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Apolipoprotein L1 (APOL1)-associated focal segmental glomerulosclerosis (FSGS) is the dominant form of FSGS in Black individuals. There are no targeted therapies for this condition, in part because the molecular mechanisms underlying APOL1's pathogenic contribution to FSGS are incompletely understood. Studying the transcriptomic landscape of APOL1 FSGS in patient kidneys is an important way to discover genes and molecular behaviors that are unique or most relevant to the human disease. With the hypothesis that the pathology driven by the high-risk APOL1 genotype is reflected in alteration of gene expression across the glomerular transcriptome, we compared expression and co-expression profiles of 15,703 genes in 16 Black patients with FSGS at high-risk vs 14 Black patients with a low-risk APOL1 genotype. Expression data from APOL1-inducible HEK293 cells and normal human glomeruli were used to pursue genes and molecular pathways uncovered in these studies. We discovered increased expression of APOL1 and nine other significant differentially expressed genes in high-risk patients. This included stanniocalcin, which has a role in mitochondrial and calcium-related processes along with differential correlations between high- and low-risk APOL1 and metabolism pathway genes. There were similar correlations with extracellular matrix- and immune-related genes, but significant loss of co-expression of mitochondrial genes in high-risk FSGS, and an NF-κB-down regulating gene, NKIRAS1, as the most significant hub gene with strong differential correlations with NDUF family (mitochondrial respiratory genes) and immune-related (JAK-STAT) genes. Thus, differences in mitochondrial gene regulation appear to underlie many differences observed between high- and low-risk Black patients with FSGS.

Precise deposition of CpG methylation is critical for mammalian development and tissue homeostasis and is often dysregulated in human diseases. The localization of de novo DNA methyltransferase DNMT3A is facilitated by its PWWP domain recognizing histone H3 lysine 36 (H3K36) methylation(1,2) and is normally depleted at CpG islands (CGIs)(3). However, methylation of CGIs regulated by Polycomb repressive complexes (PRCs) has also been observed(4–8). Here, we report that DNMT3A PWWP domain mutations identified in paragangliomas(9) and microcephalic dwarfism(10) promote aberrant localization of DNMT3A to CGIs in a PRC1-dependent manner. DNMT3A PWWP mutants accumulate at regions containing PRC1-mediated formation of monoubiquitylated histone H2A lysine 119 (H2AK119ub), irrespective of the amounts of PRC2-catalyzed formation of trimethylated histone H3 lysine 27 (H3K27me3). DNMT3A interacts with H2AK119ub-modified nucleosomes through a putative amino-terminal ubiquitin-dependent recruitment region, providing an alternative form of DNMT3A genomic targeting that is augmented by the loss of PWWP reader function. Ablation of PRC1 abrogates localization of DNMT3A PWWP mutants to CGIs and prevents aberrant DNA hypermethylation. Our study implies that a balance between DNMT3A recruitment by distinct reader domains guides de novo CpG methylation and may underlie the abnormal DNA methylation landscapes observed in select human cancer subtypes and developmental disorders.

We report a novel platform [native capillary zone electrophoresis–top-down mass spectrometry (nCZE–TDMS)] for the separation and characterization of whole nucleosomes, their histone subunits, and post-translational modifications (PTMs). As the repeating unit of chromatin, mononucleosomes (Nucs) are an ~200 kDa complex of DNA and histone proteins involved in the regulation of key cellular processes central to human health and disease. Unraveling the covalent modification landscape of histones and their defined stoichiometries within Nucs helps to explain epigenetic regulatory mechanisms. In nCZE–TDMS, online Nuc separation is followed by a three-tier tandem MS approach that measures the intact mass of Nucs, ejects and detects the constituent histones, and fragments to sequence the histone. The new platform was optimized with synthetic Nucs to significantly reduce both sample requirements and cost compared to direct infusion. Limits of detection were in the low-attomole range, with linearity of over ~3 orders of magnitude. The nCZE–TDMS platform was applied to endogenous Nucs from two cell lines distinguished by overexpression or knockout of histone methyltransferase NSD2/MMSET, where analysis of constituent histones revealed changes in histone abundances over the course of the CZE separation. We are confident the nCZE–TDMS platform will help advance nucleosome-level research in the fields of chromatin and epigenetics.

In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g., K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has broader extension. Here we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on thecisH3 tail, as determined with fully-defined heterotypic nucleosomes.In vivo, H3 tail acetylation is directly and dynamically coupled withcisH3K4 methylation levels. Together, these observations reveal an acetylation ‘chromatin switch’ on the H3 tail that modulates read-write accessibility in nucleosomes and resolve the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.

Clot in Transit in COVID-19 Introduction: Thromboembolism is a known complication of COVID-19, frequently occurring in patients receiving deep venous thrombosis (DVT) prophylaxis. This case report describes a patient with COVID-19 on DVT prophylaxis who had no other risk factors and developed a pulmonary embolism (PE) and subsequently was found to have a clot in transit in the right ventricular outflow tract on echocardiography. Case Report: 53-year-old male with no previous history of tobacco use, venous thromboembolism, malignancy, or clotting disorder was admitted with acute hypoxemic respiratory failure due to COVID-19. On initial examination, the patient was found to be hypoxic and tachycardic, requiring high flow nasal cannula. Chest x-ray showed multifocal airspace opacities consistent with COVID-19 pneumonia. CT pulmonary angiography was performed due to hypoxia and tachycardia, which revealed no evidence of PE. Laboratory results showed elevated inflammatory markers and a D-dimer of 1,700. The patient was admitted and started on dexamethasone, remdesivir, and subcutaneous heparin for DVT prophylaxis. The patient improved and oxygen was weaned down. On day 6 of hospitalization the patient developed acute dyspnea, worsening hypoxia, and tachycardia. Repeat CT pulmonary angiogram revealed multiple PE and therapeutic enoxaparin was started. An echocardiogram was performed and revealed an enlarged right ventricle and a large multi-lobulated hyperechoic mass in the right ventricular outflow tract, consist with a clot in transit. Interventional Radiology successfully performed aspiration thrombectomy, and the patient quickly improved and was discharged home on Apixaban. Discussion: As COVID-19 patients often present with hypoxemic respiratory failure and elevated D-dimer, it can be challenging for physicians to determine who should be screened for the presence of PE. Our case demonstrates the severity of hypercoagulability in COVID-19 and the importance of maintaining high suspicion for thromboembolism in COVID-19, even in patients receiving appropriate DVT prophylaxis and without risk factors. SARS-CoV-2 has been shown to bind to ACE2 on platelets and enhance thrombosis, indicating that infection itself can lead to DVT or PE. Even patient under guideline directed DVT prophylaxis frequently develop venous thromboembolism. Further investigation into how to prevent and catch pulmonary embolism in COVID-19 patients is needed. Methods such as daily D-dimer level trending, may be helpful in identifying patients at higher risk of developing PE or DVT but more research is needed to identify ideal cutoffs and DVT prophylaxis in these patients.

Rationale & Objective The current classification system for focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD) does not fully capture the complex structural changes in kidney biopsies, nor the clinical and molecular heterogeneity of these diseases. Study Design Prospective observational cohort study. Setting & Participants N=221 MCD and FSGS patients enrolled in the Nephrotic Syndrome Study Network (NEPTUNE). Exposures The NEPTUNE Digital Pathology Scoring System (NDPSS) was applied to generate scores for 37 glomerular descriptors. Outcomes Time from biopsy to complete proteinuria remission, time from biopsy to kidney disease progression (40% eGFR decline or kidney failure), and eGFR over time. Analytical Approach Cluster analysis was used to group patients with similar morphologic characteristics. Glomerular descriptors and patient clusters were assessed for associations with outcomes using adjusted Cox models and linear mixed models. Messenger RNA from glomerular tissue was used to assess differentially expressed genes between clusters and identify genes associated with individual descriptors driving cluster membership. Results Three clusters were identified: X (N=56), Y (N=68), and Z (N=97). Clusters Y and Z had higher probabilities of proteinuria remission (HR [95% CI]= 1.95 [0.99, 3.85] and 3.29 [1.52, 7.13], respectively), lower hazards of disease progression 0.22 [0.08, 0.57] and 0.11 [0.03, 0.45], respectively), and lower loss of eGFR over time compared with X. Cluster X had 1920 differentially expressed genes compared to Y+Z, which reflected activation of pathways of immune response and inflammation. Six descriptors driving the clusters individually correlated with clinical outcomes and gene expression. Limitations Low prevalence of some descriptors and biopsy at a single time point. Conclusions The NDPSS allows for categorization of FSGS/MCD patients into clinically and biologically relevant subgroups, and uncovers histologic parameters associated with clinical outcomes and molecular signatures not included in current classification systems.

We report a novel platform (native capillary zone electrophoresis – top-down mass spectrometry; nCZE-TDMS) for the separation and characterization of whole nucleosomes, their histone subunits, and PTMs. As the repeating unit of chromatin, mononucleosomes (Nucs) are a ~200 kDa complex of DNA and histone proteins involved in the regulation of key cellular processes central to human health and disease. Unraveling the covalent modification landscape of histones and their defined stoichiometries within Nucs helps to explain epigenetic regulatory mechanisms. In nCZE-TDMS, online Nuc separation is followed by a three-tier tandem MS approach that measures the intact mass of Nucs, ejects and detects the constituent histones, and fragments to sequence the histone. The new platform was optimized with synthetic Nucs to reduce both sample requirements and cost significantly compared to direct infusion. Limits of detection were in the low attomole range, with linearity over ~three orders of magnitude. The nCZE-TDMS platform was applied to endogenous Nucs from two cell lines distinguished by overexpression or knockout of histone methyltransferase NSD2/MMSET, where analysis of constituent histones revealed changes in histone abundances over the course of the CZE separation. We are confident the nCZE-TDMS platform will help advance nucleosome-level research in the fields of chromatin and epigenetics.

Channelized agricultural headwater streams are common throughout agricultural watersheds in the midwestern United States. Understanding fish-habitat relationships within these streams will provide information that can assist with developing conservation and restoration strategies for these degraded streams. From spring 2006 to fall 2010, we collected fishes and measured riparian habitat, instream habitat, and water chemistry variables from seven sites in Cedar Creek, Indiana, and 14 sites in Upper Big Walnut Creek, Ohio. We found that fish community structure was more strongly correlated with instream habitat than riparian habitat or water chemistry in both watersheds. We also observed interrelationships among instream habitat, watershed size, and fish communities within both watersheds that suggest that the hydrological changes that occur with increasing watershed size are the underlying factor for fish community changes that occur with increasing watershed size. Our results suggest that conservation and restoration efforts within channelized agricultural headwater streams in the midwestern United States, where nutrients and herbicide concentrations are low, need to address physical habitat degradation to positively influence fish community structure.

Application of pesticides within the watersheds of agricultural streams typically leads to increased instream pesticide concentrations that reduces water quality and threatens aquatic life. Pesticide reduction practices that reduce pesticide application within agricultural watersheds should reduce concentrations of pesticides within agricultural streams. Unfortunately, the influence of pesticide reduction practices on pesticides and the biota within agricultural headwater streams has not been empirically evaluated. We evaluated the watershed scale influence of atrazine reduction practices on pesticides, pesticide mixtures, and fish communities within channelized agricultural headwater streams in central Ohio. Water samples for pesticide measurements and fishes were collected in the spring and summer from a treatment stream (watershed size – 3.89 km2) that received atrazine reduction practices within 26 to 31% of its watershed during the first two years and then the watershed usage of these practices was reduced to less than 6% in the last four years. We also collected water samples and fishes during the same time from a control stream (watershed size 4.54 km2) that received atrazine reduction practices in 6% or less of its watershed during the study. Only three of 15 pesticide response variables and two of 15 fish community response variables indicated a potential effect of atrazine reduction practices. Mean differences in atrazine desethyl concentration, atrazine desethyl percent occurrence, and the number of pesticides between the control and treatment streams were greater during the time period with atrazine reduction practices than the time period without atrazine reduction practices. Mean differences in trophic guild richness and fish species composition similarity between the control and treatment streams occurred between time periods with and without atrazine reduction practices only during the summer. Our results suggest that implementing atrazine reduction practices to reduce atrazine usage within small portions (30% or less) of the watersheds of channelized agricultural headwater streams may not influence pesticides, pesticide mixtures, and fish community structure during the spring and summer.

Crayfishes (Decapoda) are common inhabitants of agricultural headwater streams in the Midwestern USA that have been impacted by physical habitat degradation and contamination by agricultural pollutants. The frequency and severity of injuries within crayfish communities are indicators of crayfish aggression, which is influenced by physical, chemical, and biotic factors. Previous studies have not evaluated the relationships of the frequency and severity of crayfish injuries with physical habitat quality, water quality, and biotic factors within agricultural headwater streams. Understanding these relationships will assist with determining if crayfish injury variables can serve as an indicator of physical habitat quality or water quality in these small degraded streams. We sampled crayfishes, documented the frequency and type of injuries, and measured instream habitat and water chemistry in 2014 and 2015 within 12 agricultural headwater streams in Indiana, Michigan, and Ohio. We documented five native crayfish species from 1641 adult captures. The most abundant species were Faxonius rusticus, Faxonius immunis, and Faxonius propinquus. Linear mixed effect model analyses indicated that four crayfish injury response variables were positively correlated (p

Conservation agriculture practices (CAs) have been internationally promoted and used for decades to enhance soil health and mitigate soil loss. An additional benefit of CAs has been mitigation of agricultural runoff impacts on aquatic ecosystems. Countries across the globe have agricultural agencies that provide programs for farmers to implement a variety of CAs. Increasingly there is a need to demonstrate that CAs can provide ecological improvements in aquatic ecosystems. Growing global concerns of lost habitat, biodiversity, and ecosystem services, increased eutrophication and associated harmful algal blooms are expected to intensify with increasing global populations and changing climate. We conducted a literature review identifying 88 studies linking CAs to aquatic ecological responses since 2000. Most studies were conducted in North America (78%), primarily the United States (73%), within the framework of the USDA Conservation Effects Assessment Project. Identified studies most frequently documented macroinvertebrate (31%), fish (28%), and algal (20%) responses to riparian (29%), wetland (18%), or combinations (32%) of CAs and/or responses to eutrophication (27%) and pesticide contamination (23%). Notable research gaps include better understanding of biogeochemistry with CAs, quantitative links between varying CAs and ecological responses, and linkages of CAs with aquatic ecosystem structure and function.

The widespread use of stream channelization and subsurface tile drainage for removing water from agricultural fields has led to the development of numerous channelized agricultural headwater streams within agricultural watersheds of the Midwestern United States, Canada, and Europe. Channelized agricultural headwater streams have been documented to serve as habitat for amphibians, but information on amphibian habitat relationships within these streams is lacking and needed for developing effective conservation strategies. We quantified instream habitat, water chemistry, and sampled amphibians from seven sites in three channelized streams in Cedar Creek, Indiana in 2008 and 2009 and five sites in five channelized streams in Upper Big Walnut Creek, Ohio in 2009. We conducted an indirect gradient analysis involving the use of principal component analysis and generalized linear mixed effect model analysis to determine which variables had the greatest influence on amphibian community and population structure. Overall, amphibian community and population structure was most strongly correlated with water chemistry rather than instream habitat within channelized agricultural headwater streams in Indiana and Ohio. Eleven of 12 amphibian response variables were most strongly correlated with either a water chemistry gradient of nitrate + nitrite and acetochlor, a gradient of total nitrogen and ammonia, or a gradient of simazine and total phosphorus. Only one amphibian response variable was most strongly correlated with an instream habitat gradient of dissolved oxygen and water depth. Our results suggest that conservation strategies that target reductions of nutrients and herbicides will provide the greatest benefits for amphibians within channelized agricultural headwater streams.

Agricultural land use leads to changes in physical and chemical characteristics of sediment that influence macroinvertebrate community diversity and abundance in streams. To the best of our knowledge the joint influence of sediment&rsquo, s physical and chemical characteristics on stream macroinvertebrates has not been assessed. We measured sediment&rsquo, s physical and chemical characteristics and sampled macroinvertebrates in eight agricultural headwater streams in Indiana, Michigan, and Ohio, United States, in 2017 and 2018 to determine the physical and chemical conditions of the sediment, to evaluate the relationships between physical and chemical characteristics of the sediment, and the relationship of macroinvertebrate communities with the sediment&rsquo, s physical and chemical characteristics. Sediments within most sites were dominated by sand or silt. pH was suitable for macroinvertebrates and nitrate, herbicide, and trace metal concentrations were below concentration levels anticipated to affect macroinvertebrate survival. Linear mixed effect model analysis results indicated that a physical gradient of percent small gravel and percent silt was positively correlated (p &lt, 0.05) with a chemical gradient of potassium concentrations, magnesium concentrations, and percent total nitrogen in the sediments. Our linear mixed effect model analysis results also indicated that Invertebrate Community Index scores were negatively correlated (p &lt, 0.05) with a chemical gradient of simazine and calcium concentrations and were negatively correlated (p &lt, 0.05) with physical gradient of grain size diversity and percent sand. Our results suggest that watershed management plans need to address physical and chemical degradation of sediment to improve macroinvertebrate biotic integrity within agricultural headwater streams in the Midwestern United States.

The aberrant transcription factor EWS FLI1 drives Ewing sarcoma but its molecular function is not completely understood. We find that EWS FLI1 reprograms gene regulatory circuits in Ewing sarcoma by directly inducing or repressing enhancers. At GGAA repeat elements which lack evolutionary conservation and regulatory potential in other cell types EWS FLI1 multimers induce chromatin opening and create de novo enhancers that physically interact with target promoters. Conversely EWS FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild type ETS transcription factors. These divergent chromatin remodeling patterns repress tumor suppressors and mesenchymal lineage regulators while activating oncogenes and potential therapeutic targets such as the kinase VRK1. Our findings demonstrate how EWS FLI1 establishes an oncogenic regulatory program governing both tumor survival and differentiation.

Summary Conversion of land for agriculture has led to the channelisation of headwater streams and reduced water quality. Resident fish populations are expected to be challenged under such conditions and may experience declines that lead to a loss of neutral genetic variation. However, species-specific responses to recent ecological changes in stream condition and/or range expansion following glacial retreat can also influence the pattern of genetic variation found within and among contemporary populations. To evaluate the relative roles of contemporary and ancient scenarios that are hypothesised to affect the genetics of populations in streams, we studied the creek chub (Semotilus atromaculatus), a common species that is tolerant of stream degradation. We screened eight microsatellite loci on 308 individuals originating from ditches and streams surrounded by agricultural and forested land cover within the St. Joseph River catchment in north-eastern Indiana and southern Michigan, U.S.A. We found weak population structure associated with land cover and, in contrast to expectation, higher allelic richness in agricultural streams. Using Bayesian coalescent modelling, the strongest pattern found within the data set was evidence of a population decline throughout the catchment that most likely preceded stream channelisation and land conversion. The results illustrate the complexity of using neutral genetic variation of populations to assay stream quality. Tolerant species may have increased gene flow in channelised streams that leads to an increase in genetic variation. Meanwhile, post-glacial landscape change and subsequent colonisation of nascent freshwater streams appears to shape genetic variation regardless of contemporary land use.

In this paper, we extend the concept of the contrast sensitivity function - used to evaluate video projectors - to the evaluation of haptic devices. We propose using human observers to determine if vibrations rendered using a given haptic device are accompanied by artifacts detectable to humans. This determination produces a performance measure that carries particular relevance to applications involving texture rendering. For cases in which a device produces detectable artifacts, we have developed a protocol that localizes deficiencies in device design and/or hardware implementation. In this paper, we present results from human vibration detection experiments carried out using three commercial haptic devices and one high performance voice coil motor. We found that all three commercial devices produced perceptible artifacts when rendering vibrations near human detection thresholds. Our protocol allowed us to pinpoint the deficiencies, however, and we were able to show that minor modifications to the haptic hardware were sufficient to make these devices well suited for rendering vibrations, and by extension, the vibratory components of textures. We generalize our findings to provide quantitative design guidelines that ensure the ability of haptic devices to proficiently render the vibratory components of textures.

Many headwater streams in the midwestern United States were channelized for agricultural drainage. Conservation practices are implemented to reduce nutrient, pesticide, and sediment loadings within these altered streams. The impact of these practices is not well understood because their ecological impacts have not been evaluated and the relationships between water chemistry and fishes are not well understood. We evaluated relationships between water chemistry and fish communities within channelized headwater streams of Cedar Creek, Indiana, and Upper Big Walnut Creek, Ohio. Measurements of water chemistry, hydrology, and fishes have been collected from 20 sites beginning in 2005. Multiple regression analyses indicated that the relationships between water chemistry and fish communities were weak, but significant (P < 0.05). Fish communities exhibited negative relationships with ammonium and nitrate plus nitrite and positive relationships with dissolved oxygen, pH, and metolachlor. The strongest observed relationships occurred within those regression models that included a combination of nutrients, herbicides, and physicochemical variables. Multiple regression analyses also indicated that five water chemistry variables exhibited significant relationships (P < 0·05) with hydrology. Our results suggest that if water chemistry is the focus of a conservation plan, then the most effective conservation practices may be those that have a combined influence on nutrients, herbicides, and physicochemical variables. Additionally, the use of a combination of conservation practices to address physical habitat and water chemistry degradation is most likely to provide the greatest benefits for fish communities within channelized headwater streams.

The low-temperature vapor deposition of silicon thin films and the ion implantation of silicon can result in the formation of amorphous silicon layers on a crystalline silicon substrate. These amorphous layers can be crystallized by a thermally activated solid-phase epitaxial (SPE) growth process. The transformations are rapid and initiate at the buried amorphous to crystalline interface within the film. The initial stages of the transformation are investigated here using a molecular dynamics simulation approach based upon a recently proposed bond order potential for silicon. The method is used first to predict an amorphous structure for a rapidly cooled silicon melt. The radial distribution function of this structure is shown to be similar to that observed experimentally. Molecular dynamics simulations of its subsequent crystallization indicate that the early stage, rate limiting mechanism appears to be removal of tetrahedrally coordinated interstitial defects in the nominally crystalline region just behind the advancing amorphous to crystalline transition front. The activation barriers for this interstitials migration within the bulk crystal lattice are calculated and are found to be comparable to the activation energy of the overall solid-phase epitaxial growth process simulated here.

The atomic-scale structures and properties of thin films are critically determined by the various kinetic processes activated during their atomic assembly. Molecular dynamics simulations of growth allow these kinetic processes to be realistically addressed at a timescale that is difficult to reach using ab initio calculations. The newest approaches have begun to enable the growth simulation to be applied for a wide range of materials. Embedded atom method potentials can be successfully used to simulate the growth of closely packed metal multilayers. Modified charge transfer ionic + embedded atom method potentials are transferable between metallic and ionic materials and have been used to simulate the growth of metal oxides on metals. New analytical bond order potentials are now enabling significantly improved molecular dynamics simulations of semiconductor growth. Selected simulations are used to demonstrate the insights that can be gained about growth processes at surfaces.

Interatomic potentials for modelling the vapour phase growth of semiconductor thin films must be able to describe the breaking and making of covalent bonds in an efficient format so that molecular dynamics simulations of thousands or millions of atoms may be performed. We review the derivation of such potentials, focusing upon the emerging role of the bond-based analytic bond-order potential (BOP). The BOP is derived through systematic coarse graining from the electronic to the atomistic modelling hierarchies. In a first step, the density functional theory (DFT) electronic structure is simplified by introducing the tight-binding (TB) bond model whose parameters are determined directly from DFT results. In a second step, the electronic structure of the TB model is coarse grained through atom-centered moments and bond-centered interference paths, thereby deriving the analytic form of the interatomic BOP. The resultant σ and π bond orders quantify the concept of single, double, triple and conjugate bonds in hydrocarbon systems and lead to a good treatment of radical formation. We show that the analytic BOP is able to predict accurately structural energy differences in quantitative agreement with TB calculations. The current development of these potentials for simulating the growth of Si and GaAs thin films is discussed.

Kitt Peak Coronal Velocity Experiment

The effects of a small-scale, rectangular synthetic air jet on the local convective heat transfer from a flat, heated surface were measured experimentally. The synthetic jet impinges normal to the surface and induces small-scale motions by zero-net mass flux, time-periodic entrainment, and ejection of ambient air at frequencies whose periods are far higher than the characteristic thermal time scale. The velocity field between the jet orifice and the target plate is measured in planar cross sections using particle image velocimetry and is related to the local heat transfer from the plate. The present work suggests that synthetic jets can lead to substantial enhancement of the local heat transfer from heated surfaces by strong mixing that disrupts the surface thermal boundary layer. The dependence of the local heat transfer coefficient on the primary parameters of jet motion is characterized over a range of operating conditions.

The photochemistry of the 13-desmethyl (DM) analogue of bacteriorhodopsin (BR) is examined by using spectroscopy, molecular orbital theory, and chromophore extraction followed by conformational analysis. The removal of the 13-methyl group permits the direct photochemical formation of a thermally stable, photochemically reversible state, P1(DM) (lambda(max) = 525 nm), which can be generated efficiently by exciting the resting state, bR(DM) with yellow or red light (lambda590 nm). Chromophore extraction analysis reveals that the retinal configuration in P1(DM) is 9-cis, identical to that of the retinal configuration in the native BR P1 state. Fourier transform infrared and Raman experiments on P1(DM) indicate an anti configuration around the C15=N bond, as would be expected of an O-state photoproduct. However, low-temperature spectroscopy and ambient, time-resolved studies indicate that the P1(DM) state forms primarily via thermal relaxation from the L(D)(DM) state. Theoretical studies on the BR binding site show that 13-dm retinal is capable of isomerizing into a 9-cis configuration with minimal steric hindrance from surrounding residues, in contrast to the native chromophore in which surrounding residues significantly obstruct the corresponding motion. Analysis of the photokinetic experiments indicates that the Arrhenius activation energy of the bR(DM) --P1(DM) transition in 13-dm-BR is less than 0.6 kcal/mol (vs 22 +/-5 kcal/mol measured for the bR --P (P1 and P2) reaction in 85:15 glycerol:water suspensions of wild type). Consequently, the P1(DM) state in 13-dm-BR can form directly from all-trans, 15-anti intermediates (bR(DM) and O(DM)) or all-trans, 15-syn (K(D)(DM)/L(D)(DM)) intermediates. This study demonstrates that the 13-methyl group, and its interactions with nearby binding site residues, is primarily responsible for channeling one-photon photochemical and thermal reactions and is limited to the all-trans and 13-cis species interconversions in the native protein.

Poorly water-soluble compounds are being found with increasing frequency among pharmacologically active new chemical entities, which is a major concern to the pharmaceutical industry. Some particle engineering technologies have been shown to enhance the dissolution of many promising new compounds that perform poorly in formulation and clinical studies (Rogers et. al., Drug Dev Ind Pharm 27:1003-1015). One novel technology, controlled precipitation, shows significant potential for enhancing the dissolution of poorly soluble compounds. In this study, controlled precipitation is introduced; and process variables, such as mixing zone temperature, are investigated. Finally, scale-up of controlled precipitation from milligram or gram to kilogram quantities is demonstrated.Dissolution enhancement capabilities were established using two poorly water-soluble model drugs, danazol and naproxen. Stabilized drug particles from controlled precipitation were compared to milled, physical blend, and bulk drug controls using particle size analysis (Coulter), X-ray powder diffraction (XRD), scanning electron microscopy (SEM), dissolution testing (USP Apparatus 2), and residual solvent analysis.Stabilized nano- and microparticles were produced from controlled precipitation. XRD and SEM analyses confirmed that the drug particles were crystalline. Furthermore, the stabilized particles from controlled precipitation exhibited significantly enhanced dissolution properties. Residual solvent levels were below FDA limits.Controlled precipitation is a viable and scalable technology that can be used to enhance the dissolution of poorly water-soluble pharmaceutical compounds.

Chitosan, a naturally occurring biopolymer, was used as a scaffold for the covalent binding of single-stranded DNA oligonucleotide probes in a fluorescence-based nucleic acid hybridization assay. Chitosan's pH dependent chemical and electrostatic properties enable its deposition on electrodes and metal surfaces, as well as on the bottom of microtiter plates. A combinatorial 96-well microtiter plate format was used to optimize chemistries and reaction conditions leading to hybridization experiments. We found the coupling of oligonucleotides using relatively common glutaraldehyde chemistry was quite robust. Our hybridization results for complementary ssDNA oligonucleotides (E. coli dnaK sequences) demonstrated linear fluorescence intensity with concentration of E. coli dnaK-specific oligonucleotide from 0.73 μM to 6.6 μM. Moreover, hybridization assays were specific as there was minimal fluorescence associated with noncomplementary groEL oligonucleotide. Finally, these results demonstrate the portability of a DNA hybridization assay based on covalent coupling to chitosan, which, in turn, can be deposited onto various surfaces. More arduous surface preparation techniques involving silanizing agents and hazardous washing reagents are eliminated using this technique. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 83: 646–652, 2003.

The ground and excited-state properties of peridinin in solution and in the peridinin-chlorophyll-protein (PCP) complex are studied by using one-photon and two-photon spectroscopy, solvent effects, and quantum theory. Two-photon excitation spectra, two-photon polarization data, and fluorescence spectra in CS2 reveal three low-lying excited singlet states in peridinin: a lowest-excited1Ag*--like state with a system origin at ∼16 200 cm-1, a 1Bu*+-like S2 state with a system origin at ∼19 300 cm-1, and a 1Bu*--like S3 state with a system origin at ∼22 000 cm-1. The 1Bu*+-like S2 state dominates the two-photon excitation spectrum of peridinin in solution and in PCP because of type II enhancement associated with a large oscillator strength (f ≈ 1.6) coupled with a change in dipole moment upon excitation (Δμ ≈ 3 D). Thus, the two-photon spectrum looks very much like the one-photon spectrum although weak vibronic bands of the 1Ag*--like state are observed at ∼17, ∼18.1, and ∼19.2 kK in the two-photon spectrum ...

Photochromic fluorinated indolylfulgides have been identified as potential candidates for a wide range of applications including optical switches, photoregulators of biological processes, and optical memory media. In humid environments or biological systems, hydrolytic stability is essential. In an effort to improve hydrolytic stability, a series of indolylfulgimides has been synthesized from a parent trifluoromethyl-substituted indolylfulgide. The nitrogen of the succinimide moiety is linked to either a dimethyl amino or one of seven substituted phenyl groups. The phenyl groups feature substituents with increasing electron-withdrawing ability. The spectral characteristics of each compound have been examined, revealing that the wavelength absorption maxima of each form increases with increasing electron-withdrawing ability of the substituted N-phenyl ring. The quantum yields of the photoreactions have been determined with the N-(phenyl)fulgimide showing a ring closure value of nearly 0.30 in toluene. In addition, the hydrolytic, thermal, and photochemical stabilities of each compound have been measured. The fulgimides exhibit at least a 200-fold enhancement of hydrolytic stability for the Z-form and over a 1000-fold enhancement for the C-form in comparison to the same form of the parent fulgide. The N-(2,3,5,6-tetrafluoro-4-trifluoromethylphenyl)fulgimide can undergo up to 3000 photochemical cycles (coloration followed by bleaching) before losing 20% of its initial absorbance at photostationary state.

The bacteriorhodopsin branched-photocycle intermediates P and Q are studied with respect to chromophore isomeric content, photochemical origin, kinetic heterogeneity, and photoreversibility. These blue-shifted species are compared to products with similar spectroscopic properties generated via thermal denaturation. We observe that the thermal and photochemical species differ in both isomeric content and binding site environment. Sequential two-photon activation of glycerol suspensions of bacteriorhodopsin containing low concentrations of water (

Bacteriorhodopsin (BR) is the photoactive proton pump found in the purple membrane of the salt marsh archaeon Halobacterium salinarum. Evolution has optimized this protein for high photochemical efficiency, thermal stability and cyclicity, as the organism must be able to function in a hot, stagnant and resource-limited environment. Photonic materials generated via organic chemistry have yet to surpass the native protein in terms of quantum efficiency or cyclicity. However, the native protein still lacks the overall efficiency necessary for commercial viability and virtually all successful photonic devices using bacteriorhodopsin are based on chemical or genetic variants of the native protein. We show that genetic engineering can provide significant improvement in the device capabilities of proteins and, in the case of bacteriorhodopsin, a 700-fold improvement has been realized in volumetric data storage. We conclude that semi-random mutagenesis and directed evolution will play a prominent role in future efforts in bioelectronic optimization.

As the other articles in this special issue well illustrate, work camps can be examined in depth from a variety of perspectives, each of which can yield interesting insights. But even survey data about the distribution of settlements across the landscape will often indicate similarities and differences in the archaeologically observed patterns. In this example, it is the differences that inspire questions about how factors such as technology, environment, class, and social structure influenced settlement patterns at two early-20th-century mining camps in southeastern Arizona.

We have developed a method for bacterial endospore detection based on the presence dipicolinic acid (dpa), a substance unique to endospores. Since the sensitivity of this technique correlates directly with the amount of dpa extracted from the spores, we examined several types of extraction techniques for their dpa extraction efficiency. The three main categories investigated are physical, germination, and chemical methods for liberation of dpa from B. subtilis endospores. Attention is concentrated on the speed, efficiency, and simplicity of the extraction techniques for optimization of endospore detection using terbium–dipicolinate photoluminescence. Although methods from all categories succeeded in extracting dpa, the technique utilizing heated dodecylamine (dda) extracted the majority of the available dpa in less than 3 min. Application of the dda extraction procedure to the terbium–dipicolinate photoluminescence method in conjunction with an increased detection capability resulted in a two-order of magnitude improvement in endospore detection. This combination of methods resulted the lowest reported limit of detection (LOD) (1000 CFU/ml) for a terbium–dipicolinate photoluminescence method in the shortest reported time (5–7 min) for the total procedure.

We describe a broad bandwidth lidar technology for the estimation of size distributions and refractive indices of aerosol clouds. The concept is to illuminate an aerosol cloud with a pulse of intense broadband light from a specially designed laser system, collect the backscattered light as a function of wavelength and analyse it with novel inversion algorithms. The laser system has a simultaneously broadband output between 1.4-1.8 µm in each pulse. This is in an eye-safe region and is optimal for detection of particles in the one to ten micrometre size range. A lidar simulation was performed to demonstrate the potential for the method and the broad bandwidth source is described and characterized for power and spectral output.

Fluorinated indolylfulgides are a class of photochromic organic compounds with potential applications in the areas of optical memory and optical switches. Absorption spectra, quantum yields, and thermal stability have been measured for a series of fluorinated adamantylidene indolylfulgides. The cyclizable form of the trifluoromethyl-substituted 5-methoxy-1,2-dimethylindolylfulgide displays the longest absorbance maxima reported for the fulgide family. The thermal stability of the cyclizable form of the fluorinated adamantylidene indolylfulgides was greater than that of their corresponding fluorinated isopropylidene analogs, as expected based upon the mechanism of decomposition for isopropylidene analogs. The pentafluoroethyl-substituted adamantylidene indolylfulgide showed only a 27% loss in absorbance after 5 weeks at 80 °C in a poly(methylmethacrylate) film. These studies have highlighted the rational design of a thermally stable cyclizable form for fluorinated indolylfulgides.

Objective To assess primary care physicians’ (PCPs) knowledge of type 2 diabetes screening guidelines (American Diabetes Association (ADA) and 2008 US Preventive Services Task Force (USPSTF)), the alignment between their self-reported adherence and actual practice, and how often PCPs recommended diabetes prevention and self-management education programs (DPP/DSME). Research design and methods An online survey of PCPs to understand knowledge and adherence toward use of USPSTF/ADA guidelines and recommendation of DPP/DSME. Patient data from electronic medical records (EMRs) for each PCP were used to identify rates of screening in eligible patients as per guidelines and the two sources were compared to assess concordance. Results Of 305 surveyed physicians, 38% reported use of both guidelines (33% use ADA only, 25% USPSTF only). Approximately one-third of physicians who reported use of USPSTF/ADA guidelines had non-concordant EMR data. Similarly, while most PCPs reported they are ‘very likely’ to screen patients with risk factors listed in guidelines, for each criterion at least one-fourth (24%) of PCPs survey responses were non-concordant with EMRs. PCPs reported they provide referral to DPP and DSME on average to 45% and 67% of their newly diagnosed patients with pre-diabetes and diabetes, respectively. Conclusion Findings show disconnect between PCPs’ perceptions of adherence to screening guidelines and actual practice, and highlight limited referrals to DPP/DSME programs. More research is needed to understand barriers to guideline consistent screening and uptake of DPP/DSME, particularly in light of recent policy changes such as the linking USPSTF criteria to reimbursement and expected Medicare DPP reimbursement in 2018.

This chapter explores the use of the “racial grotesque” as a satiric technique in several recent works in a variety of media, including sculpture and internet videos. This chapter argues that the “racial grotesque” is employed by artists to recontextualize material objects associated with the legacy of slavery. Ultimately, these material objects bear witness to and address the nation’s attempt to erase America’s complicated racial history

Sensory rhodopsin II (SRII) is unique among the archaeal rhodopsins in having an absorption maximum near 500 nm, blue shifted roughly 70 nm from the other pigments. In addition, SRII displays vibronic structure in the lambda(max) absorption band, whereas the other pigments display fully broadened band maxima. The molecular origins responsible for both photophysical properties are examined here with reference to the 2.4 A crystal structure of sensory rhodopsin II (NpSRII) from Natronobacterium pharaonis. We use semiempirical molecular orbital theory (MOZYME) to optimize the chromophore within the chromophore binding site, and MNDO-PSDCI molecular orbital theory to calculate the spectroscopic properties. The entire first shell of the chromophore binding site is included in the MNDO-PSDCI SCF calculation, and full single and double configuration interaction is included for the chromophore pi-system. Through a comparison of corresponding calculations on the 1.55 A crystal structure of bacteriorhodopsin (bR), we identify the principal molecular mechanisms, and residues, responsible for the spectral blue shift in NpSRII. We conclude that the major source of the blue shift is associated with the significantly different positions of Arg-72 (Arg-82 in bR) in the two proteins. In NpSRII, this side chain has moved away from the chromophore Schiff base nitrogen and closer to the beta-ionylidene ring. This shift in position transfers this positively charged residue from a region of chromophore destabilization in bR to a region of chromophore stabilization in NpSRII, and is responsible for roughly half of the blue shift. Other important contributors include Asp-201, Thr-204, Tyr-174, Trp-76, and W402, the water molecule hydrogen bonded to the Schiff base proton. The W402 contribution, however, is a secondary effect that can be traced to the transposition of Arg-72. Indeed, secondary interactions among the residues contribute significantly to the properties of the binding site. We attribute the increased vibronic structure in NpSRII to the loss of Arg-72 dynamic inhomogeneity, and an increase in the intensity of the second excited (1)A(g)(-) -like state, which now appears as a separate feature within the lambda(max) band profile. The strongly allowed (1)B(u)(+)-like state and the higher-energy (1)A(g)(-) -like state are highly mixed in NpSRII, and the latter state borrows intensity from the former to achieve an observable oscillator strength.

We describe a method of detecting bacterial endospores via quantitation of calcium uniquely associated with spore suspensions. The sensor is created by combining a fluorescent calcium-sensitive indicator, calcein, in a viscous membrane on planar, silica glass coupons. The sensor coupon is affixed to the distal end of an optical fiber, which provides excitation light and collects the fluorescence emission. Aqueous micro-droplets of bacterial spores are added to the sensor and the resulting increase in fluorescence intensity is monitored. This assay effectively exploits the high concentration of calcium ion found in the spore core and expressed on the surface, and fluorescence spectroscopy, as an indirect method to detect and quantify spore concentration. This sensor technology is applicable to near real-time detection of calcium in bacterial spore suspensions without interference from light scattering or other ambient biological materials such as bacteria, pollen, viruses, and fungal spores.

In late 1999, Congress enacted financial modernisation legislation that dramatically deregulated the financial services industry and expanded the powers of financial institutions in the USA. In keeping with this deregulation and expanded powers, the regulatory landscape and enforcement mechanisms also changed. While many applaud this legislation, others point to previous US experience where financial deregulation overwhelmed federal regulators and resulted in massive failures of financial institutions and, consequently, in huge federal bailouts. The authors examine here the prospect of supplementing regulation with certain forms of private intervention. Specifically, they address the question: is there a role for whistleblowing and bounty hunting as means of supplementing existing regulation in the financial services industry?

A new technique for the detection of bacterial endospores using terbium dipicolinate photoluminescence has been previously reported in the literature. The performance of this technique is adversely affected by the presence of substances that contain phosphate ions. This deficiency must be overcome before this method can be used as a viable means of detecting bacterial endospores. We have experimentally investigated methods for mitigating the phosphate problem and demonstrate that the addition of AlCl3 is a solution to the problem. Proper experimental procedures for this method are also presented.