Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of the burden of hepatitis C virus infection in Ireland

SUMMARY Information on the burden of hepatitis C virus (HCV) disease is needed to inform policy decisions on primary and secondary prevention. Specimen-based laboratory data (1989–2004) were converted to person-based data and combined with notification data (2004–2009) to describe the burden of HCV infection in Ireland. More than 10 000 people were confirmed as HCV infected in 1989–2004, with the numbers peaking in 2000. The predominant genotypes were 1 (55%) and 3 (39%). Drug use was the most likely risk factor in 80%, with receipt of blood or blood products in 16%. It is estimated that 20 000–50 000 people in Ireland are chronically infected with HCV, a population prevalence of 0·5–1·2%, which is similar to other countries in Northern Europe. This is the first published estimate of the number of chronic HCV infections in Ireland. These data will be of value in health service planning and will contribute to the understanding of HCV infection in Europe.
Sleep problems in adults with intellectual disabilities : an exploratory analysis of support workers' causal attributions, sleep quality and treatment acceptability : major research project and clinical research portfolio

Background: Sleep has been found to have an important restorative function. Any disturbance to sleep can be detrimental to both physical and mental health. Between 9-50% of adults with intellectual disabilities (ID) are reported to experience sleep disturbance. Support workers have a key role in identifying and responding to difficulties in the people they work with. Support workers‘ attributions towards the cause of these difficulties are crucial in mediating their decision to seek treatment. Their attributions may also mediate their adherence to a recommended treatment. Hence, their awareness and beliefs regarding sleep difficulties may influence their ability to recognise and seek help for sleep problems in adults they support. Method: This study utilised an exploratory vignette and questionnaire design. Questionnaires were given to 120 support workers, based in community settings, to measure their attributions to negative behaviour change and sleep problems. Support workers‘ attributional style was compared to their views on the acceptability of a variety of treatments for sleep disturbance. Support workers‘ own sleep quality was measured and compared to their attributions. Results: Support workers attributed negative behaviour change to sleep and mental health problems most strongly. Sleep problems were believed to be internal, uncontrollable and unintentional. Support workers were optimistic about treatment, particularly non-pharmacological treatments. Support workers‘ own sleep quality did not correlate with their attributions towards sleep problems or views on the different types of treatment. Conclusions: Support workers are optimistic that sleep problems in adults with ID can be treated, however further work is necessary to understand barriers to seeking out assessment and treatment for clients with ID.
Development of 65 Novel Polymorphic cDNA-SSR Markers in Common Vetch (Vicia sativa subsp. sativa) Using Next Generation Sequencing

Vetch (Vicia sativa L.) is one of the most important annual forage legumes in the World due to its multiple uses (i.e., hay, grain, silage and green manure) and high nutritional value. However, detrimental cyanoalanine toxins in its plant parts including seeds and its vulnerability to hard winter conditions are currently reducing the agronomic values of vetch varieties. Moreover, the existence in the public domain of very few genomic resources, especially molecular markers, has further hampered breeding efforts. Polymorphic simple sequence repeat markers from transcript sequences (cDNA; simple sequence repeat [SSR]) were developed for Vicia sativa subsp. sativa. We found 3,811 SSR loci from 31,504 individual sequence reads, and 300 primer pairs were designed and synthesized. In total, 65 primer pairs were found to be consistently scorable when 32 accessions were tested. The numbers of alleles ranged from 2 to 19, frequency of major alleles per locus were 0.27–0.87, the genotype number was 2–19, the overall polymorphism information content (PIC) values were 0.20–0.86, and the observed and expected heterozygosity values were 0.00–0.41 and 0.264–0.852, respectively. These markers provide a useful tool for assessing genetic diversity, population structure, and positional cloning, facilitating vetch breeding programs.
An approach to selecting keywords to track on twitter during a disaster

Several studies on Twitter usage during disasters analyze tweets collected using ad-hoc keywords pre-defined by researchers. While recent efforts have worked to improve this methodology, open questions remain about which keywords can be used to uncover tweets contributing to situational awareness (SA) and the quality of tweets returned using different terms. Herein we consider a novel methodology for uncovering relevant keywords one can use to search for tweets containing situational awareness. We provide a description of the methodology and initial results which suggest our approach may lead to better keywords to use for keyword searching during disasters.
Ultrasonography in developmental dysplasia of the hip.

→A safe, noninvasive method of imaging of the hip: it can be used both for diagnosis and to monitor treatment. →Provides advantages when combined with clinical examination: it can provide information on hip position, stability, and morphology. →More sensitive than clinical examination and therefore can be used to resolve the dilemma of whether to splint an unstable hip immediately or to delay treatment with the hope that transient instability will resolve spontaneously. →A consensus has not been reached concerning the best age for ultrasonographic screening. →Neonatal ultrasonography detects a high number of hips with possible instability that require follow-up studies. →Hip ultrasonography performed at four to six weeks of age is more accurate. →Substantial training and attention to technical details and evaluation of results are necessary to obtain reliable results. The use of ultrasonography to examine the neonatal hip was introduced and developed by Graf39. It soon became apparent that ultrasonography could provide images of the soft-tissue components of the infant hip - that is, the cartilaginous components of the femoral head and the acetabulum, the joint capsule, and the labrum. Novick et al.83 and Harcke et al.56 introduced multiplanar ultrasonography to study the infant hip in the coronal and transverse planes. Developmental dysplasia of the hip is a term used to describe an abnormal relationship between the femoral head and the acetabulum. We use this term to describe dislocation, subluxation and instability when it is possible to dislocate or locate the femoral head in the acetabulum, and a whole array of abnormalities that express inadequate acetabular development. There is now ample evidence that ultrasonography can play a major role in the detection and management of developmental dysplasia of the hip in children younger than one year of age. In Europe it is performed by orthopaedic …
Effects on performance and eggshell quality of particle size of calcium sources in laying hens' diets with different Ca concentrations

The objective of this study was to evaluate the effect of particle size of a dietary Ca source on egg production and eggshell quality when added to hens' diets that have different levels of calcium. The experiment was carried out on 216 ISA Brown hens (25 to 70 weeks of age), allocated to 9 groups of 12 replicates (cages), with two birds in each cage. A 3 3 factorial arrangement was used, with three dietary levels of calcium (3.20, 3.70 and 4.20 %) and three levels of dietary substitutions (0, 25 and 50 %) of fine particles of limestone (FPL, diameter 0.2-0.6 mm) with large particles of limestone (LPL, diameter 1.0-1.4 mm) as a Ca source. The level of Ca in the diet had no effect on egg production, mean egg weight, feed intake, feed conversion ratio or eggshell quality parameters (P>0:05). Substitution of FPL with LPL did not affect laying performance indices or eggshell quality at 30, 43 and 53 weeks of age (P>0:05); however, it increased (P<0:05) eggshell percentage, thickness, density and breaking strength in older hens (69 weeks of age). In conclusion, the results of this study demonstrated that a level of 3.20 % Ca in a layer's diet is sufficient through the entire laying cycle to maintain good egg production and eggshell quality and that partial (25 or 50 %) substitution of fine- with large-particle limestone can, irrespective of the level of Ca in the diet, improve eggshell quality in aged laying hens.
A Canonical Microcircuit for Neocortex

We have used microanatomy derived from single neurons, and in vivo intracellular recordings to develop a simplified circuit of the visual cortex. The circuit explains the intracellular responses to pulse stimulation in terms of the interactions between three basic populations of neurons, and reveals the following features of cortical processing that are important to computational theories of neocortex. First, inhibition and excitation are not separable events. Activation of the cortex inevitably sets in motion a sequence of excitation and inhibition in every neuron. Second, the thalamic input does not provide the major excitation arriving at any neuron. Instead the intracortical excitatory connections provide most of the excitation. Third, the time evolution of excitation and inhibition is far longer than the synaptic delays of the circuits involved. This means that cortical processing cannot rely on precise timing between individual synaptic inputs.
Gamma Interferon Enhances Internalization and Early Nonoxidative Killing of Salmonella enterica Serovar Typhimurium by Human Macrophages and Modifies Cytokine Responses

ABSTRACT Gamma interferon (IFN-γ) is a critical cytokine in host defense against salmonella infections, but its role in phagocytic killing of intracellular Salmonella spp. has been investigated mainly in animal rather than human cells. We measured the effect of recombinant IFN-γ (rIFN-γ) priming on bacterial internalization, intracellular killing, oxidative burst, and cytokine release during phagocytosis of Salmonella enterica serovar Typhimurium by human monocyte-derived macrophages (MDM). Eleven-day-old MDM, primed for 72 h with rIFN-γ (100 ng/ml) exhibited an increased proportion of cells with associated bacteria (31% versus 26%, P = 0.036) and a 67% increase in internalized bacteria per cell compared to unprimed cells (P = 0.025). Retrieval of viable bacteria following internalization was reduced 3.6-fold in 72-h primed versus unprimed MDM (interquartile range, 3.1 to 6.4) at 0.5 h due to enhanced early intracellular killing, and this difference was maintained up to 24 h. In contrast, cells primed for only 24 h exhibited no increase in early killing. MDM were competent to produce an early oxidative burst when stimulated with phorbol myristate acetate, which was fully abrogated by the respiratory burst inhibitor diphenyleneiodonium chloride (DPI), but infection of MDM with S. enterica serovar Typhimurium did not cause an increase in the early respiratory burst under unprimed or primed conditions, and DPI had no effect on the early killing of bacteria by primed or unprimed MDM. During 24 h following infection, rIFN-γ-primed MDM released more interleukin-12 (IL-12) and less IL-10 relative to unprimed cells. We conclude that 72-h priming with rIFN-γ increases the efficiency of internalization and nonoxidative early intracellular killing of S. enterica serovar Typhimurium by human macrophages and modifies subsequent cytokine release.
High-Q AlN/SiO2 symmetric composite thin film bulk acoustic wave resonators

High-Q, bulk acoustic wave composite resonators based on a symmetric layer sequence of SiO2-AlN-SiO2 sandwiched between electrodes have been developed. Acoustic isolation was achieved by means of deep silicon etching to obtain membrane type thin film bulk acoustic wave resonators (TFBARs). Three different device versions were investigated. The SiO2 film thicknesses were varied (0 nm, 70 nm, 310 nm, and 770 nm) while the piezoelectric AlN film had a constant thickness of 1.2 mum. The sputter-deposited AlN film grown on the amorphous, sputter-deposited SiO2 layer exhibited a d33,f of 4.0 pm/V. Experimental results of quality factors (Q) and coupling coefficients (kt 2) are in agreement with finite element calculations. A Q of 2000 is observed for the first harmonic of the 310 nm oxide devices. The most intense resonance of the 770 nm oxide device is the third harmonic reaching Q factors of 1450. The temperature drift reveals the impact of the SiO2 layers, which is more pronounced on the first harmonic, reducing the TCF to 4 ppm/K for the 3rd harmonic of the 310 nm oxide devices.
New Treatments for Rhabdomyosarcoma: The Importance of Target Practice

To address the poor outcomes in rhabdomyosarcoma, particularly the alveolar subtype, new therapies are needed. Potential cancer-specific alterations that may be molecular targets include gene fusions or copy number changes. Following the latter strategy, an attractive antigene approach was developed to inhibit MYCN oncogene expression in rhabdomyosarcoma. Clin Cancer Res; 18(3); 595–7. ©2011 AACR.
Finding the chromatic number by means of critical graphs

We propose a new exact algorithm for finding the chromatic number of a graph G. The algorithm attempts to determine the smallest possible induced subgraph G' of G which has the same chromatic number as G. Such a subgraph is said critical since all proper induced sub-graph of G' have a chromatic number strictly smaller than G'. The proposed method is particularly helpful when a k-coloring of a non-critical graph is known, and it has to be proved that no (k-1)-coloring of G exists. Computational experiments on random graphs and on DIMACS benchmark problems demonstate that the new proposed algorithm can solve larger problem than previous known exact methods.
Attention-Based Recurrent Neural Network Models for Joint Intent Detection and Slot Filling

Attention-based encoder-decoder neural network models have recently shown promising results in machine translation and speech recognition. In this work, we propose an attention-based neural network model for joint intent detection and slot filling, both of which are critical steps for many speech understanding and dialog systems. Unlike in machine translation and speech recognition, alignment is explicit in slot filling. We explore different strategies in incorporating this alignment information to the encoder-decoder framework. Learning from the attention mechanism in encoder-decoder model, we further propose introducing attention to the alignment-based RNN models. Such attentions provide additional information to the intent classification and slot label prediction. Our independent task models achieve state-of-the-art intent detection error rate and slot filling F1 score on the benchmark ATIS task. Our joint training model further obtains 0.56% absolute (23.8% relative) error reduction on intent detection and 0.23% absolute gain on slot filling over the independent task models.
Regulation of expression of microRNAs by DNA methylation in lung cancer

Abstract Differential expression of miRNAs has been linked with lung carcinogenesis. Recent studies have indicated that DNA hypermethylation can lead to silencing of tumor suppressor miRNA-encoding genes. Restoration of tumor suppressor miRNAs using inhibitors of DNA methyltransferases has been shown to suppress cell proliferation, angiogenesis, invasion and metastasis implying that modulation of methylation of specific miRNAs can be used as novel therapeutic targets in lung cancer. In this review, we highlight tremendous progress which has been made in the identification of methylation-mediated silencing of miRNAs and their contribution in lung carcinogenesis along with the clinical utility of methylated miRNAs.
Lipid Oxidation in Carriers of Lecithin: Cholesterol Acyltransferase Gene Mutations

Objective—Lecithin:cholesterol acyltransferase (LCAT) has been shown to play a role in the depletion of lipid oxidation products, but this has so far not been studied in humans. In this study, we investigated processes and parameters relevant to lipid oxidation in carriers of functional LCAT mutations. Methods and Results—In 4 carriers of 2 mutant LCAT alleles, 63 heterozygotes, and 63 family controls, we measured activities of LCAT, paraoxonase 1, and platelet-activating factor-acetylhydrolase; levels of lysophosphatidylcholine molecular species, arachidonic and linoleic acids, and their oxidized derivatives; immunodetectable oxidized phospholipids on apolipoprotein (apo) B–containing and apo(a)-containing lipoproteins; IgM and IgG autoantibodies to malondialdehyde-low-density lipoprotein and IgG and IgM apoB-immune complexes; and the antioxidant capacity of high-density lipoprotein (HDL). In individuals with LCAT mutations, plasma LCAT activity, HDL cholesterol, apoA-I, arachidonic acid, and its oxidized derivatives, oxidized phospholipids on apo(a)-containing lipoproteins, HDL-associated platelet-activating factor-acetylhydrolase activity, and the antioxidative capacity of HDL were gene-dose–dependently decreased. Oxidized phospholipids on apoB-containing lipoproteins was increased in heterozygotes (17%; P<0.001) but not in carriers of 2 defective LCAT alleles. Conclusion—Carriers of LCAT mutations present with significant reductions in LCAT activity, HDL cholesterol, apoA-I, platelet-activating factor-acetylhydrolase activity, and antioxidative potential of HDL, but this is not associated with parameters of increased lipid peroxidation; we did not observe significant changes in the oxidation products of arachidonic acid and linoleic acid, immunoreactive oxidized phospholipids on apo(a)-containing lipoproteins, and IgM and IgG autoantibodies against malondialdehyde-low-density lipoprotein. These data indicate that plasma LCAT activity, HDL-associated platelet-activating factor-acetylhydrolase activity, and HDL cholesterol may not influence the levels of plasma lipid oxidation products.
Effect of Dietary Apigenin on Colonic Ornithine Decarboxylase Activity, Aberrant Crypt Foci Formation, and Tumorigenesis in Different Experimental Models

Abstract: The efficacy of dietary apigenin, a dietary flavonoid, in colon cancer prevention was investigated by evaluating the inhibition of the ornithine decarboxylase (ODC) activity and the formation of aberrant crypt foci (ACF) and by studying the ability of apigenin to block colon carcinogenesis in two mouse models. First, the activity of ODC was measured in colon cancer cells (Caco-2) and in the colon epithelium of CF-1 mice. Apigenin at 10 and 30 μM significantly inhibited the ODC activity of Caco-2 cells by 26% and 57%, respectively. Colonic ODC activity in CF-1 mice was reduced with 0.1% dietary apigenin by 42% compared with the control, but this difference was not statistically significant. Second, ACF formation was evaluated in azoxymethane (AOM)-induced CF-1 mice. Female CF-1 mice at 6 wk of age were i.p. injected with 5 mg/kg body weight (BW) AOM once to induce ACF. ACF formation in CF-1 mice was reduced by 50% (P < 0.05) with 0.1% dietary apigenin fed for 6 wk when compared with the control. Dietary apigenin inhibited ACF only in the distal region of the CF-1 mouse colon. Finally, tumorigenesis studies were conducted using two different mouse models: AOM-induced CF-1 mice and Min mice with mutant adenomatous polyposis coli (APC) gene. Female CF-1 mice at 6 wk of age were i.p. injected with 10 mg/kg BW AOM weekly for 6 (AOM Study I) or 4 (AOM Study II) wk to induce tumors. CF-1 mice were fed diets containing 0.025% or 0.1% apigenin for 23-25 wk. Female Min mice were fed diets for 10 wk beginning at 5 wk of age. In two AOM-treated mouse colon tumor studies 0.025% and 0.1% dietary apigenin modestly reduced tumors in the group fed 0.025% apigenin (25% incidence in comparison with 65% in the controls) in a non-dose response manner. Apigenin failed to inhibit adenoma formation in the Min mouse study. These results suggest that dietary apigenin showed promise in cancer prevention by reducing the ODC activity and ACF formation, however, clear evidence of cancer prevention was not obtained in mouse tumor studies. Further investigation of the potential chemopreventive effect of apigenin in carcinogenesis is warranted.
Characterization of two pigeon paramyxovirus type 1 isolates in China

For over three decades, there has been a continuing panzootic caused by a virulent variant avian paramyxovirus type 1 strain, the so-called pigeon paramyxovirus type 1. It is found primarily in racing pigeons, but it has also spread to wild birds and poultry. In this study, two pigeon paramyxovirus type 1 strains, SD12 and BJ13, obtained from diseased pigeons in China, were characterized. Phylogenetic analysis based on complete sequences allowed characterization of both strains as genotype VI, class II. Further phylogenetic analysis of a 374-nucleotide section of the fusion gene showed that SD12 fell into lineage VIbii-d and BJ13 into VIbii-f. The deduced amino acid sequence of the cleavage site of the fusion protein confirmed that both isolates contained the virulent motif 112K/RRQKR↓F117 at the cleavage site. Nevertheless, the values of intracerebral pathogenicity indices showed the SD12 isolate to be a velogenic strain and BJ13 isolate to be a mesogenic strain. The SD12 isolate was further investigated via clinical observation, RNA detection, histopathology and viral serology in experimentally infected 3-week-old chickens. It showed a mild pathological phenotype in chickens, with viral replication restricted to a few tissues. The molecular mechanism for the SD12 isolate to have a virulent motif but low levels of virulence for chickens requires further study.
Expression and Localization of an Hsp70 Protein in the Microsporidian Encephalitozoon cuniculi

Microsporidia spore surface proteins are an important, under investigated aspect of spore/host cell attachment and infection. For comparison analysis of surface proteins, we required an antibody control specific for an intracellular protein. An endoplasmic reticulum-associated heat shock protein 70 family member (Hsp70; ECU02_0100; “C1”) was chosen for further analysis. DNA encoding the C1 hsp70 was amplified, cloned and used to heterologously express the C1 Hsp70 protein, and specific antiserum was generated. Two-dimensional Western blotting analysis showed that the purified antibodies were monospecific. Immunoelectron microscopy of developing and mature E. cuniculi spores revealed that the protein localized to internal structures and not to the spore surface. In spore adherence inhibition assays, the anti-C1 antibodies did not inhibit spore adherence to host cell surfaces, whereas antibodies to a known surface adhesin (EnP1) did so. In future studies, the antibodies to the ‘C1' Hsp70 will be used to delineate spore surface protein expression.