Global transcription of CRISPR loci in the human oral cavity

© 2015 Lum et al.; licensee BioMed Central. Background: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are active in acquired resistance against bacteriophage and plasmids in a number of environments. In the human mouth, CRISPR loci evolve to counteract oral phage, but the expression of these CRISPR loci has not previously been investigated. We sequenced cDNA from CRISPR loci found in numerous different oral bacteria and compared with oral phage communities to determine whether the transcription of CRISPR loci is specifically targeted towards highly abundant phage present in the oral environment. Results: We found that of the 529,027 CRISPR spacer groups studied, 88 % could be identified in transcripts, indicating that the vast majority of CRISPR loci in the oral cavity were transcribed. There were no strong associations between CRISPR spacer repertoires and oral health status or nucleic acid type. We also compared CRISPR repertoires with oral bacteriophage communities, and found that there was no significant association between CRISPR transcripts and oral phage, regardless of the CRISPR type being evaluated. We characterized highly expressed CRISPR spacers and found that they were no more likely than other spacers to match oral phage. By reassembling the CRISPR-bearing reads into longer CRISPR loci, we found that the majority of the loci did not have spacers matching viruses found in the oral cavities of the subjects studied. For some CRISPR types, loci containing spacers matching oral phage were significantly more likely to have multiple spacers rather than a single spacer matching oral phage. Conclusions: These data suggest that the transcription of oral CRISPR loci is relatively ubiquitous and that highly expressed CRISPR spacers do not necessarily target the most abundant oral phage

Phenotypes and Clinical Genotypes of Bruxism Patients: A Systematic Review

Background. Bruxism is a phenomenon where psychological and exogenous biological factors act in greater percentage. Several genetic polymorphisms have been described in GABAA receptors, and some have been associated with motor limitations, such as the rs1805057 polymorphism of the GABRB1 gene (GABAA), which found a haplotype associated with a lower limitation in movement in acute pain processes. The aim to identify the clinical phenotypes in bruxism patients. Eligibility criteria were as follows: observational studies, case control studies, odds ratios, bruxism, patients, and a keyword search that included [[bruxism]], OR [[temporomandibular joint disorders]] OR [[sleep bruxism]], OR [[awake bruxism]], OR [[polymorphism]] or [[GABAA]], or [[serotonin]] , using the Boolean operators AND, OR and NOT. Were included 210 identified records in databases; 50 records from other sources; 117 records were deleted after determining they were duplicates; 42 studies were included in qualitative synthesis ; finally, who met inclusion requirements 5 studies were included in synthesis. The comparison of global DNA methylation profiles in patients with bruxism shows a possible genetic influence on their etiology, indicating that patients with HTR2A rs2770304 alleles are at increased risk. the HTR2A rs2770304 allele leads to an increased risk of bruxism

Formation of calcium sulfate through the aggregation of sub-3 nanometre primary species

The formation pathways of gypsum remain uncertain. Here, using truly in situ and fast time-resolved small-angle X-ray scattering, we quantify the four-stage solution-based nucleation and growth of gypsum (CaSO4 ·2H2O), an important mineral phase on Earth and Mars. The reaction starts through the fast formation of well-defined, primary species of <3 nm in length (stage I), followed in stage II by their arrangement into domains. The variations in volume fractions and electron densities suggest that these fast forming primary species contain Ca-SO4-cores that self-assemble in stage III into large aggregates. Within the aggregates these well-defined primary species start to grow (stage IV), and fully crystalize into gypsum through a structural rearrangement. Our results allow for a quantitative understanding of how natural calcium sulfate deposits may form on Earth and how a terrestrially unstable phase-like bassanite can persist at low-water activities currently dominating the surface of Mars

Efficacy of Thermotherapy to Treat Cutaneous Leishmaniasis Caused by Leishmania tropica in Kabul, Afghanistan: A Randomized, Controlled Trial

BACKGROUND: Pentavalent antimony is the agent recommended for treatment of cutaneous leishmaniasis (CL). Its use is problematic, because it is expensive and because of the potential for drug-associated adverse effects during a lengthy and painful treatment course. METHODS: We tested the efficacy of thermotherapy for the treatment of CL due to Leishmania tropica in a randomized, controlled trial in Kabul, Afghanistan. We enrolled 401 patients with a single CL lesion and administered thermotherapy using radio-frequency waves (1 treatment of ≥1 consecutive application at 50°C for 30 s) or sodium stibogluconate (SSG), administered either intralesionally (a total of 5 injections of 25 mL every 57 days, depending on lesion size) or intramuscularly (20 mg/kg daily for 21 days). RESULTS: Cure, defined as complete reepithelialization at 100 days after treatment initiation, was observed in 75 (69.4%) of 108 patients who received thermotherapy, 70 (75.3%) of 93 patients who received intralesional SSG, and 26 (44.8%) of 58 patients who received intramuscular SSG. The OR for cure with thermotherapy was 2.80 (95% confidence interval [CI], 1.455.41), compared with intramuscular SSG treatment (P = .002). No statistically significant difference was observed in the odds of cure in comparison of intralesional SSG and thermotherapy treatments. The OR for cure with intralesional SSG treatment was 3.75 (95% CI, 1.867.54), compared with intramuscular SSG treatment (P 100 days, respectively; P = .003). CONCLUSIONS: Thermotherapy is an effective, comparatively well-tolerated, and rapid treatment for CL, and it should be considered as an alternative to antimony treatment

How Short-Lived Ikaite Affects Calcite Crystallization

The pathways of CaCO₃ crystallization are manifold, often involving one or several metastable amorphous or nanocrystalline intermediate phases. The presence of such intermediates is often overlooked, because they are short-lived and/or occur at small molar fractions. However, their occurrence does not just impact the mechanisms and pathways of formation of the final stable CaCO₃ phase, but also affects their crystal size, shape, and structure. Here we document the presence of a short-lived intermediate through in situ and time-resolved small and wide-angle X-ray scattering combined with high resolution electron microscope observations. When ikaite forms concomitant with the dissolution of amorphous calcium carbonate (ACC) but prior to calcite formation, fairly large glendonite-type calcite crystals grow despite the presence of citrate ligands that usually reduce crystal size. These were ideal seeding crystals for further crystallization from supersaturated ions in solution. In contrast, in the absence of ikaite the crystallization of calcite proceeds through transformation from ACC, resulting in fine-grained spherulitic calcite with sizes ∼8 times smaller than when ikaite was present. Noteworthy is that the formation of the intermediate ikaite, although it consumes less than 3 mol % of the total precipitated CaCO₃, still clearly affected the calcite formation mechanism

Dendritic Spine Shape Analysis: A Clustering Perspective

Functional properties of neurons are strongly coupled with their morphology. Changes in neuronal activity alter morphological characteristics of dendritic spines. First step towards understanding the structure-function relationship is to group spines into main spine classes reported in the literature. Shape analysis of dendritic spines can help neuroscientists understand the underlying relationships. Due to unavailability of reliable automated tools, this analysis is currently performed manually which is a time-intensive and subjective task. Several studies on spine shape classification have been reported in the literature, however, there is an on-going debate on whether distinct spine shape classes exist or whether spines should be modeled through a continuum of shape variations. Another challenge is the subjectivity and bias that is introduced due to the supervised nature of classification approaches. In this paper, we aim to address these issues by presenting a clustering perspective. In this context, clustering may serve both confirmation of known patterns and discovery of new ones. We perform cluster analysis on two-photon microscopic images of spines using morphological, shape, and appearance based features and gain insights into the spine shape analysis problem. We use histogram of oriented gradients (HOG), disjunctive normal shape models (DNSM), morphological features, and intensity profile based features for cluster analysis. We use x-means to perform cluster analysis that selects the number of clusters automatically using the Bayesian information criterion (BIC). For all features, this analysis produces 4 clusters and we observe the formation of at least one cluster consisting of spines which are difficult to be assigned to a known class. This observation supports the argument of intermediate shape types.Comment: Accepted for BioImageComputing workshop at ECCV 201

Ileosigmoid fistula and delayed ileal obstruction secondary to blunt abdominal trauma: a case report

<p>Abstract</p> <p>Introduction</p> <p>Abdominal trauma is a source of significant mortality and morbidity. Bowel injury as a result of blunt abdominal trauma is usually evident within hours or days of the accident.</p> <p>Case presentation</p> <p>A 38-year-old Caucasian Greek man presented with a subtle and delayed small bowel obstruction caused by a post-traumatic ileosigmoid fistula and ileal stricture four months after a road traffic accident.</p> <p>Conclusion</p> <p>Delayed occurrence of post-traumatic small bowel stricture and ileosigmoid fistula is an uncommon surgical emergency. General surgeons as well as emergency physicians should bear this manifestation in mind should a patient return to the hospital several weeks or even years after blunt abdominal trauma with symptoms or signs of bowel obstruction.</p

An assessment of functioning and non-functioning distractors in multiple-choice questions: a descriptive analysis

<p>Abstract</p> <p>Background</p> <p>Four- or five-option multiple choice questions (MCQs) are the standard in health-science disciplines, both on certification-level examinations and on in-house developed tests. Previous research has shown, however, that few MCQs have three or four functioning distractors. The purpose of this study was to investigate non-functioning distractors in teacher-developed tests in one nursing program in an English-language university in Hong Kong.</p> <p>Methods</p> <p>Using item-analysis data, we assessed the proportion of non-functioning distractors on a sample of seven test papers administered to undergraduate nursing students. A total of 514 items were reviewed, including 2056 options (1542 distractors and 514 correct responses). Non-functioning options were defined as ones that were chosen by fewer than 5% of examinees and those with a positive option discrimination statistic.</p> <p>Results</p> <p>The proportion of items containing 0, 1, 2, and 3 functioning distractors was 12.3%, 34.8%, 39.1%, and 13.8% respectively. Overall, items contained an average of 1.54 (SD = 0.88) functioning distractors. Only 52.2% (n = 805) of all distractors were functioning effectively and 10.2% (n = 158) had a choice frequency of 0. Items with more functioning distractors were more difficult and more discriminating.</p> <p>Conclusion</p> <p>The low frequency of items with three functioning distractors in the four-option items in this study suggests that teachers have difficulty developing plausible distractors for most MCQs. Test items should consist of as many options as is feasible given the item content and the number of plausible distractors; in most cases this would be three. Item analysis results can be used to identify and remove non-functioning distractors from MCQs that have been used in previous tests.</p

Feature selection for chemical sensor arrays using mutual information

We address the problem of feature selection for classifying a diverse set of chemicals using an array of metal oxide sensors. Our aim is to evaluate a filter approach to feature selection with reference to previous work, which used a wrapper approach on the same data set, and established best features and upper bounds on classification performance. We selected feature sets that exhibit the maximal mutual information with the identity of the chemicals. The selected features closely match those found to perform well in the previous study using a wrapper approach to conduct an exhaustive search of all permitted feature combinations. By comparing the classification performance of support vector machines (using features selected by mutual information) with the performance observed in the previous study, we found that while our approach does not always give the maximum possible classification performance, it always selects features that achieve classification performance approaching the optimum obtained by exhaustive search. We performed further classification using the selected feature set with some common classifiers and found that, for the selected features, Bayesian Networks gave the best performance. Finally, we compared the observed classification performances with the performance of classifiers using randomly selected features. We found that the selected features consistently outperformed randomly selected features for all tested classifiers. The mutual information filter approach is therefore a computationally efficient method for selecting near optimal features for chemical sensor arrays

Density-dependence of functional development in spiking cortical networks grown in vitro

During development, the mammalian brain differentiates into specialized regions with distinct functional abilities. While many factors contribute to functional specialization, we explore the effect of neuronal density on the development of neuronal interactions in vitro. Two types of cortical networks, dense and sparse, with 50,000 and 12,000 total cells respectively, are studied. Activation graphs that represent pairwise neuronal interactions are constructed using a competitive first response model. These graphs reveal that, during development in vitro, dense networks form activation connections earlier than sparse networks. Link entropy analysis of dense net- work activation graphs suggests that the majority of connections between electrodes are reciprocal in nature. Information theoretic measures reveal that early functional information interactions (among 3 cells) are synergetic in both dense and sparse networks. However, during later stages of development, previously synergetic relationships become primarily redundant in dense, but not in sparse networks. Large link entropy values in the activation graph are related to the domination of redundant ensembles in late stages of development in dense networks. Results demonstrate differences between dense and sparse networks in terms of informational groups, pairwise relationships, and activation graphs. These differences suggest that variations in cell density may result in different functional specialization of nervous system tissue in vivo.Comment: 10 pages, 7 figure