Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery.

The obesity pandemic in the obstetrical population plus increased frequency of Cesarean delivery (CD) has increased vulnerability to surgical site infection (SSI). Here we characterized the microbiome at the site of skin incision before and after CD. Skin and relevant surgical sites were sampled before and after surgical antisepsis from obese (n = 31) and non-obese (n = 27) pregnant women. We quantified bacterial biomass by qPCR, microbial community composition by 16sRNA sequencing, assigned operational taxonomic units, and stained skin biopsies from incision for bacteria and biofilms. In obese women, incision site harbors significantly higher bacterial biomass of lower diversity. Phylum Firmicutes predominated over Actinobacteria, with phylotypes Clostridales and Bacteroidales over commensal Staphylococcus and Propionbacterium spp. Skin dysbiosis increased post-surgical prep and at end of surgery. Biofilms were identified post-prep in the majority (73%) of skin biopsies. At end of surgery, incision had significant gains in bacterial DNA and diversity, and obese women shared more genera with vagina and surgeon's glove in CD. Our findings suggest microbiota at incision differs between obese and non-obese pregnant women, and changes throughout CD. An interaction between vaginal and cutaneous dysbiosis at the incision site may explain the a priori increased risk for SSI among obese pregnant women.

Comparison of the Lund and Browder table to computed tomography scan three-dimensional surface area measurement for a pediatric cohort.

BACKGROUND: Treating burns effectively requires accurately assessing the percentage of the total body surface area (%TBSA) affected by burns. Current methods for estimating %TBSA, such as Lund and Browder (L&B) tables, rely on historic body statistics. An increasingly obese population has been blamed for increasing errors in %TBSA estimates. However, this assumption has not been experimentally validated. We hypothesized that errors in %TBSA estimates using L&B were due to differences in the physical proportions of today's children compared with children in the early 1940s when the chart was developed and that these differences would appear as body mass index (BMI)-associated systematic errors in the L&B values versus actual body surface areas. MATERIALS AND METHODS: We measured the TBSA of human pediatric cadavers using computed tomography scans. Subjects ranged from 9 mo to 15 y in age. We chose outliers of the BMI distribution (from the 31st percentile at the low through the 99th percentile at the high). We examined surface area proportions corresponding to L&B regions. RESULTS: Measured regional proportions based on computed tomography scans were in reasonable agreement with L&B, even with subjects in the tails of the BMI range. The largest deviation was 3.4%, significantly less than the error seen in real-world %TBSA estimates. CONCLUSIONS: While today's population is more obese than those studied by L&B, their body region proportions scale surprisingly well. The primary error in %TBSA estimation is not due to changing physical proportions of today's children and may instead lie in the application of the L&B table.

Investigating skin-to-skin care patterns with extremely preterm infants in the NICU and their effect on early cognitive and communication performance: a retrospective cohort study.

OBJECTIVES: The primary objective of the study was to investigate how patterns of skin-to-skin care might impact infant early cognitive and communication performance. DESIGN: This was a retrospective cohort study. SETTING: This study took place in a level-IV all-referral neonatal intensive care unit in the Midwest USA specialising in the care of extremely preterm infants. PARTICIPANTS: Data were collected from the electronic medical records of all extremely preterm infants (gestational age <27 weeks) admitted to the unit during 2010-2011 and who completed 6-month and 12-month developmental assessments in the follow-up clinic (n=97). OUTCOME MEASURES: Outcome measures included the cognitive and communication subscales of the Bayley Scales of Infant Development, Third Edition (Bayley-III); and skin-to-skin patterns including: total hours of maternal and paternal participation throughout hospitalisation, total duration in weeks and frequency (hours per week). ANALYSIS: Extracted data were analysed through a multistep process of logistic regressions, t-tests, χ2 tests and Fisher's exact tests followed with exploratory network analysis using novel visual analytic software. RESULTS: Infants who received above the sample median in total hours, weekly frequency and total hours from mothers and fathers of skin-to-skin care were more likely to score ≥80 on the cognitive and communication scales of the Bayley-III. However, the results were not statistically significant (p>0.05). Mothers provided the majority of skin-to-skin care with a sharp decline at 30 weeks corrected age, regardless of when extremely preterm infants were admitted. Additional exploratory network analysis suggests that medical and skin-to-skin factors play a parallel, non-synergistic role in contributing to early cognitive and communication performance as assessed through the Bayley-III. CONCLUSIONS: This study suggests an association between early and frequent skin-to-skin care with extremely preterm infants and early cognitive and communication performance.

MoFlow: visualizing conformational changes in molecules as molecular flow improves understanding.

BACKGROUND: Current visualizations of molecular motion use a Timeline-analogous representation that conveys "first the molecule was shaped like this, then like this...". This scheme is orthogonal to the Pathline-like human understanding of motion "this part of the molecule moved from here to here along this path". We present MoFlow, a system for visualizing molecular motion using a Pathline-analogous representation. RESULTS: The MoFlow system produces high-quality renderings of molecular motion as atom pathlines, as well as interactive WebGL visualizations, and 3D printable models. In a preliminary user study, MoFlow representations are shown to be superior to canonical representations for conveying molecular motion. CONCLUSIONS: Pathline-based representations of molecular motion are more easily understood than timeline representations. Pathline representations provide other advantages because they represent motion directly, rather than representing structure with inferred motion.

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues.

Protein alignments are commonly used to evaluate the similarity of protein residues, and the derived consensus sequence used for identifying functional units (e.g., domains). Traditional consensus-building models fail to account for interpositional dependencies - functionally required covariation of residues that tend to appear simultaneously throughout evolution and across the phylogentic tree. These relationships can reveal important clues about the processes of protein folding, thermostability, and the formation of functional sites, which in turn can be used to inform the engineering of synthetic proteins. Unfortunately, these relationships essentially form sub-motifs which cannot be predicted by simple "majority rule" or even HMM-based consensus models, and the result can be a biologically invalid "consensus" which is not only never seen in nature but is less viable than any extant protein. We have developed a visual analytics tool, StickWRLD, which creates an interactive 3D representation of a protein alignment and clearly displays covarying residues. The user has the ability to pan and zoom, as well as dynamically change the statistical threshold underlying the identification of covariants. StickWRLD has previously been successfully used to identify functionally-required covarying residues in proteins such as Adenylate Kinase and in DNA sequences such as endonuclease target sites.

Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests.

INTRODUCTION: In 2011, the BioVis symposium of the IEEE VisWeek conferences inaugurated a new variety of data analysis contest. Aimed at fostering collaborations between computational scientists and biologists, the BioVis contest provided real data from biological domains with emerging visualization needs, in the hope that novel approaches would result in powerful new tools for the community. In 2011 and 2012 the theme of these contests was expression Quantitative Trait Locus analysis, within and across tissues respectively. In 2013 the topic was updated to protein sequence and mutation visualization. METHODS: The contest was framed in the context of a real protein with numerous mutations that had lost function, and the question posed "what minimal set of changes would you propose to rescue function, or how could you support a biologist attempting to answer that question?". The data was grounded in actual experimental results in triosephosphate isomerase(TIM) enzymes. Seven teams composed of 36 individuals submitted entries with proposed solutions and approaches to the challenge. Their contributions ranged from careful analysis of the visualization and analytical requirements for the problem through integration of existing tools for analyzing the context and consequences of protein mutations, to completely new tools addressing the problem. RESULTS: Judges found valuable and novel contributions in each of the entries, including interesting ways to hierarchicalize the protein into domains of informational interaction, tools for simultaneously understanding both sequential and spatial order, and approaches for conveying some types of inter-residue dependencies. In this manuscript we document the problem presented to the contestants, summarize the biological contributions of their entries, and suggest opportunities that this work has highlighted for even more improved tools in the future.