Mechanisms for collective inversion-symmetry breaking in dabconium perovskite ferroelectrics

Dabconium hybrid perovskites include a number of recently-discovered ferroelectric phases with large spontaneous polarisations. The origin of ferroelectric response has been rationalised in general terms in the context of hydrogen bonding, covalency, and strain coupling. Here we use a combination of simple theory, Monte Carlo simulations, and density functional theory calculations to assess the ability of these microscopic ingredients—together with the always-present throughspace dipolar coupling—to account for the emergence of polarisation in these particular systems whilst not in other hybrid perovskites. Our key result is that the combination of A-site polarity, preferred orientation along h111i directions, and ferroelastic strain coupling drives precisely the ferroelectric transition observed experimentally. We rationalise the absence of polarisation in many hybrid perovskites, and arrive at a set of design rules for generating FE examples beyond the dabconium family alone

SFSSClass: an integrated approach for miRNA based tumor classification

Background: MicroRNA (miRNA) expression profiling data has recently been found to be particularly important in cancer research and can be used as a diagnostic and prognostic tool. Current approaches of tumor classification using miRNA expression data do not integrate the experimental knowledge available in the literature. A judicious integration of such knowledge with effective miRNA and sample selection through a biclustering approach could be an important step in improving the accuracy of tumor classification. Results: In this article, a novel classification technique called SFSSClass is developed that judiciously integrates a biclustering technique SAMBA for simultaneous feature (miRNA) and sample (tissue) selection (SFSS), a cancer-miRNA network that we have developed by mining the literature of experimentally verified cancer-miRNA relationships and a classifier uncorrelated shrunken centroid (USC). SFSSClass is used for classifying multiple classes of tumors and cancer cell lines. In a part of the investigation, poorly differentiated tumors (PDT) having non diagnostic histological appearance are classified while training on more differentiated tumor (MDT) samples. The proposed method is found to outperform the best known accuracy in the literature on the experimental data sets. For example, while the best accuracy reported in the literature for classifying PDT samples is similar to 76.5%, the accuracy of SFSSClass is found to be similar to 82.3%. The advantage of incorporating biclustering integrated with the cancer-miRNA network is evident from the consistently better performance of SFSSClass (integration of SAMBA, cancer-miRNA network and USC) over USC (eg., similar to 70.5% for SFSSClass versus similar to 58.8% in classifying a set of 17 MDT samples from 9 tumor types, similar to 91.7% for SFSSClass versus similar to 75% in classifying 12 cell lines from 6 tumor types and similar to 382.3% for SFSSClass versus similar to 41.2% in classifying 17 PDT samples from 11 tumor types). Conclusion: In this article, we develop the SFSSClass algorithm which judiciously integrates a biclustering technique for simultaneous feature (miRNA) and sample (tissue) selection, the cancer-miRNA network and a classifier. The novel integration of experimental knowledge with computational tools efficiently selects relevant features that have high intra-class and low interclass similarity. The performance of the SFSSClass is found to be significantly improved with respect to the other existing approaches

The myofibroblast, multiple origins for major roles in normal and pathological tissue repair

Myofibroblasts differentiate, invade and repair injured tissues by secreting and organizing the extracellular matrix and by developing contractile forces. When tissues are damaged, tissue homeostasis must be re-established, and repair mechanisms have to rapidly provide harmonious mechanical tissue organization, a process essentially supported by (myo)fibroblasts. Under physiological conditions, the secretory and contractile activities of myofibroblasts are terminated when the repair is complete (scar formation) but the functionality of the tissue is only rarely perfectly restored. At the end of the normal repair process, myofibroblasts disappear by apoptosis but in pathological situations, myofibroblasts likely remain leading to excessive scarring. Myofibroblasts originate from different precursor cells, the major contribution being from local recruitment of connective tissue fibroblasts. However, local mesenchymal stem cells, bone marrow-derived mesenchymal stem cells and cells derived from an epithelial-mesenchymal transition process, may represent alternative sources of myofibroblasts when local fibroblasts are not able to satisfy the requirement for these cells during repair. These diverse cell types probably contribute to the appearance of myofibroblast subpopulations which show specific biological properties and which are important to understand in order to develop new therapeutic strategies for treatment of fibrotic and scarring diseases

Functionally Orthologous Viral and Cellular MicroRNAs Studied by a Novel Dual-Fluorescent Reporter System

Recent research raised the possibility that some viral microRNAs (miRNAs) may function as orthologs of cellular miRNAs. In the present work, to study the functional orthologous relationships of viral and cellular miRNAs, we first constructed a dual-fluorescent protein reporter vector system for the easy determination of miRNA function. By expressing the miRNAs and the indicator and internal control fluorescent proteins individually from a single vector, this simple reporter system can be used for miRNA functional assays that include visualizing miRNA activity in live cells. Sequence alignments indicated that the simian virus 40 (SV40) encoded miRNA sv40-mir-S1-5p contains a seed region identical to that of the human miRNA hsa-miR423-5p. Using the new reporter system, it was found that sv40-mir-S1-5p and hsa-miR423-5p downregulate the expression of common artificial target mRNAs and some predicted biological targets of hsa-miR423-5p, demonstrating that they are functional orthologs. The human immunodeficiency virus 1 (HIV-1) encoded hiv1-miR-N367 also contains a seed sequence identical to that of the human miRNA hsa-miR192. Functional assays showed that hiv1-miR-N367 and hsa-miR192 could downregulate common artificial and predicted biological targets, suggesting that these miRNAs may also act as functional orthologs. Thus, this study presents a simple and universal system for testing miRNA function and identifies two new pairs of functional orthologs, sv40-mir-S1-5p and hsa-miR423-5p as well as hiv-1-miR-N367 and hsa-miR192. These findings also expand upon our current knowledge of functional homology and imply that a more general phenomenon of orthologous relationships exists between viral and cellular miRNAs

RNAi in the regulation of mammalian viral infections

Although RNA interference (RNAi) is known to play an important part in defense against viruses of invertebrates, its contribution to mammalian anti-viral defense has been a matter of dispute. This is surprising because all components of the RNAi machinery necessary for robust RNAi-mediated restriction of viruses are conserved in mammals, and the introduction of synthetic small interfering RNAs (siRNAs) into cells efficiently silences the replication of viruses that contain siRNA complementary sequences in those cells. Here, I discuss the reasons for the dispute, and review the evidence that RNAi is a part of the physiological defense of mammalian cells against viral infections

Tension-type headache and sleep apnea in the general population

The main objective of this study is to investigate the relationship between tension-type headache and obstructive sleep apnea in the general population. The method involves a cross-sectional population-based study. A random age and gender stratified sample of 40,000 persons aged 20–80 years residing in Akershus, Hedmark or Oppland County, Norway were drawn by the National Population Register. A postal questionnaire containing the Berlin Questionnaire was used to classify respondents to be of either high or low risk of obstructive sleep apnea. Included in this study were 297 persons with high risk and 134 persons with low risk of sleep apnea, aged 30–65 years. They underwent an extensive clinical interview, a physical and a neurological examination by physicians, and in-hospital polysomnography. Those with apnea hypopnoea index (AHI) ≥5 were classified with obstructive sleep apnea. Tension-type headache was diagnosed according to the International Classification of Headache Disorders. Results showed the prevalence of frequent and chronic tension-type headache was 18.7 and 2.1% in the participants with obstructive sleep apnea. The logistic regression analyses showed no significant relationship between tension-type headache and obstructive sleep apnea, with adjusted odds ratios for frequent tension-type headache of 0.95 (0.55–1.62) and chronic tension-type headache of 1.91 (0.37–9.85). The results did not change when using cut-off of moderate (AHI ≥15) and severe (AHI ≥30) obstructive sleep apnea. Thus, we did not find any significant relationship between tension-type headache and the AHI. The presence and severity of sleep apneas seem not to influence presence and attack-frequency of tension-type headache in the general population

Value of supplemental interventions to enhance the effectiveness of physical exercise during respiratory rehabilitation in COPD patients. A Systematic Review

BACKGROUND: There is a controversy about the additional benefit of various supplemental interventions used in clinical practice to further enhance the effectiveness of respiratory rehabilitation in patients with Chronic obstructive pulmonary disease (COPD). The aim of this research was to assess randomised controlled trials (RCTs) testing the additional benefit of supplemental interventions during respiratory rehabilitation in COPD patients. METHODS: Systematic review with literature searches in six electronic databases, extensive hand-searching and contacting of authors. Two reviewers selected independently eligible RCTs, rated the methodological quality and extracted the data, which were analyzed considering the minimal important difference of patient-important outcomes where possible. FINDINGS: We identified 20 RCTs whereof 18 provided sufficient data for analysis. The methodological quality was low and sample sizes were too small for most trials to produce meaningful results (median total sample size = 28). Data from five trials showed that supplemental oxygen during exercise did not have clinically meaningful effects on health-related quality of life while improvements of exercise capacity may be even larger for patients exercising on room air. RCTs of adding assisted ventilation, nutritional supplements or a number of anabolically acting drugs do not provide sufficient evidence for or against the use any of these supplemental interventions. INTERPRETATION: There is insufficient evidence for most supplemental interventions during respiratory rehabilitation to estimate their additional value, partly due to methodological shortcomings of included RCTs. Current data do not suggest benefit from supplemental oxygen during exercise, although the methodological quality of included trials limits conclusions. To appropriately assess any of the various supplemental interventions used in clinical practice, pragmatic trials on respiratory rehabilitation of COPD patients need to consider methodological aspects as well as appropriate sample sizes

Surface Hardness Impairment of Quorum Sensing and Swarming for Pseudomonas aeruginosa

The importance of rhamnolipid to swarming of the bacterium Pseudomonas aeruginosa is well established. It is frequently, but not exclusively, observed that P. aeruginosa swarms in tendril patterns—formation of these tendrils requires rhamnolipid. We were interested to explain the impact of surface changes on P. aeruginosa swarm tendril development. Here we report that P. aeruginosa quorum sensing and rhamnolipid production is impaired when growing on harder semi-solid surfaces. P. aeruginosa wild-type swarms showed huge variation in tendril formation with small deviations to the “standard” swarm agar concentration of 0.5%. These macroscopic differences correlated with microscopic investigation of cells close to the advancing swarm edge using fluorescent gene reporters. Tendril swarms showed significant rhlA-gfp reporter expression right up to the advancing edge of swarming cells while swarms without tendrils (grown on harder agar) showed no rhlA-gfp reporter expression near the advancing edge. This difference in rhamnolipid gene expression can be explained by the necessity of quorum sensing for rhamnolipid production. We provide evidence that harder surfaces seem to limit induction of quorum sensing genes near the advancing swarm edge and these localized effects were sufficient to explain the lack of tendril formation on hard agar. We were unable to artificially stimulate rhamnolipid tendril formation with added acyl-homoserine lactone signals or increasing the carbon nutrients. This suggests that quorum sensing on surfaces is controlled in a manner that is not solely population dependent

In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans

The question whether fatty acids can be converted into glucose in humans has a long standing tradition in biochemistry, and the expected answer is “No”. Using recent advances in Systems Biology in the form of large-scale metabolic reconstructions, we reassessed this question by performing a global investigation of a genome-scale human metabolic network, which had been reconstructed on the basis of experimental results. By elementary flux pattern analysis, we found numerous pathways on which gluconeogenesis from fatty acids is feasible in humans. On these pathways, four moles of acetyl-CoA are converted into one mole of glucose and two moles of CO2. Analyzing the detected pathways in detail we found that their energetic requirements potentially limit their capacity. This study has many other biochemical implications: effect of starvation, sports physiology, practically carbohydrate-free diets of inuit, as well as survival of hibernating animals and embryos of egg-laying animals. Moreover, the energetic loss associated to the usage of gluconeogenesis from fatty acids can help explain the efficiency of carbohydrate reduced and ketogenic diets such as the Atkins diet