Inferring hidden Markov models from noisy time sequences: a method to alleviate degeneracy in molecular dynamics

We present a new method for inferring hidden Markov models from noisy time sequences without the necessity of assuming a model architecture, thus allowing for the detection of degenerate states. This is based on the statistical prediction techniques developed by Crutchfield et al., and generates so called causal state models, equivalent to hidden Markov models. This method is applicable to any continuous data which clusters around discrete values and exhibits multiple transitions between these values such as tethered particle motion data or Fluorescence Resonance Energy Transfer (FRET) spectra. The algorithms developed have been shown to perform well on simulated data, demonstrating the ability to recover the model used to generate the data under high noise, sparse data conditions and the ability to infer the existence of degenerate states. They have also been applied to new experimental FRET data of Holliday Junction dynamics, extracting the expected two state model and providing values for the transition rates in good agreement with previous results and with results obtained using existing maximum likelihood based methods.Comment: 19 pages, 9 figure

Legacy and Novel Per- and Polyfluoroalkyl Substances in Juvenile Seabirds from the U.S. Atlantic Coast

Per- and polyfluoroalkyl substances (PFAS) are anthropogenic, globally distributed chemicals. Legacy PFAS, including perfluorooctane sulfonate (PFOS), have been regularly detected in marine fauna but little is known about their current levels or the presence of novel PFAS in seabirds. We measured 36 emerging and legacy PFAS in livers from 31 juvenile seabirds from Massachusetts Bay, Narragansett Bay, and the Cape Fear River Estuary (CFRE), United States. PFOS was the major legacy perfluoroalkyl acid present, making up 58% of concentrations observed across all habitats (range: 11–280 ng/g). Novel PFAS were confirmed in chicks hatched downstream of a fluoropolymer production site in the CFRE: a perfluorinated ether sulfonic acid (Nafion byproduct 2; range: 1–110 ng/g) and two perfluorinated ether carboxylic acids (PFO4DA and PFO5DoDA; PFO5DoDA range: 5–30 ng/g). PFOS was inversely associated with phospholipid content in livers from CFRE and Massachusetts Bay individuals, while δ 13C, an indicator of marine versus terrestrial foraging, was positively correlated with some long-chain PFAS in CFRE chick livers. There is also an indication that seabird phospholipid dynamics are negatively impacted by PFAS, which should be further explored given the importance of lipids for seabirds

Transcript analysis reveals a specific HOX signature associated with positional identity of human endothelial cells.

The endothelial cell has a remarkable ability for sub-specialisation, adapted to the needs of a variety of vascular beds. The role of developmental programming versus the tissue contextual environment for this specialization is not well understood. Here we describe a hierarchy of expression of HOX genes associated with endothelial cell origin and location. In initial microarray studies, differential gene expression was examined in two endothelial cell lines: blood derived outgrowth endothelial cells (BOECs) and pulmonary artery endothelial cells. This suggested shared and differential patterns of HOX gene expression between the two endothelial lines. For example, this included a cluster on chromosome 2 of HOXD1, HOXD3, HOXD4, HOXD8 and HOXD9 that was expressed at a higher level in BOECs. Quantative PCR confirmed the higher expression of these HOXs in BOECs, a pattern that was shared by a variety of microvascular endothelial cell lines. Subsequently, we analysed publically available microarrays from a variety of adult cell and tissue types using the whole "HOX transcriptome" of all 39 HOX genes. Using hierarchical clustering analysis the HOX transcriptome was able to discriminate endothelial cells from 61 diverse human cell lines of various origins. In a separate publically available microarray dataset of 53 human endothelial cell lines, the HOX transcriptome additionally organized endothelial cells related to their organ or tissue of origin. Human tissue staining for HOXD8 and HOXD9 confirmed endothelial expression and also supported increased microvascular expression of these HOXs. Together these observations suggest a significant involvement of HOX genes in endothelial cell positional identity

Prevalence and Correlates of Common Mental Disorders among Mothers of Young Children in Kilimanjaro Region of Tanzania.

Although poor maternal mental health is a major public health problem, with detrimental effects on the individual, her children and society, information on its correlates in low-income countries is sparse. This study investigates the prevalence of common mental disorders (CMD) among at-risk mothers, and explores its associations with sociodemographic factors. This population-based survey of mothers of children aged 0-36 months used the 14-item Shona Symptom Questionnaire (SSQ). Mothers whose response was "yes" to 8 or more items on the scale were defined as "at risk of CMD." Of the 1,922 mothers (15-48 years), 28.8% were at risk of CMD. Risk of CMD was associated with verbal abuse, physical abuse, a partner who did not help with the care of the child, being in a polygamous relationship, a partner with low levels of education, and a partner who smoked cigarettes. Cohabiting appeared to be protective. Taken together, our results indicate the significance of the quality of relations with one's partner in shaping maternal mental health. The high proportion of mothers who are at risk of CMD emphasizes the importance of developing evidence-based mental health programmes as part of the care package aimed at improving maternal well-being in Tanzania and other similar settings

Evaluation of brine disposal from the bryan mound site of the strategic petroleum reserve program final report

On March 10, 1980, the Department of Energy's Strategic Petroleum Reserve Program began leaching the Bryan Mound salt dome and discharging the resulting brine into the coastal waters off Freeport, Texas. During the months of March and April, a team of scientists and engineers from Texas A and M University conducted an intensive environmental study of the area surrounding the diffuser site. A pipeline has been laid from the Bryan Mound site to a location 12.5 statute miles (20 km) offshore. The last 3060 ft (933 m) of this pipeline is a 52-port diffuser through which brine can be discharged at a maximum rate of 680,000 barrels per day. Initially, 16 ports were open which permitted a maximum discharge rate of 350,000 barrels per day and a continuous brine discharge was achieved on March 13, 1980. The purpose of this report is to describe the findings of the project team during the intensive postdisposal study period of March and April, 1980. The major areas of investigation are physical oceanography, analysis of the discharge plume, water and sediment quality, nekton, benthos, phytoplankton, zooplankton, and data management. Document type: Repor

Measuring the total infrared light from galaxy clusters at z=0.5-1.6: connecting stellar populations to dusty star formation

Massive galaxy clusters undergo strong evolution from z~1.6 to z~0.5, with overdense environments at high-z characterized by abundant dust-obscured star formation and stellar mass growth which rapidly give way to widespread quenching. Data spanning the near- to far-infrared (IR) spectrum can directly trace this transformation; however, such studies have largely been limited to the massive galaxy end of cluster populations. In this work, we present ``total light" stacking techniques spanning 3.4-500{\mu}m aimed at revealing the total cluster IR emission, including low mass members and potential intracluster dust. We detail our procedures for WISE, Spitzer, and Herschel imaging, including corrections to recover the total stacked emission in the case of high fractions of detected galaxies. We apply our stacking techniques to 232 well-studied massive (log M200/Msun~13.8) clusters across multiple z bins, recovering extended cluster emission at all wavelengths, typically at >5sigma. We measure the averaged near- to far-IR radial profiles and SEDs, quantifying the total stellar and dust content. The near-IR radial profiles are well described by an NFW model with a high (c~7) concentration parameter. Dust emission is similarly concentrated, albeit suppressed at small radii (r<0.2Mpc). The measured SEDs lack warm dust, consistent with the colder SEDs expected for low mass galaxies. We derive total stellar masses consistent with the theoretical Mhalo-M_star relation and specific-star formation rates that evolve strongly with redshift, echoing that of massive (log Mstar/Msun>10) cluster galaxies. Separating out the massive galaxy population reveals that the majority of cluster far-IR emission (~70-80%) is provided by the low mass constituents, which differs from field galaxies. This effect may be a combination of mass-dependent quenching and excess dust in low mass cluster galaxies.Comment: 32 pages, 16 figures, 7 tables. Submitted to MNRAS, comments welcome