparison group yields an unfavorable outcome, the individual is dismayed and experiences stress that impinges negatively on his health. In a recent study, Hounkpatin et al. (2016) conduct an inquiry aimed at deciphering which measure of low reflects better the adverse psychosocial effect of low on health. Hounkpatin et al. pit against each other two indices that they characterize as competing: the relative deprivation (Yitzhaki Index) of individual i, RDi ; and the income rank position of individual i, Ri . In this Rejoinder we show that because a measure of rank is embodied in the RDi index and the Ri index can be elicited from the RDi index, these two indices need not be viewed as competing. Furthermore, we formulate a composite measure of deprivation, CRDi , which can be used to assess more fully the psychosocial effect of individual i's low on his health.
ICP-MS trace element analysis in serum and whole blood
2020-05-20

Trace elements and minerals are compounds that are essential for the support of a variety of biological functions and play an important role in the formation of and the defense against oxidative stress. Here we describe a technique, allowing sequential detection of the trace elements (K, Zn, Se, Cu, Mn, Fe, Mg) in serum and whole blood by an ICP-MS method using single work-up, which is a simple, quick and robust method for the sequential measurement and quantification of the trace elements Sodium (Na), Potassium (K), Calcium (Ca), Zinc (Zn), Selenium (Se), Copper (Cu), Iron (Fe), Manganese (Mn) and Magnesium (Mg) in whole blood as well as Copper (Cu), Selenium (Se), Zinc (Zn), Iron (Fe), Magnesium (Mg), Manganese (Mn), Chromium (Cr), Nickel (Ni), Gold (Au) and Lithium (Li) in human serum. For analysis, only 100 μl of serum or whole blood is sufficient, which make this method suitable for detecting trace element deficiency or excess in newborns and infants. All samples were processed and analyzed by ICP-MS (Agilent Technologies). The accuracy, precision, linearity and the limit of quantification (LOQ), Limit of Blank (LOB) and the limit of detection (LOD) of the method were assessed. Recovery rates were between 80-130% for most of the analyzed elements; repeatabilities (Cv %) calculated were below 15% for most of the measured elements. The validity of the proposed methodology was assessed by analyzing a certified human serum and whole blood material with known concentrations for all elements; the method described is ready for routine use in biomonitoring studies.
Meta-analysis of the effects of transcranial direct current stimulation on inhibitory control
2020-05-20

Based on the studies included, our meta-analytic approach substantiates previously observed differences between brain regions, i.e., involvement of the right inferior frontal gyrus (rIFG) vs. the right dorsolateral prefrontal cortex (rDLPFC) in inhibitory control. Results indicate a small moderating effect of tDCS on inhibitory control in single-session studies and highlight the relevance of technical and behavioral parameters.