Culturally Tailored, Family-Centered, Behavioral Obesity Intervention for Latino-American Preschool-aged Children

http://dx.doi.org/10.1542/peds.2011-376

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi

A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon’s second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults

The gut mycobiome of the Human Microbiome Project healthy cohort

Background: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. Results: Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96. 8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. Conclusions: Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual’s mycobiome is no more similar to itself over time than to another person’s. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples

Processes associated with ionic current rectification at a 2D-titanate nanosheet deposit on a microhole poly(ethylene terephthalate) substrate

Films of titanate nanosheets (approx. 1.8-nm layer thickness and 200-nm size) having a lamellar structure can form electrolyte-filled semi-permeable channels containing tetrabutylammonium cations. By evaporation of a colloidal solution, persistent deposits are readily formed with approx. 10-μm thickness on a 6-μm-thick poly(ethylene-terephthalate) (PET) substrate with a 20-μm diameter microhole. When immersed in aqueous solution, the titanate nanosheets exhibit a p.z.c. of − 37 mV, consistent with the formation of a cation conducting (semi-permeable) deposit. With a sufficiently low ionic strength in the aqueous electrolyte, ionic current rectification is observed (cationic diode behaviour). Currents can be dissected into (i) electrolyte cation transport, (ii) electrolyte anion transport and (iii) water heterolysis causing additional proton transport. For all types of electrolyte cations, a water heterolysis mechanism is observed. For Ca 2+ and Mg 2+ ions, water heterolysis causes ion current blocking, presumably due to localised hydroxide-induced precipitation processes. Aqueous NBu 4 + is shown to ‘invert’ the diode effect (from cationic to anionic diode). Potential for applications in desalination and/or ion sensing are discussed. [Figure not available: see fulltext.]. </p

PEP-FOLD: an online resource for de novo peptide structure prediction

Rational peptide design and large-scale prediction of peptide structure from sequence remain a challenge for chemical biologists. We present PEP-FOLD, an online service, aimed at de novo modelling of 3D conformations for peptides between 9 and 25 amino acids in aqueous solution. Using a hidden Markov model-derived structural alphabet (SA) of 27 four-residue letters, PEP-FOLD first predicts the SA letter profiles from the amino acid sequence and then assembles the predicted fragments by a greedy procedure driven by a modified version of the OPEP coarse-grained force field. Starting from an amino acid sequence, PEP-FOLD performs series of 50 simulations and returns the most representative conformations identified in terms of energy and population. Using a benchmark of 25 peptides with 9–23 amino acids, and considering the reproducibility of the runs, we find that, on average, PEP-FOLD locates lowest energy conformations differing by 2.6 Å Cα root mean square deviation from the full NMR structures. PEP-FOLD can be accessed at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOL

'H, I, J, K, L, M, N, O, PEE! Get it? Pee!': Siblings' shared humour in childhood

Humour is a central feature of social interactions in childhood that has received little attention. In a sample of 86 7‐year‐old children (M age = 7.82 years, SD = 0.80), we investigated patterns and individual differences in spontaneous humour observed during free play with their older (M age = 9.55 years, SD = 0.88) or their younger sibling (M age = 5.87 years, SD = 0.96). We coded children's instances, categories, and responses to humour. We investigated the nature of children's humour on the dyadic and individual level. Humour was common, and siblings’ production of humour was highly interdependent between play partners. Dyadic humour differed according to structural features of the sibling relationship (age, gender composition), and 7‐year‐old focal children's humour varied according to gender. This study contributes to knowledge regarding the dyadic nature of children's humour and individual patterns of humour beyond the preschool years

Dinucleotide controlled null models for comparative RNA gene prediction

<p>Abstract</p> <p>Background</p> <p>Comparative prediction of RNA structures can be used to identify functional noncoding RNAs in genomic screens. It was shown recently by Babak <it>et al</it>. [BMC Bioinformatics. 8:33] that RNA gene prediction programs can be biased by the genomic dinucleotide content, in particular those programs using a thermodynamic folding model including stacking energies. As a consequence, there is need for dinucleotide-preserving control strategies to assess the significance of such predictions. While there have been randomization algorithms for single sequences for many years, the problem has remained challenging for multiple alignments and there is currently no algorithm available.</p> <p>Results</p> <p>We present a program called SISSIz that simulates multiple alignments of a given average dinucleotide content. Meeting additional requirements of an accurate null model, the randomized alignments are on average of the same sequence diversity and preserve local conservation and gap patterns. We make use of a phylogenetic substitution model that includes overlapping dependencies and site-specific rates. Using fast heuristics and a distance based approach, a tree is estimated under this model which is used to guide the simulations. The new algorithm is tested on vertebrate genomic alignments and the effect on RNA structure predictions is studied. In addition, we directly combined the new null model with the RNAalifold consensus folding algorithm giving a new variant of a thermodynamic structure based RNA gene finding program that is not biased by the dinucleotide content.</p> <p>Conclusion</p> <p>SISSIz implements an efficient algorithm to randomize multiple alignments preserving dinucleotide content. It can be used to get more accurate estimates of false positive rates of existing programs, to produce negative controls for the training of machine learning based programs, or as standalone RNA gene finding program. Other applications in comparative genomics that require randomization of multiple alignments can be considered.</p> <p>Availability</p> <p>SISSIz is available as open source C code that can be compiled for every major platform and downloaded here: <url>http://sourceforge.net/projects/sissiz</url>.</p

Wireless transmission of biosignals for hyperbaric chamber applications

[EN] This paper presents a wireless system to send biosignals outside a hyperbaric chamber avoiding wires going through the chamber walls. Hyperbaric chambers are becoming more and more common due to new indications of hyperbaric oxygen treatments. Metallic walls physically isolate patients inside the chamber, where getting a patient's vital signs turns into a painstaking task. The paper proposes using a ZigBee-based network to wirelessly transmit the patient's biosignals to the outside of the chamber. In particular, a wearable battery supported device has been designed, implemented and tested. Although the implementation has been conducted to transmit the electrocardiography signal, the device can be easily adapted to consider other biosignals.The authors would like to thanks the University of Balearic Islands (UIB), the Miguel Hernandez University (UMH), MEDIBAROX unit of the Perpetuo Socorro Hospital and the "Catedra de Medicina Hiperbarica" (UMH) for their support allowing the use of its facilities for this work. The authors would also like to thank Borja Mas Boned for his help designing the LabVIEW application. This research has been carried out with funding and promotion of "Catedra de Medicina Hiperbarica" of the Miguel Hernandez University. http://nbio.umh.es/es/2010/12/01/catedra-de-medicina-hiperbarica-medibarox/.Perez-Vidal, C.; Gracia Calandin, LI.; Carmona, C.; Alorda, B.; Salinas, A. (2017). Wireless transmission of biosignals for hyperbaric chamber applications. PLoS ONE. 12(3):1-19. https://doi.org/10.1371/journal.pone.0172768S119123Sureda, A., Batle, J. M., Martorell, M., Capó, X., Tejada, S., Tur, J. A., & Pons, A. (2016). Antioxidant Response of Chronic Wounds to Hyperbaric Oxygen Therapy. PLOS ONE, 11(9), e0163371. doi:10.1371/journal.pone.0163371Branco, B. H. M., Fukuda, D. H., Andreato, L. V., Santos, J. F. da S., Esteves, J. V. D. C., & Franchini, E. (2016). The Effects of Hyperbaric Oxygen Therapy on Post-Training Recovery in Jiu-Jitsu Athletes. PLOS ONE, 11(3), e0150517. doi:10.1371/journal.pone.0150517Xu, Y., Ji, R., Wei, R., Yin, B., He, F., & Luo, B. (2016). The Efficacy of Hyperbaric Oxygen Therapy on Middle Cerebral Artery Occlusion in Animal Studies: A Meta-Analysis. PLOS ONE, 11(2), e0148324. doi:10.1371/journal.pone.0148324Lin, B.-S., Lin, B.-S., Chou, N.-K., Chong, F.-C., & Chen, S.-J. (2006). RTWPMS: A Real-Time Wireless Physiological Monitoring System. IEEE Transactions on Information Technology in Biomedicine, 10(4), 647-656. doi:10.1109/titb.2006.874194Hu, S., Wei, H., Chen, Y., & Tan, J. (2012). A Real-Time Cardiac Arrhythmia Classification System with Wearable Sensor Networks. Sensors, 12(9), 12844-12869. doi:10.3390/s120912844Burns, A., Greene, B. R., McGrath, M. J., O’Shea, T. J., Kuris, B., Ayer, S. M., … Cionca, V. (2010). SHIMMER™ – A Wireless Sensor Platform for Noninvasive Biomedical Research. IEEE Sensors Journal, 10(9), 1527-1534. doi:10.1109/jsen.2010.2045498Gil, Y., Wu, W., & Lee, J. (2012). A Synchronous Multi-Body Sensor Platform in a Wireless Body Sensor Network: Design and Implementation. Sensors, 12(8), 10381-10394. doi:10.3390/s120810381Chin-Teng Lin, Kuan-Cheng Chang, Chun-Ling Lin, Chia-Cheng Chiang, Shao-Wei Lu, Shih-Sheng Chang, … Li-Wei Ko. (2010). An Intelligent Telecardiology System Using a Wearable and Wireless ECG to Detect Atrial Fibrillation. IEEE Transactions on Information Technology in Biomedicine, 14(3), 726-733. doi:10.1109/titb.2010.2047401W. Y. Chung, Y. D. Lee, and S. J. Jung, &apos;A Wireless Sensor Network Compatible Wearable U-Healthcare Monitoring System Using Integrated Ecg, Accelerometer and Spo2&apos;, Conf Proc IEEE Eng Med Biol Soc, 2008 (2008), 1529–32.ZigBee Alliance; http://www.zigbee.org/Mahmood, A., Javaid, N., & Razzaq, S. (2015). A review of wireless communications for smart grid. Renewable and Sustainable Energy Reviews, 41, 248-260. doi:10.1016/j.rser.2014.08.036J.S. Lee, Y.W. Su, and C.C. Shen, &quot;A comparative study of wireless protocols: Bluetooth, UWB, ZigBee, and Wi-Fi, 33rd Annual Conference of the IEEE Industrial Electronics Society (IECON), 2007, pp. 46–51.P.P. Parikh, M.G. Kanabar, and T.S. Sidhu, &quot;Opportunities and challenges of wireless communication technologies for smart grid applications, IEEE PES General Meeting, 2010, pp. 1–7.Fadlullah, Z. M., Fouda, M. M., Kato, N., Takeuchi, A., Iwasaki, N., & Nozaki, Y. (2011). Toward intelligent machine-to-machine communications in smart grid. IEEE Communications Magazine, 49(4), 60-65. doi:10.1109/mcom.2011.5741147A.C. Olteanu, G.D. Oprina, N. Tapus, and S. Zeisberg, &quot;Enabling mobile devices for home automation using ZigBee, 19th IEEE International Conference on Control Systems and Computer Science, 2013, pp. 189–195.Shang, Y. (2014). Vulnerability of networks: Fractional percolation on random graphs. Physical Review E, 89(1). doi:10.1103/physreve.89.012813R. Barea-Navarro. Biomedical Instrumentation. Chapter 3. University of Alcala

Ensuring respect for persons in COMPASS: A cluster randomised pragmatic clinical trial

Cluster randomised clinical trials present unique challenges in meeting ethical obligations to those who are treated at a randomised site. Obtaining informed consent for research within the context of clinical care is one such challenge. In order to solve this problem it is important that an informed consent process be effective and efficient, and that it does not impede the research or the healthcare. The innovative approach to informed consent employed in the COMPASS study demonstrates the feasibility of upholding ethical standards without imposing undue burden on clinical workflows, staff members or patients who may participate in the research by virtue of their presence in a cluster randomised facility. The COMPASS study included 40 randomised sites and compared the effectiveness of a postacute stroke intervention with standard care. Each site provided either the comprehensive postacute stroke intervention or standard care according to the randomisation assignment. Working together, the study team, institutional review board and members of the community designed an ethically appropriate and operationally reasonable consent process which was carried out successfully at all randomised sites. This achievement is noteworthy because it demonstrates how to effectively conduct appropriate informed consent in cluster randomised trials, and because it provides a model that can easily be adapted for other pragmatic studies. With this innovative approach to informed consent, patients have access to the information they need about research occurring where they are seeking care, and medical researchers can conduct their studies without ethical concerns or unreasonable logistical impediments. Trial registration number NCT02588664, recruiting. This article covers the development of consent process that is currentlty being employed in the study