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Two haloalkaliphilic bacteria isolated from industrial brine solutions were characterized via molecular, physiological, and in silico metabolic pathway analyses. Genomes from the organisms, designated Halomonas BC1 and BC2, were sequenced; 16S ribosomal subunit-based phylogenetic analysis revealed a high level of similarity to each other and to Halomonas meridiana. Both strains were moderate halophiles with near optimal specific growth rates (≥60 % μ) observed over <0.1-5 % (w/v) NaCl and pH ranging from 7.4 to 10.2. Isolate BC1 was further characterized by measuring uptake or synthesis of compatible solutes under different growth conditions; in complex medium, uptake and accumulation of external glycine betaine was observed while ectoine was synthesized de novo in salts medium. Transcriptome analysis of isolate BC1 grown on glucose or citrate medium measured differences in glycolysis- and gluconeogenesis-based metabolisms, respectively. The annotated BC1 genome was used to build an in silico, genome-scale stoichiometric metabolic model to study catabolic energy strategies and compatible solute synthesis under gradients of oxygen and nutrient availability. The theoretical analysis identified energy metabolism challenges associated with acclimation to high salinity and high pH. The study documents central metabolism data for the industrially and scientifically important haloalkaliphile genus Halomonas. [ABSTRACT FROM AUTHOR]

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin. [ABSTRACT FROM AUTHOR]

Research Objective: To compare quality outcomes from surgical procedures performed at freestanding ambulatory surgery centers (ASCs) and hospital-based outpatient departments (HOPDs).Data Sources: Patient-level ambulatory surgery (1997-2004), hospital discharge (1997-2004), and vital statistics data (1997-2004) for the state of Florida were assembled and analyzed.Study Design: We used a pooled, cross-sectional design. Logistic regressions with time fixed-effects were estimated separately for the 12 most common ambulatory surgical procedures. Our quality outcomes were risk-adjusted 7-day and 30-day mortality and 7-day and 30-day unexpected hospitalizations. Risk-adjustment for patient demographic characteristics and severity of illness were calculated using the DCG/HCC methodology adjusting for primary diagnosis only and separately for all available diagnoses.Principal Findings: Although neither ASCs nor HOPDs performed better overall, we found some difference by procedure that varied based on the risk-adjustment approach used.Conclusions: There appear to be important variations in quality outcomes for certain procedures, which may be related to differences in organizational structure, processes, and strategies between ASCs and HOPDs. The study also confirms the importance of risk-adjustment for comorbidities when using administrative data, particularly for procedures that are sensitive to differences in severity. [ABSTRACT FROM AUTHOR]

The measurement of the optical transmission matrix (TM) of an opaque material is an advanced form of space-variant aberration correction. Beyond imaging, TM-based methods are emerging in a range of fields, including optical communications, micro-manipulation, and computing. In many cases, the TM is very sensitive to perturbations in the configuration of the scattering medium it represents. Therefore, applications often require an up-to-the-minute characterisation of the fragile TM, typically entailing hundreds to thousands of probe measurements. Here, we explore how these measurement requirements can be relaxed using the framework of compressive sensing, in which the incorporation of prior information enables accurate estimation from fewer measurements than the dimensionality of the TM we aim to reconstruct. Examples of such priors include knowledge of a memory effect linking the input and output fields, an approximate model of the optical system, or a recent but degraded TM measurement. We demonstrate this concept by reconstructing the full-size TM of a multimode fibre supporting 754 modes at compression ratios down to ∼5% with good fidelity. We show that in this case, imaging is still possible using TMs reconstructed at compression ratios down to ∼1% (eight probe measurements). This compressive TM sampling strategy is quite general and may be applied to a variety of other scattering samples, including diffusers, thin layers of tissue, fibre optics of any refractive profile, and reflections from opaque walls. These approaches offer a route towards the measurement of high-dimensional TMs either quickly or with access to limited numbers of measurements.

Non-line-of-sight (NLOS) imaging is a rapidly growing field seeking to form images of objects outside the field of view, with potential applications in autonomous navigation, reconnaissance, and even medical imaging. The critical challenge of NLOS imaging is that diffuse reflections scatter light in all directions, resulting in weak signals and a loss of directional information. To address this problem, we propose a method for seeing around corners that derives angular resolution from vertical edges and longitudinal resolution from the temporal response to a pulsed light source. We introduce an acquisition strategy, scene response model, and reconstruction algorithm that enable the formation of 2.5-dimensional representations-a plan view plus heights-and a 180 ∘ field of view for large-scale scenes. Our experiments demonstrate accurate reconstructions of hidden rooms up to 3 meters in each dimension despite a small scan aperture (1.5-centimeter radius) and only 45 measurement locations.

ADC is a potential post treatment imaging biomarker in colorectal liver metastasis however measurements are affected by respiratory motion. This is compounded by increased statistical uncertainty in ADC measurement with decreasing tumour volume. In this prospective study we applied a retrospective motion correction method to improve the image quality of 15 tumour data sets from 11 patients. We compared repeatability of ADC measurements corrected for motion artefact against non-motion corrected acquisition of the same data set. We then applied an error model that estimated the uncertainty in ADC repeatability measurements therefore taking into consideration tumour volume. Test-retest differences in ADC for each tumour, was scaled to their estimated measurement uncertainty, and 95% confidence limits were calculated, with a null hypothesis that there is no difference between the model distribution and the data. An early post treatment scan (within 7 days of starting treatment) was acquired for 12 tumours from 8 patients. When accounting for both motion artefact and statistical uncertainty due to tumour volumes, the threshold for detecting significant post treatment changes for an individual tumour in this data set, reduced from 30.3% to 1.7% (95% limits of agreement). Applying these constraints, a significant change in ADC (5 th and 20 th percentiles of the ADC histogram) was observed in 5 patients post treatment. For smaller studies, motion correcting data for small tumour volumes increased statistical efficiency to detect post treatment changes in ADC. Lower percentiles may be more sensitive than mean ADC for colorectal metastases.

Computing the amounts of light arriving from different directions enables a diffusely reflecting surface to play the part of a mirror in a periscope-that is, perform non-line-of-sight imaging around an obstruction. Because computational periscopy has so far depended on light-travel distances being proportional to the times of flight, it has mostly been performed with expensive, specialized ultrafast optical systems 1-12 . Here we introduce a two-dimensional computational periscopy technique that requires only a single photograph captured with an ordinary digital camera. Our technique recovers the position of an opaque object and the scene behind (but not completely obscured by) the object, when both the object and scene are outside the line of sight of the camera, without requiring controlled or time-varying illumination. Such recovery is based on the visible penumbra of the opaque object having a linear dependence on the hidden scene that can be modelled through ray optics. Non-line-of-sight imaging using inexpensive, ubiquitous equipment may have considerable value in monitoring hazardous environments, navigation and detecting hidden adversaries.

Several human skin diseases and disorders are associated with two groups of fungi, the dermatophytes and Malassezia. Although these skin-related problems are not generally life threatening, they are among the most common diseases and disorders of mankind. These fungi are phylogenetically divergent, with the dermatophytes within the Ascomycota and Malassezia within Basidiomycota. Genome analysis indicates that the adaptations to the skin environment are different in these two groups of fungi. Malassezia are dependent on host lipids and secrete lipases and phospholipases that likely release host fatty acids. The dermatophytes encode multiple enzymes with potential roles in modulating host interactions: polyketide synthases, nonribosomal peptide synthetases, LysM, proteases, kinases, and pseudokinases. These two fungal groups have maximized their interactions with the host using two very different mechanisms., (Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.)

Introduction: This study uses the most recent data from the nationally representative National Youth Tobacco Survey (NYTS) to examine the use of alternative tobacco products among U.S. cigarette smokers and non-cigarette smokers aged 14-17. Alternative tobacco product use is defined as use of one or more of the following products: smokeless tobacco, cigars, pipes, bidis, or kreteks., Methods: Using the results from the 2004, 2006, and 2009 NYTS, multivariate logistic regressions were used to investigate separately the extent of alternative tobacco product use in current cigarette smokers and in those who reported not smoking cigarettes controlling for demographic and other independent influences., Results: The results indicate that for adolescent smokers and nonsmokers, the use of one type of alternative tobacco product made it much more likely the individual would use one or more of the other alternative tobacco products. Non-cigarette smokers using these tobacco products appeared to exhibit symptoms of nicotine dependence comparable to those of cigarette smokers., Conclusions: More information on adolescent use of alternative tobacco products is needed. Current cigarette use declined 3.4% annually over 2004-2009 for the NYTS 14- to 17-year-old population, but this cohort's use of alternative tobacco products was unchanged. The number of adolescents aged 14-17 who did not smoke cigarettes but used alternative tobacco products increased 5.9% per year over the same period. Current surveillance measures need to be expanded in order to gain a more comprehensive understanding of adolescent alternative tobacco use.

Introduction: Youth who smoke daily have diverse methods for obtaining cigarettes, which range from commercial sources to essentially black market transactions. This study examines access to cigarettes, attitudes toward tobacco, and the demographic characteristics of youth who are daily cigarette smokers., Methods: Biennial data from the Florida Youth Tobacco Survey, a representative sample of Florida public middle- and high-school students, were used. Daily smoking was categorized into ordinal categories of increasing intensity. Analysis was done with a logistic partial proportional odds model, which allowed the effects of the independent predictors to vary according to smoking intensity., Results: The multivariate analysis revealed that males and females have different methods of obtaining cigarettes. Moreover, certain modes of access to cigarettes were related to daily smoking intensity. Males who obtained cigarettes from their parents or stole them from a store were much more likely to have a higher intensity of daily smoking. Females who gave someone money to buy their cigarettes or bought them from a person were more likely to smoke more cigarettes per day. Males, but not females, also perceived that increasing the number of cigarettes smoked per day provides social benefits in the form of more friends., Conclusions: Understanding how daily youth smokers obtain cigarettes is necessary if effective antitobacco policies are to be developed for these individuals. Daily youth smokers are at increased risk of becoming addicted to nicotine, making them more likely to transition to daily adult smoking.

This paper examines the empirical consistency of the Diagnosis Cost Groups/Hierarchical Condition Categories (DCG/HCC) risk-adjustment method for comparing 7-day mortality between hospital-based outpatient departments (HOPDs) and freestanding ambulatory surgery centers (ASCs). We used patient level data for the three most common outpatient procedures provided during the 1997-2004 period in Florida. We estimated base-line logistic regression models without any diagnosis-based risk adjustment and compared them to logistic regression models with the DCG/HCC risk-adjustment, and to conditional logit models with a matched cohort risk-adjustment approach. We also evaluated models that adjusted for primary diagnoses only, and then for all available diagnoses, to assess how the frequently absent secondary diagnoses fields in ambulatory surgical data affect risk-adjustment. We found that risk-adjustment using both diagnosis-based methods resulted in similar 7-day mortality estimates for HOPD patients in comparison with ASC patients in two out of three procedures. We conclude that the DCG/HCC risk-adjustment method is relatively consistent and stable, and recommend this risk-adjustment method for health policy research and practice with ambulatory surgery data. We also recommend using risk-adjustment with all available diagnoses.

Purpose: To assess the amount of local rural hospital outpatient department (HOPD) bypass for outpatient procedures., Methods: We analyzed data on colonoscopies and upper gastrointestinal endoscopies performed in the state of Florida over the period 1997-2004., Findings: Approximately, 53% of colonoscopy and 45% of upper gastrointestinal endoscopy patients bypassed their local rural hospital for treatment at either a free-standing ambulatory surgical center (ASC) or a nonlocal hospital outpatient department. Independent predictors of bypass included risk-adjusted severity of the patient's medical condition, insurance status, and race. Patients treated in ASCs were predominately healthier, white and commercially insured. Nonlocal HOPDs tend to treat a sicker cohort of patients who were publicly insured or under managed care., Conclusions: The results indicate that patients who bypass their local HOPD to an ASC differ from those bypassing to a nonlocal HOPD, and that patient factors influencing bypass for outpatient procedures differ from those influencing inpatient bypass. From a policy perspective, as procedures continue to migrate from the inpatient to the outpatient setting, bypassing the local rural hospital for treatment elsewhere could create conditions that negatively impact rural hospital operations.

This study explores associations between patient outcomes (7- and 30-day hospitalization and mortality) and healthcare provider (physician and facility) volumes of outpatient colonoscopy, cataract removal, and upper gastrointestinal endoscopy performed in outpatient surgical settings in Florida. Findings indicate that patients treated by high-volume physicians or facilities had lower adjusted odds ratios for hospitalizations and mortality. When physician and facility volume were assessed simultaneously, physician volume accounted for larger effects than facility volume in hospitalization models. When assessing both physician and facility volume together for mortality, facility volume was a stronger predictor of mortality outcomes at 30 days. Further examinations of associations of outpatient physician and facility volumes and patient outcomes are suggested.

Background: Little is known about quality outcomes in accredited and nonaccredited ambulatory surgical centers (ASCs). Quality outcomes in ASCs accredited by either the Accreditation Association for Ambulatory Health Care (AAAHC) or The Joint Commission were compared with those of nonaccredited ASCs in Florida., Methods: Patient-level ambulatory surgery and hospital discharge data from Florida for 2004 were merged and analyzed. Multivariate logistic regressions were estimated separately for the five most common ambulatory surgical procedures: colonoscopy, cataract removal, upper gastroendoscopy, arthroscopy, and prostate biopsy. Statistical models examined differences in risk-adjusted 7-day and 30-day unexpected hospitalizations between nationally accredited and nonaccredited ASCs. In addition to risk adjustment, each model controlled for facility volume of procedure and patient demographic characteristics including gender, race, age, and insurance type., Results: In multivariate analyses that controlled for facility volume and patient characteristics, patients at Joint Commission-accredited facilities were still significantly less likely to be hospitalized after colonoscopy. Specifically, compared with patients treated in nonaccredited ASCs regulated by the state agency, patients treated at those facilities were 10.9% less likely to be hospitalized within 7 days (adjusted odds ratio [OR] = 0.891; 95% confidence interval [C.I.], 0.799-0.993) and 9.4% less likely to be hospitalized within 30 days (adjusted OR = 0.906; 95% C.I., 0.850-0.966). No other differences in unexpected hospitalization rates were detected in the other procedures examined., Discussion: With the exception of one procedure, systematic differences in quality of care do not exist between ASCs that are accredited by AAAHC, those accredited by the Joint Commission, or those not accredited in Florida.

Background: Hospitals have been slow to adopt information technology (IT) largely because of a lack of generalizable evidence of the value associated with such adoption., Purpose: To explore the relationship between IT adoption and quality of care in acute-care hospitals., Methods: Primary data on hospital IT adoption were combined with secondary hospital discharge data. Regression analyses were used to examine the relationship between various measures of IT adoption and several quality indicators after controlling for confounders. Adoption of IT was measured using a previously validated method that considers clinical, administrative, and strategic IT capabilities of acute-care hospitals. Quality measures included the Inpatient Quality Indicators developed by the Agency for Healthcare Research and Quality., Results: Data from 98 hospitals were available for analyses. Hospitals adopted an average of 11.3 (45.2%) clinical IT applications, 15.7 (74.8%) administrative IT applications, and 5 (50%) strategic IT applications. In multivariate regression analyses, hospitals that adopted a greater number of IT applications were significantly more likely to have desirable quality outcomes on seven Inpatient Quality Indicator measures, including risk-adjusted mortality from percutaneous transluminal coronary angioplasty, gastrointestinal hemorrhage, and acute myocardial infarction. An increase in clinical IT applications was also inversely correlated with utilization of incidental appendectomy, and an increase in the adoption of strategic IT applications was inversely correlated with risk-adjusted mortality from craniotomy and laparoscopic cholecystectomy., Practice Implications: Hospital adoption of IT is associated with desirable quality outcomes across hospitals in Florida. These findings will assist hospital leaders interested in understanding better the effect of costly IT adoption on quality of care in their institutions.

Fungi in the genus Malassezia are ubiquitous skin residents of humans and other warm-blooded animals. Malassezia are involved in disorders including dandruff and seborrheic dermatitis, which together affect >50% of humans. Despite the importance of Malassezia in common skin diseases, remarkably little is known at the molecular level. We describe the genome, secretory proteome, and expression of selected genes of Malassezia globosa. Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta, a close relative implicated in similar skin disorders. Adaptation to the skin environment and associated pathogenicity may be due to unique metabolic limitations and capabilities. For example, the lipid dependence of M. globosa can be explained by the apparent absence of a fatty acid synthase gene. The inability to synthesize fatty acids may be complemented by the presence of multiple secreted lipases to aid in harvesting host lipids. In addition, an abundance of genes encoding secreted hydrolases (e.g., lipases, phospholipases, aspartyl proteases, and acid sphingomyelinases) was found in the M. globosa genome. In contrast, the phylogenetically closely related plant pathogen Ustilago maydis encodes a different arsenal of extracellular hydrolases with more copies of glycosyl hydrolase genes. M. globosa shares a similar arsenal of extracellular hydrolases with the phylogenetically distant human pathogen, Candida albicans, which occupies a similar niche, indicating the importance of host-specific adaptation. The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex.

The surgery literature is filled with reports on racial or gender disparities in quality. However, whether patient demographics are risk factors for complications or death from ambulatory surgical procedures is unknown. This study explores whether racial, age, and gender outcome disparities exist after ambulatory surgeries. Patients studied included adults (>18 years) receiving common ambulatory surgical procedures (N = 3,174,436) in either a freestanding ambulatory surgical center or a hospital-based outpatient department during 1997-2004 in Florida. Results demonstrate that African Americans were at a significantly increased risk for either mortality or unexpected hospitalization in 4 of the 5 procedures examined, even after controlling for confounders. For women, unexpected hospital admission or mortality was less likely to occur after almost all procedures examined. Thus, many of the racial and gender disparities in the inpatient surgical literature are also observed in the ambulatory setting. More research is needed to determine the source of these disparities.

Most of the studies linking the use of information technology (IT) to improved patient safety have been conducted in academic medical centers or have focused on a single institution or IT application. Our study explored the relationship between overall IT adoption and patient safety performance across hospitals in Florida. Primary data on hospital IT adoption were combined with secondary hospital discharge data. Regression analyses were used to examine the relationship between measures of IT adoption and the Patient Safety Indicators (PSIs) of the Agency for Healthcare Research and Quality. We found that eight PSIs were related to at least one measure of IT adoption. Compared with administrative IT adoption, clinical IT adoption was related to more patient safety outcome measures. Hospitals with the most sophisticated and mature IT infrastructures performed significantly better on the largest number of PSIs. Adoption of IT is associated with desirable performance on many important measures of hospital patient safety. Hospital leaders and other decision makers who are examining IT systems should consider the impact of IT on patient safety.

Protein protease inhibitors could potentially be used to stabilize proteases in commercial products such as liquid laundry detergents. However, many protein protease inhibitors are susceptible to hydrolysis inflicted by the protease. We have engineered Streptomyces subtilisin inhibitor (SSI) to resist proteolysis by adding an interchain disulfide bond and removing a subtilisin cleavage site at leucine 63. When these stabilizing changes were combined with changes to optimize the affinity for subtilisin, the resulting inhibitor provided complete protease stability for at least 5 months at 31 degrees C in a subtilisin-containing liquid laundry detergent and allowed full recovery of the subtilisin activity upon the dilution that occurs in a North American washing machine.