Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased antigen and bacterial uptake in follicle associated epithelium induced by chronic psychological stress in rats

Background: Chronic stress affects the course of inflammatory bowel disease and experimental colitis, and may also initiate intestinal inflammation in rats. Aim: To investigate the effects of stress on the M cell containing follicle associated epithelium, specialised in antigen uptake. Subjects and methods: Wistar rats were submitted to acute water avoidance stress for one hour or chronic water avoidance stress for 1 hour/day for 10 consecutive days. Permeability to 51Cr-edta, horseradish peroxidase, and chemically killed Escherichia coli K-12 was studied in both villus and follicle associated epithelium in Ussing chambers. Segments were further examined by light, electron, and confocal microscopy. Results: Acute stress increased horseradish peroxidase flux in villus as well as in follicle associated epithelium. Chronic stress further increased permeability to horseradish peroxidase in villus and follicle associated epithelium, in the latter by almost fourfold. Moreover, chronic stress induced over 30 times increased E coli passage in follicle associated epithelium whereas there was no significant increase in villus epithelium. Bacterial uptake was confirmed by confocal microscopy showing fluorescent bacteria penetrating and passing through the epithelial surface. Conclusions: These results show that the barrier function of follicle associated epithelium can be modulated, and that chronic stress enhances the uptake of luminal antigens and bacteria via the follicle associated epithelium. This can increase antigen exposure in Peyer’s patches thereby having implications in the initiation of proinflammatory immune responses within the intestinal mucosa.
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals

Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. To address this question, we investigated transcriptional dynamics in the ichthyosporean Creolimax fragrantissima, a relative of animals that undergoes coenocytic development. We find that Creolimax utilizes dynamic regulation of alternative splicing, long inter-genic non-coding RNAs and co-regulated gene modules associated with animal multicellularity in a cell-type specific manner. Moreover, our study suggests that the different cell types of the three closest animal relatives (ichthyosporeans, filastereans and choanoflagellates) are the product of lineage-specific innovations. Additionally, a proteomic survey of the secretome reveals adaptations to a fungal-like lifestyle. In summary, the diversity of cell types among protistan relatives of animals and their complex genome regulation demonstrates that the last unicellular ancestor of animals was already capable of elaborate specification of cell types. DOI: http://dx.doi. org/10.7554/eLife.08904. 001
Molecular Analysis of Codon 548 in the rpoB Gene Involved in Mycobacterium tuberculosis Resistance to Rifampin

ABSTRACT Most Mycobacterium tuberculosis rifampin-resistant strains have been associated with mutations in an 81-bp rifampin resistance-determining region (RRDR) in the gene rpoB. However, if this region alone were targeted, rifampin-resistant strains with mutations outside the RRDR would not be detected. In this study, among 51 rifampin-resistant clinical isolates analyzed by sequencing 1,681-bp-long DNA fragments containing the RRDR, 47 isolates contained mutations within the RRDR, three isolates contained mutations both within and outside the RRDR, and only one isolate had a single missense mutation (Arg548His) located outside the RRDR. A drug susceptibility test of recombinant Mycobacterium smegmatis and M. tuberculosis isolates carrying mutated rpoB (Arg548His) showed an increased MIC for rifampin compared to that of the control strains. Modeling of the Arg548His mutant RpoB-DNA complex revealed that the His548 side chain formed a more stable hydrogen bond structure than did Arg548, reducing the flexibility of the rifampin-resistant cluster II region of RpoB, suggesting that the RpoB Arg548His mutant does not effectively interact with rifampin and results in bacterial resistance to the drug. This is the first report on the relationship between the mutation in codon 548 of RpoB and rifampin resistance in tuberculosis. The novel mutational profile of the rpoB gene described here will contribute to the comprehensive understanding of rifampin resistance patterns and to the development of a useful tool for simple and rapid drug susceptibility tests.
Genome-Wide Association and Transcriptome Analyses Reveal Candidate Genes Underlying Yield-determining Traits in Brassica napus

Yield is one of the most important yet complex crop traits. To improve our understanding of the genetic basis of yield establishment, and to identify candidate genes responsible for yield improvement in Brassica napus, we performed genome-wide association studies (GWAS) for seven yield-determining traits [main inflorescence pod number (MIPN), branch pod number (BPN), pod number per plant (PNP), seed number per pod (SPP), thousand seed weight, main inflorescence yield (MIY), and branch yield], using data from 520 diverse B. napus accessions from two different yield environments. In total, we detected 128 significant single nucleotide polymorphisms (SNPs), 93 of which were revealed as novel by integrative analysis. A combination of GWAS and transcriptome sequencing on 21 haplotype blocks from samples pooled by four extremely high-yielding or low-yielding accessions revealed the differential expression of 14 crucial candiate genes (such as Bna.MYB83, Bna.SPL5, and Bna.ROP3) associated with multiple traits or containing multiple SNPs associated with the same trait. Functional annotation and expression pattern analyses further demonstrated that these 14 candiate genes might be important in developmental processes and biomass accumulation, thus affecting the yield establishment of B. napus. These results provide valuable information for understanding the genetic mechanisms underlying the establishment of high yield in B. napus, and lay the foundation for developing high-yielding B. napus varieties.
Testing a Simplified Method for Measuring Velocity Integration in Saccades Using a Manipulation of Target Contrast

A growing number of studies in vision research employ analyses of how perturbations in visual stimuli influence behavior on single trials. Recently, we have developed a method along such lines to assess the time course over which object velocity information is extracted on a trial-by-trial basis in order to produce an accurate intercepting saccade to a moving target. Here, we present a simplified version of this methodology, and use it to investigate how changes in stimulus contrast affect the temporal velocity integration window used when generating saccades to moving targets. Observers generated saccades to one of two moving targets which were presented at high (80%) or low (7.5%) contrast. In 50% of trials, target velocity stepped up or down after a variable interval after the saccadic go signal. The extent to which the saccade endpoint can be accounted for as a weighted combination of the pre- or post-step velocities allows for identification of the temporal velocity integration window. Our results show that the temporal integration window takes longer to peak in the low when compared to high contrast condition. By enabling the assessment of how information such as changes in velocity can be used in the programming of a saccadic eye movement on single trials, this study describes and tests a novel methodology with which to look at the internal processing mechanisms that transform sensory visual inputs into oculomotor outputs.
Cervical Ossification of Posterior Longitudinal Ligament in X-Linked Hypophosphatemic Rickets Revealing Homogeneously Increased Vertebral Bone Density

There is no report that describes in detail the radiological and intraoperative findings of rickets with symptomatic cervical ossification of the posterior longitudinal ligament. Here, we describe a case of X-linked hypophosphatemic rickets with cervical ossification of the posterior longitudinal ligament presenting unique radiological and intraoperative findings. The patient presented progressive tetraparesis. Magnetic resonance imaging studies revealed severe cervical spinal cord compression caused by ossification of the posterior longitudinal ligament. Computed tomography scans revealed homogeneously increased vertebral bone density. An expansive laminoplasty was performed. At surgery, homogeneously hard lamina bone was burdened in drilling and opening of the laminae. The patient's neurological symptoms were improved postoperatively. Bony fusion of the hinges occurred postoperatively. Therefore, expansive laminoplasty could be performed for symptomatic cervical ossification of the posterior longitudinal ligament with X-linked hypophosphatemic rickets. However, unusual bone characters should be taken into consideration for careful operation during surgery.
Measuring mealtime difficulties: eating, feeding and meal behaviours in older adults with dementia.

AIMS AND OBJECTIVES The purpose of this integrative review is to examine the instruments currently available for clinical use specifically to assess mealtime difficulties, a concept subsuming the domains of eating, feeding and meal behaviours in older adults with dementia; and to determine the quality and practicality of those instruments for use in clinical practice. BACKGROUND Dementia is a leading cause of death globally and the 5th leading cause of death in the USA for adults over 65. Nutritional status is vital to well-being, therefore, instruments to measure eating, feeding and meal behaviours are important. Instruments measuring these behaviours can be used to plan effective interventions to alleviate the behaviours and improve oral intake. DESIGN Integrative review. METHOD Database searches of EBSCOHost, PubMed, CINAHL, ScienceDirect, AgeLine and HaPI using various keyword combinations related to meal, eating and feeding behaviours in dementia as well as keywords related to instruments, scales or measurement. Abstracts and articles were analysed to identify instruments used in research and clinically to measure eating, feeding and meal behaviours in dementia. RESULTS Twelve observational instruments were identified and organised into categories of eating, feeding and meal behaviours for older adults with dementia. Instruments were described by concepts measured. CONCLUSIONS The majority of instruments identified do not report adequate psychometric testing in the literature. One instrument is identified reporting extensive testing for reliability and validity and has been recommended for clinical practice--The Edinburgh Feeding Evaluation in Dementia (EdFED) scale. RELEVANCE TO CLINICAL PRACTICE The EdFED has been identified as a valid and reliable instrument for measuring feeding difficulties and is available for use in clinical practice. In using the EdFED, interventions can be planned to monitor feeding difficulties and promote nutritional status of older adults with dementia.
Optimization of a Vertical Protection Level Equation for Dual Frequency SBAS

The advent of dual frequency Satellite Based Augmentation Systems (SBAS) will allow the aviation community to address some of the shortcomings of the current SBAS Minimum Operational Performance Standards (MOPS), in particular of the Vertical Protection Level (VPL), and also to adapt it to threats for a dual frequency user. First, satellite faults will become the dominant source of error – because the ionospheric delay threat is canceled. Second, it was discovered that there are nominal biases that cannot be corrected by the ground and that cause the current VPL to be inflated. Finally, actual data collected in support of system performance has shown that the statistics exhibit non-gaussian behavior. A Vertical Protection Level equation that addresses these points was proposed in [1]. This equation accounts explicitly for possible nominal biases and for the fact that the position error bound is dominated by one possible fault at a given time. The equation was evaluated using a Service Volume analysis tool and it was shown that it could provide significant benefits over the current equation. These simulations computed user coefficients (the coefficients that project the pseudorange onto the user position) based on a Least Squares (LS) approach. The LS approach is not optimal for the proposed VPL equation. In this paper we show that choosing optimally the coefficients that project the pseudoranges onto the position domain could significantly increase the performance of an SBAS based on the equation described in [1]. To this purpose, we will describe an algorithm that minimizes the Vertical Protection Level. Then, we will evaluate the availability benefits that can be obtained using the optimal algorithm using a Service Volume Analysis tool.
Apolipoprotein C-III, n-3 polyunsaturated fatty acids, and "insulin-resistant" T-455C APOC3 gene polymorphism in heart disease patients: example of gene-diet interaction.

BACKGROUND Apolipoprotein C-III (apo C-III) is a marker of cardiovascular disease risk associated with triglyceride (TG)-rich lipoproteins. The T-455C polymorphism in the insulin-responsive element of the APOC3 gene influences TG and apo C-III concentrations. Long-chain n-3 polyunsaturated fatty acids (PUFAs) contained in fish have well-known apo C-III-lowering properties. METHODS We investigated the possibility of an interactive effect between the APOC3 gene variant and erythrocyte n-3 PUFAs, suitable markers of dietary intake of fatty acids, on apo C-III concentrations in a population of 848 heart disease patients who had coronary angiography. RESULTS In the population as a whole, apo C-III concentrations were significantly inversely correlated with total erythrocyte PUFAs, but the correlation was not significant when only -455CC homozygous individuals were taken into account. In the total population and in subgroups with the -455TT and -455CT genotypes, the relative proportions of individuals presenting with increased apo C-III (i.e., above the 75th percentile value calculated on the entire population after exclusion of individuals taking lipids-lowering medications) decreased progressively as the n-3 PUFA and docosahexaenoic acid concentrations increased. The opposite situation was observed in the homozygous -455CC subgroup, in whom increasing erythrocyte n-3 PUFA and docosahexaenoic acid concentrations were associated with higher proportions of individuals with high apo C-III. A formal interactive effect between genotype and n-3 PUFAs was confirmed even after adjustment for possible confounding variables [age, sex, body mass index, smoking, coronary artery disease (CAD)/CAD-free status, or use of lipid-lowering medications] by logistic models. CONCLUSION Patients homozygous for the -455C APOC3 variant are poorly responsive to the apo C-III-lowering effects of n-3 PUFAs.
Rate-distortion optimization for video compression

The rate-distortion efficiency of video compression schemes is based on a sophisticated interaction between various motion representation possibilities, waveform coding of differences, and waveform coding of various refreshed regions. Hence, a key problem in high-compression video coding is the operational control of the encoder. This problem is compounded by the widely varying content and motion found in typical video sequences, necessitating the selection between different representation possibilities with varying rate-distortion efficiency. This article addresses the problem of video encoder optimization and discusses its consequences on the compression architecture of the overall coding system. Based on the well-known hybrid video coding structure, Lagrangian optimization techniques are presented that try to answer the question: what part of the video signal should be coded using what method and parameter settings?
Experimental Evaluation of Memory Effects on TCP Traffic in Congested Networks

Today the Internet is a worldwide-interconnected computer network that transmits data by packet switching based on the TCP/IP protocol suite. Internet has TCP as the main protocol of the transport layer. The performance of TCP is studied by many researchers. They are trying to analytically characterizing the throughput of TCP’s congestion control mechanism. Internet routers were widely believed to need big memory spaces. Commercial routers today have huge packet memory spaces, often storing millions of packets, under the assumption that big memory spaces lead to good statistical multiplexing and hence efficient use of expensive long-haul links. In this paper, we summarize the works and present the experimental study result with big memory space size and give a qualitative analysis of the result. Our conclusion is that the, round-trip time (RTT) is not increased by linear, but by quadric when the memory space size of the bottleneck is big enough. Our goal is to estimate the average queue length of the memory space size and develop a TCP model based on RTT and the average queue length.
Hyperglycemia and a Common Variant of GCKR Are Associated With the Levels of Eight Amino Acids in 9,369 Finnish Men

We investigated the association of glycemia and 43 genetic risk variants for hyperglycemia/type 2 diabetes with amino acid levels in the population-based Metabolic Syndrome in Men (METSIM) Study, including 9,369 nondiabetic or newly diagnosed type 2 diabetic Finnish men. Plasma levels of eight amino acids were measured with proton nuclear magnetic resonance spectroscopy. Increasing fasting and 2-h plasma glucose levels were associated with increasing levels of several amino acids and decreasing levels of histidine and glutamine. Alanine, leucine, isoleucine, tyrosine, and glutamine predicted incident type 2 diabetes in a 4.7-year follow-up of the METSIM Study, and their effects were largely mediated by insulin resistance (except for glutamine). We also found significant correlations between insulin sensitivity (Matsuda insulin sensitivity index) and mRNA expression of genes regulating amino acid degradation in 200 subcutaneous adipose tissue samples. Only 1 of 43 risk single nucleotide polymorphisms for type 2 diabetes or hyperglycemia, the glucose-increasing major C allele of rs780094 of GCKR, was significantly associated with decreased levels of alanine and isoleucine and elevated levels of glutamine. In conclusion, the levels of branched-chain, aromatic amino acids and alanine increased and the levels of glutamine and histidine decreased with increasing glycemia, reflecting, at least in part, insulin resistance. Only one single nucleotide polymorphism regulating hyperglycemia was significantly associated with amino acid levels.
A robust neural network classifier to model the compressive strength of high performance concrete using feature subset selection

High performance concrete (HPC) is a mixture of cement, fine aggregate, coarse aggregate, water and other ingredients. Modeling the compressive strength of HPC (or concrete strength) is a difficult task in building materials because it is influenced by the proportions of various ingredients within the HPC. Researchers have tried to confront this difficulty by modeling the strength of concrete using artificial neural networks (ANN). The influence of ingredients on concrete strength still remains unknown due to the "black box" nature of ANN. This paper investigates the influence of ingredients on concrete strength modeling using feature selection. A robust ANN-model using the knowledge from feature selection has been developed to predict the strength effectively. Experimental results have shown that the proposed model is efficient with respect to runtime and prediction.
Evolutionary reactive behavior for mobile robots navigation

Mobile robot's navigation and obstacle avoidance in an unknown environment is analyzed in this paper. From the guidance of position sensors, artificial neural network (ANN) based controllers settle the desired trajectory between current and a target point. Evolutionary algorithms were used to choose the best controller. This approach, known as evolutionary robotics (ER), commonly resorts to very simple ANN architectures. Although they include temporal processing, most of them do not consider the learned experience in the controller's evolution. Thus, the ER research presented in this article, focuses on the specification and testing of the ANN based controllers implemented when genetic mutations are performed from one generation to another. Discrete-time recurrent neural networks based controllers were tested, with two variants: plastic neural networks (PNN) and standard feedforward (FFNN) networks. Also the way in which evolution was performed was analyzed. As a result, controlled mutation do not exhibit major advantages against the noncontrolled one, showing that diversity is more powerful than controlled adaptation.
Identification and macrophage‐activating activity of glycolipids released from intracellular Mycobacterium bovis BCG

Intracellular mycobacteria release cell wall glycolipids into the endosomal network of infected macrophages. Here, we characterize the glycolipids of Mycobacterium bovis BCG (BCG) that are released into murine bone marrow‐derived macrophages (BMMØ). Intracellularly released mycobacterial lipids were harvested from BMMØ that had been infected with 14C‐labelled BCG. Released BCG lipids were resolved by thin‐layer chromatography, and they migrated similarly to phosphatidylinositol dimannosides (PIM2), mono‐ and diphosphatidylglycerol, phosphatidylethanolamine, trehalose mono‐ and dimycolates and the phenolic glycolipid, mycoside B. Culture‐derived BCG lipids that co‐migrated with the intracellularly released lipids were purified and identified by electrospray ionization mass spectrometry. When delivered on polystyrene microspheres, fluorescently tagged BCG lipids were also released into the BMMØ, in a manner similar to release from viable or heat‐killed BCG bacilli. To determine whether the released lipids elicited macrophage responses, BCG lipid‐coated microspheres were delivered to interferon gamma‐primed macrophages (BMMØ or thioglycollate‐elicited peritoneal macrophages), and reactive nitrogen intermediates as well as tumour necrosis factor‐alpha and monocyte chemoattractant protein‐1 production were induced. When fractionated BCG lipids were delivered on the microspheres, PIM2 species reproduced the macrophage‐activating activity of total BCG lipids. These results demonstrate that intracellular mycobacteria release a heterogeneous mix of lipids, some of which elicit the production of proinflammatory cytokines from macrophages that could potentially contribute to the granulomatous response in tuberculous diseases.
Methods for Subtyping and Molecular Comparison of Human Viral Genomes

SUMMARY The development over the past two decades of molecular methods for manipulation of RNA and DNA has afforded molecular virologists the ability to study viral genomes in detail that has heretofore not been possible. There are many molecular techniques now available for typing and subtyping of viruses. The available methods include restriction fragment length polymorphism analysis, Southern blot analysis, oligonucleotide fingerprint analysis, reverse hybridization, DNA enzyme immunoassay, RNase protection analysis, single-strand conformation polymorphism analysis, heteroduplex mobility assay, nucleotide sequencing, and genome segment length polymorphism analysis. The methods have certain advantages and disadvantages which should be considered in their application to specific viruses or for specific purposes. These techniques are likely to become more widely used in the future for epidemiologic studies and for investigations into the pathophysiology of virus infections.