Miracle-dz/UniFAR-FTUs huggingface dataset:
Lignin-Modifying Enzymes of Flavodon flavus, a Basidiomycete Isolated from a Coastal Marine Environment

ABSTRACT A basidiomycetous fungus Flavodon flavus (Klotzsch) Ryvarden (strain 312), isolated from decaying sea grass from a coral lagoon off the west coast of India, mineralized nearly 24% of14C-labeled synthetic lignin to14CO2 in 24 days. When grown in low-nitrogen medium (2.4 mM N) this fungus produced three major classes of extracellular lignin-modifying enzymes (LMEs): manganese-dependent peroxidase (MNP), lignin peroxidase (LIP), and laccase. Low MNP and laccase activities were seen in high-nitrogen medium (24 mM N), but no LIP activity was seen. In media containing lignocellulosic substrates such as pine, poplar, or sugarcane bagasse as the sole source of carbon and nitrogen, relatively high MNP and moderate levels of laccases were seen, but LIP production either was not seen or was minimal. LME production was also seen in media prepared with artificial seawater. Fast protein liquid chromatography and isoelectric focusing resolved LMEs into four isozymes each of MNP and LIP, while laccase isozymes were resolved into two groups, one group containing seven isozymes (pIs 4 to 6) and the other group containing at least three isozymes (pIs < 3). The molecular masses of the different isozymes were 43 to 99 kDa for MNP, 40 and 41.5 kDa for LIP, and 43 and 99 kDa for laccase. F. flavus showed effective degradation of various dye pollutants in media prepared with or without artificial seawater. This is the first report on the production of all three major classes of LMEs by F. flavus and points to the bioremediation potential of this organism in terrestrial as well as marine environments.
Probabilistic Model for Listeria monocytogenes Growth during Distribution, Retail Storage, and Domestic Storage of Pasteurized Milk

ABSTRACT A survey on the time-temperature conditions of pasteurized milk in Greece during transportation to retail, retail storage, and domestic storage and handling was performed. The data derived from the survey were described with appropriate probability distributions and introduced into a growth model of Listeria monocytogenes in pasteurized milk which was appropriately modified for taking into account strain variability. Based on the above components, a probabilistic model was applied to evaluate the growth of L. monocytogenes during the chill chain of pasteurized milk using a Monte Carlo simulation. The model predicted that, in 44.8% of the milk cartons released in the market, the pathogen will grow until the time of consumption. For these products the estimated mean total growth of L. monocytogenes during transportation, retail storage, and domestic storage was 0.93 log CFU, with 95th and 99th percentiles of 2.68 and 4.01 log CFU, respectively. Although based on EU regulation 2073/2005 pasteurized milk produced in Greece belongs to the category of products that do not allow the growth of L. monocytogenes due to a shelf life (defined by law) of 5 days, the above results show that this shelf life limit cannot prevent L. monocytogenes from growing under the current chill chain conditions. The predicted percentage of milk cartons—initially contaminated with 1 cell/1-liter carton—in which the pathogen exceeds the safety criterion of 100 cells/ml at the time of consumption was 0.14%. The probabilistic model was used for an importance analysis of the chill chain factors, using rank order correlation, while selected intervention and shelf life increase scenarios were evaluated. The results showed that simple interventions, such as excluding the door shelf from the domestic storage of pasteurized milk, can effectively reduce the growth of the pathogen. The door shelf was found to be the warmest position in domestic refrigerators, and it was most frequently used by the consumers for domestic storage of pasteurized milk. Furthermore, the model predicted that a combination of this intervention with a decrease of the mean temperature of domestic refrigerators by 2°C may allow an extension of pasteurized milk shelf life from 5 to 7 days without affecting the current consumer exposure to L. monocytogenes.
Authoritarian regime types revisited: updated data in comparative perspective

This article introduces a modified and updated version of the authoritarian regime type dataset first introduced by Hadenius and Teorell. The basic logic and merits of this dataset is presented, previously published criticism of the index is addressed and practical advice for potential users is provided. The dataset is also compared theoretically and empirically with the datasets provided by Cheibub et al., and Geddes et al. It is argued that the choice of dataset is likely to have a substantial effect on the results of empirical research. The different datasets all have their respective strengths and weaknesses. However, our typology of authoritarianism distinguishes itself from the alternative categorisations in that it recognises the heterogeneous character of electoral regimes and provides a category corresponding to the theoretically interesting class of ‘electoral authoritarian’ regimes.
The use of mini-CEX in UK foundation training six years following its introduction: Lessons still to be learned and the benefit of formal teaching regarding its utility

Background: The mini-clinical evaluation exercise (mini-CEX) is a widely used tool with a strong theoretical basis. It was introduced to UK foundation training in 2005. Aims: To assess current experiences, opinions and attitudes towards mini-CEX amongst foundation doctors, and explore what factors underpin these. Methods: Data were collected from foundation trainees via an on-line questionnaire. Results: Ninety-eight per cent of respondents had used mini-CEX during FY1, however, only 32% had ever received formal teaching regarding its use. In terms of understanding of the purpose of mini-CEX, only 30% of trainees commented on there being a formative aspect or requirement for feedback. The majority of trainees did not feel that mini-CEX was a useful part of their training. The main themes were the poor attitude and understanding of assessors and difficulties finding sufficient time. However, those who had received formal teaching as students regarding the use of mini-CEX were significantly more likely as postgraduates to find it beneficial (p = 0.031). Conclusions: A more concerted effort to educate trainees and assessors regarding the correct use of mini-CEX will enhance its educational value. Increased education during undergraduate training regarding use of formative assessment may lead to more effective utilisation in the postgraduate setting.
Fast Image/Video Contrast Enhancement Based on Weighted Thresholded Histogram Equalization

A fast and effective method for image contrast enhancement is presented. In the proposed method, the probability distribution function (histogram) of an image is modified by weighting and thresholding before the histogram equalization (HE) is performed. We show that such an approach provides a convenient and effective mechanism to control the enhancement process, while being adaptive to various types of images. We also discuss application of the proposed method in video enhancement. Experimental results are presented and compared with results from other contemporary methods.
MORPHOLOGIC AND MOLECULAR STUDY OF HEMOPARASITES IN WILD CORVIDS AND EVIDENCE OF SEQUENCE IDENTITY WITH PLASMODIUM DNA DETECTED IN CAPTIVE BLACK-FOOTED PENGUINS (SPHENISCUS DEMERSUS)

Abstract: A morphologic and molecular epidemiologic investigation was conducted on a captive African black-footed penguin (Spheniscus demersus) colony with a history of Plasmodium infections at La Palmyre Zoo (France). Each penguin received 12.5 mg of pyrimethamine twice a week as a prophylaxis every year from April to November. Although Plasmodium parasites were not detected in blood smears and tissues collected from the penguins, various blood parasites were recorded in blood smears from wild Eurasian magpies (Pica pica) and carrion crows (Corvus corone) sampled at the same time in the study area. These parasites consisted of several Plasmodium spp. (P. lenoblei, P. dorsti, P. bioccai, P. relictum, P. dherteae, P. beaucournui, P. maior, P. tranieri, and P. snounoui), Parahaemoproteus spp. , Trypanosoma spp. , and Leucocytozoon spp. On the other hand, nested polymerase chain reaction enabled detection of Plasmodium DNA in 28/44 (64%) penguins, 15/25 (60%) magpies, and 4/9 (44%) crows. Sequencing and phylogenetic analyses indicated that the parasite DNA amplified from the penguins, magpies, and crows were similar. Magpies and crows could therefore act as a reservoir for penguin Plasmodium infections, which may be more prevalent than previously thought. Morphologic characterization of the Plasmodium spp. detected in the penguins, as well as further biological and epidemiologic studies, are needed to fully understand the transmission of Plasmodium parasites to captive penguins.
Synthesis, export, and assembly of Aeromonas salmonicida A-layer analyzed by transposon mutagenesis

Suicide plasmid pJB4JI, containing transposon Tn5 and phage Mu, was introduced into Aeromonas salmonicida 449 which produces a surface protein array known as the A-layer. Kanamycin-resistant exconjugants of 449 with altered ability to produce the A-layer were selected by virtue of their altered colonial morphology and color on medium containing the dye Congo red. Analysis of culture supernatants, periplasmic shock fluid, outer membranes, and whole-cell lysates by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting with a monoclonal antibody to A-protein revealed five classes of single-insertion mutations that affected the ability of cells to produce and export A-protein and to assemble the A-layer. These studies suggest that A-protein is produced from a single chromosomal gene. The subunits subsequently pass through the periplasm and across the outer membrane. At least one gene product is required for this export. Assembly of A-layer on the cell surface then requires the presence of O polysaccharide chains on the lipopolysaccharide. In one case, insertion of Tn5 resulted in loss of ability to produce both A-protein and lipopolysaccharide with O polysaccharide chains, suggesting that synthesis of A-protein and synthesis of lipopolysaccharide may involve coordinate regulation.
The effect of stem length on femoral component positioning in canine total hip arthroplasty.

OBJECTIVE To determine the effects of femoral prosthesis stem length on positioning of the femoral component within the canine femur. STUDY DESIGN An in vitro experimental study. SAMPLE POPULATION Eleven adult, mixed breed, canine cadaver femurs. METHODS Polymethylmethacrylate centralized Biomedtrix size 5, 6, and 7 standard and 1cm shortened implants were placed in specimens, manipulated to achieve maximal displacements of the implant tip in each plane, and radiographed. Measurements of the implant angle, tip offset, and minimal tip to endosteal surface distance were obtained with image processing software. The effects of implant length and size on implant positioning were evaluated with the use of Student's t, chi(2) exact, and 2-way ANOVA testing. RESULTS Statistically significant increases were noted in tip to caudal cortex distance in the sagittal plane, and available angle variability and tip offset variability in the transverse plane for shortened size 6 and 7 stems relative to the standard stems. No significant differences were noted in size 5 stems. Statistically significant increases in tip to caudal cortex distance and transverse plane available angle variability for standard 6 compared to standard 7 stems were noted. CONCLUSIONS Shortened stems result in statistical improvement of several variables of femoral component positioning. However, the improvement appears to be clinically negligible. CLINICAL RELEVANCE Alteration of current stem lengths is not recommended. The use of undersized standard implants may improve femoral component positioning in total hip arthroplasty.
How the body shapes the way we think - a new view on intelligence

How could the body influence our thinking when it seems obvious that the brain controls the body? In How the Body Shapes the Way We Think, Rolf Pfeifer and Josh Bongard demonstrate that thought is not independent of the body but is tightly constrained, and at the same time enabled, by it. They argue that the kinds of thoughts we are capable of have their foundation in our embodiment -- in our morphology and the material properties of our bodies. This crucial notion of embodiment underlies fundamental changes in the field of artificial intelligence over the past two decades, and Pfeifer and Bongard use the basic methodology of artificial intelligence -- "understanding by building" -- to describe their insights. If we understand how to design and build intelligent systems, they reason, we will better understand intelligence in general. In accessible, nontechnical language, and using many examples, they introduce the basic concepts by building on recent developments in robotics, biology, neuroscience, and psychology to outline a possible theory of intelligence. They illustrate applications of such a theory in ubiquitous computing, business and management, and the psychology of human memory. Embodied intelligence, as described by Pfeifer and Bongard, has important implications for our understanding of both natural and artificial intelligence.
‘Sometimes I want to play by myself’: Understanding what friendship means to children with autism in mainstream primary schools

Research has shown that friendship impacts the overall experience of mainstream school for autistic children. Using a unique combination of quantitative, qualitative and social network methods, we investigated the extent and nature of autistic children’s friendships from their perspective and from those of their mothers, teachers and classroom peers. Consistent with previous research, children with autism (n = 12), aged between 9 and 11 years, rated their friendships to be of poorer quality than their non-autistic classroom peers (n = 11). There was, however, much variability in autistic children’s ratings, which, unexpectedly, was related to neither children’s cognitive ability nor their theory of mind ability. Encouragingly, the children generally reported satisfaction with their friendships, and although no child was socially isolated, the degree of inclusion in friendship networks varied widely. Furthermore, autistic children’s social motivation emerged as a key factor in parents’ and teachers’ reports in determining both the nature and extent of their friendships. Adults played an active role in supporting children’s friendships, but this sometimes conflicted with what the children wanted. These findings highlight the need to ascertain the perspectives of young people with autism on their friendships and to consider the social and ethical implications of when and how to intervene.
The effect of paracetamol (acetaminophen) on fentanyl metabolism in vitro

Background: Fentanyl is a synthetic opioid widely used in anesthesia and analgesia. In experimental animals and in humans it has been shown that most fentanyl biotransformation occurs in the liver, where this opioid is converted primarily to its N‐dealkylated derivative, norfentanyl. Recent studies have shown that fentanyl is metabolized to norfentanyl via cytochrome P‐450 3A4 (CYP3A4). CYP3A4 is responsible for the metabolism of numerous other therapeutic agents, including those administered concurrently with fentanyl (e.g., nifedipine, lidocaine, erythromycin and cyclosporine). Paracetamol is also metabolized by the CYP3A family, with a Km that is nearly equal to therapeutic blood concentrations. Since paracetamol is widely used, its potential interaction with fentanyl metabolism would be of great interest.
Do central terminals of intact myelinated primary afferents sprout into the superficial dorsal horn of rat spinal cord after injury to a neighboring peripheral nerve?

In order to investigate whether normal myelinated primary afferent axons sprout into the territories of adjacent injured peripheral nerve fibers in the superficial dorsal horn of the spinal cord, adult rats underwent either sectioning of the saphenous or femoral nerves on one side, or else unilateral denervation of the skin of the posterior thigh. Two weeks later cholera toxin B subunit (CTb), which is normally transported selectively by myelinated somatic primary afferents, was injected into the ipsilateral (intact) sciatic nerve. The relationship between CTb, vasoactive intestinal peptide (VIP), and binding of Bandeiraea simplicifolia isolectin B4 (IB4) was then examined in the ipsilateral dorsal horn of the second to fifth lumbar spinal segments (L2–L5). Sectioning of the femoral or saphenous nerves resulted in a reduction of IB4 binding in laminae I–II in the medial third of the dorsal horn of L2, L3, and the upper part of L4. VIP‐immunoreactivity was upregulated in exactly the same regions in which IB4‐binding was reduced. These correspond to the areas that were previously innervated by unmyelinated afferents in the sectioned nerves. CTb‐labeling was detected in regions known to receive input from myelinated sciatic afferents: lamina I and a band extending from the inner part of lamina II (IIi) to lamina V in the L3–5 segments, and the deepest part of the dorsal horn in L2. Importantly, no CTb‐labeling was detected in the outer part of lamina II (IIo) in the denervated areas. Sectioning of branches of the posterior cutaneous nerve of the thigh resulted in a reduction of IB4‐binding and upregulation of VIP‐immunoreactivity in the lateral part of the superficial dorsal horn of caudal L4 and L5. Again, CTb‐immunoreactivity showed the normal sciatic pattern in L4–L5, with no labeling detected in lamina IIo in the denervated region. These results do not support the suggestion that the central terminals of intact myelinated afferents sprout into regions of lamina II occupied by adjacent nerves that have been axotomized peripherally. J. Comp. Neurol. 474:427–437, 2004. © 2004 Wiley‐Liss, Inc.
ZJM‐289, a novel nitric oxide donor, alleviates the cerebral ischaemic–reperfusion injury in rats

1. Current studies indicate that nitric oxide (NO) plays a dual role as both a protective and pathogenic factor in focal cerebral ischaemia depending on the level, location, source and environment. The present study hypothesized that the NO donor ZJM‐289 could inhibit cerebral ischaemia–reperfusion (I/R) injury and investigated the mechanism of the beneficial events.
Effects of Angiotensin II on Rat Pancreatic Stellate Cells

The aim of the study was to identify pancreatic stellate cells (PSCs) as a potential target of angiotensin II (ATII) action because recently a local renin-angiotensin system (RAS) has been described in the pancreas. PSCs were isolated from male Wistar rats and investigated for ATII receptor expression and ATII-induced calcium transients, contractions, proliferation, and &agr;-smooth muscle actin expression. Quiescent and activated PSCs expressed the ATII receptor subtype AT1 but not AT2. Addition of ATII led to a rapid elevation of intracellular calcium ([Ca2+]i). The sensitivity toward ATII with respect to calcium transients did not change during the transdifferentiation process. In activated PSCs, ATII dose dependently induced PSC cell contraction. Furthermore, ATII induced an activation of the c-Jun-N-terminal kinase (JNK) and extracellular regulated kinase (Erk), which was inhibited after intracellular calcium chelation by BAPTA-AM. The p38 mitogen-activated protein kinase (p38MAPK) was also activated by ATII. BAPTA-AM itself induced p38MAPK activation, which was not further enhanced by ATII. ATII stimulated PSC proliferation, while PSC transdifferentiation, as indicated by &agr;-smooth muscle actin expression and collagen type I secretion, was not enhanced. The data suggest that PSCs are targets of ATII action with potential pathophysiological relevance.
The Associations Between Urbanicity and Physical Activity and Sitting Time in Mexico.

BACKGROUND Approximately 17.4% of people in Mexico self-report physical activity levels below the World Health Organization's guidelines and an average sedentary time of 16 hours per day.1 Low physical activity has been associated with noncommunicable disease risk factors and previous research suggests that urbanicity might be an important determinant of physical activity. The aim of this study was to measure urbanicity in Mexico and assess if it is associated with physical activity and sitting time. METHODS A sample of 2880 men and 4211 women aged 20 to 69 was taken from the 2012 Mexico National Health and Nutrition Survey and multivariable linear regression models were used to examine the association between physical activity, sitting time and urbanicity; adjusting for sex, education level, socioeconomic status and Body Mass Index. The urbanicity score and the 7 urbanicity subscores were estimated from the CENSUS 2010. RESULTS The subscores of demographic, economic activity, diversity and communication were negatively associated with physical activity. Sitting time was positively associated with the overall urbanicity, and the demographic and health subscores. CONCLUSIONS There was evidence of associations between urbanicity and physical activity in Mexico.
Structure and functional properties of the Bacillus subtilis transcriptional repressor Rex

The transcription factor Rex has been implicated in regulation of the expression of genes important for fermentative growth and for growth under conditions of low oxygen tension in several Gram‐positive bacteria. Rex senses the redox poise of the cell through changes in the NADH/NAD+ ratio. The crystal structures of two essentially identical Rex proteins, from Thermus aquaticus and T. thermophilus, have previously been determined in complex with NADH. Here we present the crystal structure of the Rex protein from Bacillus subtilis, as well as extensive studies of its affinity for nucleotides and DNA, using surface plasmon resonance, isothermal titration calorimetry and electrophoretic mobility shift assays. We show that Rex has a very high affinity for NADH but that its affinity for NAD+ is 20 000 times lower. However, the NAD+ affinity is increased by a factor of 30 upon DNA binding, suggesting that there is a positive allosteric coupling between DNA binding and NAD+ binding. The crystal structures of two pseudo‐apo forms (from crystals soaked with NADH and cocrystallized with ATP) show a very different conformation from the previously determined Rex:NADH complexes, in which the N‐terminal domains are splayed away from the dimer core. A mechanism is proposed whereby conformational changes in a C‐terminal domain‐swapped helix mediate the transition from a flexible DNA binding form to a locked NADH‐bound form incapable of binding DNA.