Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

Changes in the midpalatal and pterygopalatine sutures induced by micro-implant-supported skeletal expander, analyzed with a novel 3D method based on CBCT imaging

Abstract Background Mini-implant-assisted rapid palatal expansion (MARPE) appliances have been developed with the aim to enhance the orthopedic effect induced by rapid maxillary expansion (RME). Maxillary Skeletal Expander (MSE) is a particular type of MARPE appliance characterized by the presence of four mini-implants positioned in the posterior part of the palate with bi-cortical engagement. The aim of the present study is to evaluate the MSE effects on the midpalatal and pterygopalatine sutures in late adolescents, using high-resolution CBCT. Specific aims are to define the magnitude and sagittal parallelism of midpalatal suture opening, to measure the extent of transverse asymmetry of split, and to illustrate the possibility of splitting the pterygopalatine suture. Methods Fifteen subjects (mean age of 17.2 years; range, 13.9–26.2 years) were treated with MSE. Pre- and post-treatment CBCT exams were taken and superimposed. A novel methodology based on three new reference planes was utilized to analyze the sutural changes. Parameters were compared from pre- to post-treatment and between genders non-parametrically using the Wilcoxon sign rank test. For the frequency of openings in the lower part of the pterygopalatine suture, the Fisher’s exact test was used. Results Regarding the magnitude of midpalatal suture opening, the split at anterior nasal spine (ANS) and at posterior nasal spine (PNS) was 4.8 and 4.3 mm, respectively. The amount of split at PNS was 90% of that at ANS, showing that the opening of the midpalatal suture was almost perfectly parallel antero-posteriorly. On average, one half of the anterior nasal spine (ANS) moved more than the contralateral one by 1.1 mm. Openings between the lateral and medial plates of the pterygoid process were detectable in 53% of the sutures (P < 0.05). No significant differences were found in the magnitude and frequency of suture opening between males and females. Correlation between age and suture opening was negligible (R 2 range, 0.3–4.2%). Conclusions Midpalatal suture was successfully split by MSE in late adolescents, and the opening was almost perfectly parallel in a sagittal direction. Regarding the extent of transverse asymmetry of the split, on average one half of ANS moved more than the contralateral one by 1.1 mm. Pterygopalatine suture was split in its lower region by MSE, as the pyramidal process was pulled out from the pterygoid process. Patient gender and age had a negligible influence on suture opening for the age group considered in the study

Arginase strongly impairs neuronal nitric oxide-mediated airway smooth muscle relaxation in allergic asthma

BACKGROUND: Using guinea pig tracheal preparations, we have recently shown that endogenous arginase activity attenuates inhibitory nonadrenergic noncholinergic (iNANC) nerve-mediated airway smooth muscle relaxation by reducing nitric oxide (NO) production – due to competition with neuronal NO-synthase (nNOS) for the common substrate, L-arginine. Furthermore, in a guinea pig model of allergic asthma, airway arginase activity is markedly increased after the early asthmatic reaction (EAR), leading to deficiency of agonist-induced, epithelium-derived NO and subsequent airway hyperreactivity. In this study, we investigated whether increased arginase activity after the EAR affects iNANC nerve-derived NO production and airway smooth muscle relaxation. METHODS: Electrical field stimulation (EFS; 150 mA, 4 ms, 4 s, 0.5 – 16 Hz)-induced relaxation was measured in tracheal open-ring preparations precontracted to 30% with histamine in the presence of 1 μM atropine and 3 μM indomethacin. The contribution of NO to EFS-induced relaxation was assessed by the nonselective NOS inhibitor N(ω)-nitro-L-arginine (L-NNA, 100 μM), while the involvement of arginase activity in the regulation of EFS-induced NO production and relaxation was investigated by the effect of the specific arginase inhibitor N(ω)-hydroxy-nor-L-arginine (nor-NOHA, 10 μM). Furthermore, the role of substrate availability to nNOS was measured in the presence of exogenous L-arginine (5.0 mM). RESULTS: At 6 h after ovalbumin-challenge (after the EAR), EFS-induced relaxation (ranging from 3.2 ± 1.1% at 0.5 Hz to 58.5 ± 2.2% at 16 Hz) was significantly decreased compared to unchallenged controls (7.1 ± 0.8% to 75.8 ± 0.7%; P < 0.05 all). In contrast to unchallenged controls, the NOS inhibitor L-NNA did not affect EFS-induced relaxation after allergen challenge, indicating that NO deficiency underlies the impaired relaxation. Remarkably, the specific arginase inhibitor nor-NOHA normalized the impaired relaxation to unchallenged control (P < 0.05 all), which effect was inhibited by L-NNA (P < 0.01 all). Moreover, the effect of nor-NOHA was mimicked by exogenous L-arginine. CONCLUSION: The results clearly demonstrate that increased arginase activity after the allergen-induced EAR contributes to a deficiency of iNANC nerve-derived NO and decreased airway smooth muscle relaxation, presumably via increased substrate competition with nNOS

Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families

The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion/deletion, and by mutations that create or disrupt stem base pairing. We analyzed the evolution of stem lengths and constructed substitution matrices describing the changes responsible for the variation in the RNA stem length. In addition, we used principal component analysis of the stem length data to determine the most variable stems in different families of RNA. This data provides new insights into the evolution of RNA secondary structures and patterns of variation in the lengths of double helical regions of RNA molecules. Our findings will facilitate design of improved mutational models for RNA structure evolution

Developing country consumers’ acceptance of biofortified foods: a synthesis

The success of biofortified staple crops depends on whether they are accepted and consumed by target populations. In the past 8 years, several studies were undertaken to understand consumers’ acceptance of foods made with biofortified staple crops. Consumer acceptance is measured in terms of their sensory evaluation and economic valuation of biofortified varieties vis-à-vis conventional ones. These studies apply expert sensory panel and hedonic trait analyses methods adopted from food sciences literature, as well as various preference elicitation methods (including experimental auctions, revealed choice experiments, and stated choice experiments) adopted from experimental economics literature. These studies also test the impact of various levers on consumers’ evaluation and valuation for biofortified foods. These levers include (i) nutrition information and the media through which such information is conveyed; (ii) the length and content of nutrition information; (iii) different branding options; (iv) the nature (national or international) of the branding/certification agency that is endorsing the biofortified staple food; and (v) the nature (national or international) of the agency that is delivering the biofortified staple food. This paper brings together evidence on consumer acceptance of biofortified crops on 5 crops across 7 countries in Africa, Asia and Latin America. The results of these studies are expected to aid in the development of biofortified crops that consumers like, as well as in the development of appropriate marketing and consumer awareness or information campaigns to encourage the switch in consumption from traditional staples to biofortified ones

Barriers to home care for terminally ill Turkish and Moroccan migrants, perceived by GPs and nurses: a survey

BACKGROUND: Previous qualitative research proved that relatives of elderly terminally ill Turkish and Moroccan immigrants experience several barriers to the use of Dutch professional home care. The aim of this study was to explore how general practitioners and home care nurses perceive the home care for terminally ill Turkish and Moroccan migrants and their families in the Netherlands. METHODS: Questionnaires were sent to home care organizations and GPs working in areas where most of these migrants are living. 93 nurses and 78 GPs provided information about their experiences and opinions regarding home care for this group of patients. The data were analyzed by descriptive statistics. RESULTS: GPs refer relatively few patients from these migrant groups to home care. They often find it difficult to assess the needs of these patients and their families. In 40% of the GPs' cases in which terminally ill Turkish and Moroccan migrants were not referred to home care, the GP regretted this afterwards: the patients had not received sufficient qualified care, and their informal carers had often become overburdened. In addition, home care nurses often express dissatisfaction with the home care given to terminally ill Turkish or Moroccan patients, because of communication problems, the patients' lack of knowledge of the disease, or difficulties in making suitable appointments with the patient or with the family. CONCLUSIONS: Nurses and GPs cite chiefly similar factors influencing access to and use of home care as family members did in a previous study. However, according to GPs and nurses, the main barrier to the use of home care concerns communication problems, while relatives cited the preference for family care as the main reason for abstaining from the use of home care. (aut. ref.

Inter-examiner reliability of the diagnosis of cervical pillar hyperplasia (CPH) and the correlation between CPH and spinal degenerative joint disease (DJD)

BACKGROUND: Cervical pillar hyperplasia (CPH) is a recently described phenomenon of unknown aetiology. Its clinical importance is poorly understood at the present time; therefore, the objective of this study was to determine (1) the inter-examiner reliability of detecting CPH and (2) if there is a clinically important correlation (r > 0.4) between the number of cervical spine levels showing signs of degenerative joint disease (DJD) and CPH. METHODS: The sample consisted of 320 radiographs of human male and female subjects who ranged from 40 to 79 years of age. The inter-examiner reliability of assessing the presence/absence of pillar hyperplasia was evaluated on 50 neutral lateral radiographs by two examiners using line drawings and it was quantified using the kappa coefficient of concordance. To determine the presence/absence of hyperplastic pillars as well as the presence/absence of DJD at each intervertebral disc and zygapophysial joint, 320 AP open mouth, AP lower cervical and neutral lateral radiographs were then examined. The unpaired t-test at the 5% level of significance was performed to test for a statistically significant difference between the number of levels affected by DJD in patients with and without hyperplasia. The Spearman's rho at the 5% level of significance was performed to quantify the correlation between DJD and age. RESULTS: The inter-examiner reliability of detecting cervical pillar hyperplasia was moderate with a kappa coefficient of 0.51. The unpaired t-test indicated that there was no statistically significant difference (p > 0.05) between the presence/absence of cervical pillar hyperplasia and the number of levels affected by DJD in an age-matched population, regardless of whether all elements were considered together, or the discs and facets were analyzed separately. A Spearman correlation rank of 0.67 (p < 0.05) suggested a moderately strong correlation between the number of elements (i.e. discs/facets) affected, and the age of the individual. CONCLUSION: Cervical pillar hyperplasia is a reasonable concept that requires further research. Its evaluation is easy to learn and acceptably reliable. Previous research has suggested that CPH may affect the cervical lordosis, and therefore, alter biomechanics which may result in premature DJD. This current study, however, indicates that, globally, CPH does not appear to be related to the development of DJD

A Career in Surgical Oncology: Finding Meaning, Balance, and Personal Satisfaction

The practice of surgical oncology provides opportunities for both personal distress as well as personal satisfaction. While many surgical oncologists experience career burnout, others derive great meaning and satisfaction from their work. In this article, we review the literature on surgeon burnout, discuss potential personal and professional consequences, and consider steps individual surgeons can take to promote personal and professional satisfaction

Impact of protein supplementation during endurance training on changes in skeletal muscle transcriptome

Background: Protein supplementation improves physiological adaptations to endurance training, but the impact on adaptive changes in the skeletal muscle transcriptome remains elusive. The present analysis was executed to determine the impact of protein supplementation on changes in the skeletal muscle transcriptome following 5- weeks of endurance training. Results: Skeletal muscle tissue samples from the vastus lateralis were taken before and after 5-weeks of endurance training to assess changes in the skeletal muscle transcriptome. One hundred and 63 genes were differentially expressed after 5-weeks of endurance training in both groups (q-value 0.05). Endurance training primarily affected expression levels of genes related to extracellular matrix and these changes tended to be greater in PRO than in CON. Conclusions: Protein supplementation subtly impacts endurance training-induced changes in the skeletal muscle transcriptome. In addition, our transcriptomic analysis revealed that the extracellular matrix may be an important factor for skeletal muscle adaptation in response to endurance training. This trial was registered at clinicaltrials.gov as NCT03462381, March 12, 201