Reduced chemistry for butanol isomers at engine-relevant conditions

Butanol has received significant research attention as a second-generation biofuel in the past few years. In the present study, skeletal mechanisms for four butanol isomers were generated from two widely accepted, well-validated detailed chemical kinetic models for the butanol isomers. The detailed models were reduced using a two-stage approach consisting of the directed relation graph with error propagation and sensitivity analysis. During the reduction process, issues were encountered with pressure-dependent reactions formulated using the logarithmic pressure interpolation approach; these issues are discussed and recommendations made to avoid ambiguity in its future implementation in mechanism development. The performance of the skeletal mechanisms generated here was compared with that of detailed mechanisms in simulations of autoignition delay times, laminar flame speeds, and perfectly stirred reactor temperature response curves and extinction residence times, over a wide range of pressures, temperatures, and equivalence ratios. The detailed and skeletal mechanisms agreed well, demonstrating the adequacy of the resulting reduced chemistry for all the butanol isomers in predicting global combustion phenomena. In addition, the skeletal mechanisms closely predicted the time-histories of fuel mass fractions in homogeneous compression-ignition engine simulations. The performance of each butanol isomer was additionally compared with that of a gasoline surrogate with an antiknock index of 87 in a homogeneous compression-ignition engine simulation. The gasoline surrogate was consumed faster than any of the butanol isomers, with tert-butanol exhibiting the slowest fuel consumption rate. While n-butanol and isobutanol displayed the most similar consumption profiles relative to the gasoline surrogate, the two literature chemical kinetic models predicted different orderings.Comment: 39 pages, 16 figures. Supporting information available via https://doi.org/10.1021/acs.energyfuels.6b0185

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.

In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3' untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites

The Impact of Weather on Influenza and Pneumonia Mortality in New York City, 1975–2002: A Retrospective Study

The substantial winter influenza peak in temperate climates has lead to the hypothesis that cold and/or dry air is a causal factor in influenza variability. We examined the relationship between cold and/or dry air and daily influenza and pneumonia mortality in the cold season in the New York metropolitan area from 1975–2002. We conducted a retrospective study relating daily pneumonia and influenza mortality for New York City and surroundings from 1975–2002 to daily air temperature, dew point temperature (a measure of atmospheric humidity), and daily air mass type. We identified high mortality days and periods and employed temporal smoothers and lags to account for the latency period and the time between infection and death. Unpaired t-tests were used to compare high mortality events to non-events and nonparametric bootstrapped regression analysis was used to examine the characteristics of longer mortality episodes. We found a statistically significant (p = 0.003) association between periods of low dew point temperature and above normal pneumonia and influenza mortality 17 days later. The duration (r = −0.61) and severity (r = −0.56) of high mortality episodes was inversely correlated with morning dew point temperature prior to and during the episodes. Weeks in which moist polar air masses were common (air masses characterized by low dew point temperatures) were likewise followed by above normal mortality 17 days later (p = 0.019). This research supports the contention that cold, dry air may be related to influenza mortality and suggests that warning systems could provide enough lead time to be effective in mitigating the effects

Controlled release nanoparticulate matter delivery system

A controlled release nanoparticulate matter delivery system includes a plurality of thermoresponsive modules containing a respective nanoparticulate matter. Each thermoresponsive module is selectively operable in at least one of a heating mode that releases the nanoparticulate matter and a cooling mode that inhibits release of the nanoparticulate matter. A control module is in electrical communication with the plurality of thermoresponsive modules. The control module is configured to determine a temperature of each thermoresponsive module and to select the at least one heating mode and cooling mode based on the temperature. The heating and cooling mode may be selected in response to a desired dosing profile and/or a biometric condition.Board of Regents, University of Texas Syste

Pilot study of the safety and effect of adalimumab on pain, physical function, and musculoskeletal disease in mucopolysaccharidosis types I and II.

Mucopolysaccharidosis I and II are lysosomal storage disorders that, despite treatment with hematopoietic cell transplantation (HCT) and/or enzyme replacement therapy (ERT), continue to cause significant skeletal abnormalities leading to pain, stiffness, physical dysfunction, and short stature. Tumor necrosis factor - alpha (TNF-α) is elevated in individuals with MPS I and II and associated with pain and physical dysfunction. Therefore, we evaluated the safety and effects of the TNF-α inhibitor adalimumab in patients with MPS I and II in a 32-week, randomized, double blind, placebo-controlled, crossover study of adalimumab at a dose of 20 mg (weight 15-<30 kg) or 40 mg (weight ≥ 30 kg) administered subcutaneously every other week or saline placebo for 16 weeks. Participants were evaluated at baseline, week 16, and week 32 with the Children's Health Questionnaire - Parent Form 50 (CHQ-PF50), the Pediatric Pain Questionnaire (PPQ), range-of-motion (ROM) measurements, anthropometry, six-minute walk test (6MWT), hand dynamometer, and laboratory evaluations for safety. The primary outcome was safety and primary efficacy outcome was bodily pain (BP) measured by the CHQ-PF50. Two subjects, one with MPS I and one with MPS II, completed the study. Adalimumab was well tolerated and there were no serious adverse events. Standardized BP scores for age and gender were higher (i.e. less pain) at the end of the treatment versus placebo phase for both subjects. Subject #1 became unblinded during treatment due to skin erythema. Behavior measured by both CHQ-PF50 and parental report improved during treatment compared to placebo in both subjects. ROM improved by > 5° in seven of eight joints in Subject #1 and five of eight joints in Subject #2 (range 7.0° to 52.8°). There was no change in the PPQ, 6MWT, or hand dynamometer. Data from this small pilot study suggest that treatment with adalimumab is safe, tolerable, and may improve ROM, physical function, and possibly pain, in children with MPS I or II. However, additional clinical trials are needed before this therapy should be recommended as part of clinical care

Neurogenic to Gliogenic Fate Transition Perturbed by Loss of HMGB2

Mouse cortical development relies heavily on a delicate balance between neurogenesis and gliogenesis. The lateral ventricular zone produces different classes of excitatory pyramidal cells until just before birth, when the production of astroglia begins to prevail. Epigenetic control of this fate shift is of critical importance and chromatin regulatory elements driving neuronal or astroglial development play an vital role. Different classes of chromatin binding proteins orchestrate the transcriptional repression of neuronal-specific genes, while allowing for the activation of astrocyte-specific genes. Through proteomic analysis of embryonic neural progenitor cells (NPCs) our group had previously identified high mobility group B2 (HMGB2), a chromatin protein dynamically expressed throughout embryonic development. In the current study using cultures of perinatal NPCs from HMGB2+/+ and HMGB2-/- mice we discovered that vital elements of the polycomb group (PcG) epigenetic complexes polycomb repressive complexes 1 and 2 (PRC1/2) were downregulated during the differentiation process of HMGB2-null NPCs. These epigenetic changes led to downstream changes in specific histone modification levels, specifically the trimethylation of H3K27, and a subsequent shift in the perinatal neurogenesis to gliogenesis fate transition. Collectively these results demonstrate that chromatin binding proteins, such as HMGB2, can have significant effects on the epigenetic landscape of perinatal neural stem/progenitor cells

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs

RNAs assume sophisticated structures that are active in myriad cellular processes. In this review, we highlight newly identified ribozymes, riboswitches, and small RNAs, some of which control the function of cellular metabolic and gene expression networks. We then examine recent developments in genome-wide RNA structure probing technologies that are yielding new insights into the structural landscape of the transcriptome. Finally, we discuss how these RNA ‘structomic’ methods can address emerging questions in RNA systems biology, from the mechanisms behind long non-coding RNAs to new bases for human diseases

Environmental Correlates of Breeding in the Crested Caracara (Caracara cheriway)

We evaluated the influence of weather on reproduction of the Crested Caracara (Caracara cheriway) in an agricultural landscape in south-central Florida. We used a mixed logistic-regression modeling approach within an information-theoretic framework to examine the influence of total rainfall, rainfall frequency, and temperature on the number of breeding pairs, timing of breeding, nest success, and productivity of Crested Caracaras during 1994–2000. The best models indicated an influence of rainfall frequency and laying period on reproduction. More individuals nested and more pairs nested earlier during years with more frequent rainfall in late summer and early fall. Pairs that nested later in each breeding season had smaller clutches, lower nest success and productivity, and higher probability of nest failure. More frequent rainfall during early spring months that are usually characterized by water deficit (March–May), more frequent rainfall during the fall drawdown period (September–November), and a shorter winter dry period showed some association with higher probability of brood reduction and lower nest success. The proportion of nests that failed was higher in wet years, when total rainfall during the breeding season (September–April) was \u3e10% above the 20-year average. Rainfall may influence reproduction in Crested Caracaras indirectly through food resources. As total rainfall increased during February–April, when most pairs are feeding nestlings or dependent fledglings, the proportion of drawdown-dependent species (those that become available as rainfall decreases and wetlands become isolated and shallow) in the diet of Crested Caracaras declined, which may indicate reduced availability of foraging habitat for this primarily terrestrial raptor

De Novo Microdeletion Spanning YWHAE and CRK in an Individual with Intellectual Disability and Stunted Growth

In this report, we present a case of a 20-year-old female with congenital intellectual disability, stunted growth, and hypothyroidism. Competitive genetic hybridization (CHG) revealed a loss of a portion of 17p13.3 at least 195 Kb in size, not present in either parent. This area of chromosome 17 is associated with Miller-Dieker Syndrome (MDS) and Isolated Lissencephaly Sequence (ILS), but these conditions are related predominantly to PAFAH1B1, which is not included in the patient’s deletion

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

SummaryThe Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service.Availability and implementationRCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org)