Crime and Building Rehabilitation or Demolition: A Dose-Response Analysis.

Thousands of buildings in Cleveland, Ohio were demolished or rehabilitated since the Great Recession in the 2000s. Recent evidence suggests removing vacant and decaying buildings reduces violent and firearm-involved crime. This study examines the dose-response relationship between demolitions, rehabilitations, and crime.

Space-filling and benthic competition on coral reefs.

Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors.

Multi-dimensional clinical phenotyping of a national cohort of adult cystic fibrosis patients.

Background: Cystic Fibrosis (CF) is a multi-systemic disorder resulting from genetic variation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene which can result in bronchiectasis, chronic sinusitis, pancreatic malabsorption, cholestatic liver disease and distal intestinal obstructive syndrome. This study generates multi-dimensional clinical phenotypes that capture the complexity and spectrum of the disease manifestations seen in adult CF patients using statistically robust techniques.

Methods: Pre-transplant clinical data from adult (age ≥18 years) CF patients (n = 992) seen in six regionally distinct US CF centers between 1/1/2014 and 6/30/2015 were included.

A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes.

Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the family have been shown to produce only one type of CIS-a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term injection systems (BIS).

Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics.

Background: Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated water systems. The Bayesian SourceTracker approach uses deep-sequencing marker gene libraries (16S ribosomal RNA) to determine the proportional contributions of bacteria from many potential source environments to a given sink environment simultaneously. Since its development, SourceTracker has been applied to an extensive diversity of studies, from beach contamination to human behavior.

Functional Connectivities Are More Informative Than Anatomical Variables in Diagnostic Classification of Autism.

Machine learning techniques have been implemented to reveal brain features that distinguish people with autism spectrum disorders (ASDs) from typically developing (TD) peers. However, it remains unknown whether different neuroimaging modalities are equally informative for diagnostic classification. We combined anatomical magnetic resonance imaging (aMRI), diffusion weighted imaging (DWI), and functional connectivity MRI (fcMRI) using conditional random forest (CRF) for supervised learning to compare how informative each modality was in diagnostic classification.

Cardiomyocyte cell cycle dynamics and proliferation revealed through cardiac-specific transgenesis of fluorescent ubiquitinated cell cycle indicator (FUCCI).

Rationale: Understanding and manipulating the cardiomyocyte cell cycle has been the focus of decades of research, however the ultimate goal of activating mitotic activity in adult mammalian cardiomyocytes remains elusive and controversial. The relentless pursuit of controlling cardiomyocyte mitosis has been complicated and obfuscated by a multitude of indices used as evidence of cardiomyocyte cell cycle activity that lack clear identification of cardiomyocyte "proliferation" versus cell cycle progression, endoreplication, endomitosis, and even DNA damage. Unambiguous appreciation of the complexity of cardiomyocyte replication that avoids oversimplification and misinterpretation is desperately needed.

Cardiac c-Kit Biology Revealed by Inducible Transgenesis.

Rationale: Biological significance of c-Kit as a cardiac stem cell marker and role(s) of c-Kit+ cells in myocardial development or response to pathological injury remain unresolved because of varied and discrepant findings. Alternative experimental models are required to contextualize and reconcile discordant published observations of cardiac c-Kit myocardial biology and provide meaningful insights regarding clinical relevance of c-Kit signaling for translational cell therapy.

Objective: The main objectives of this study are as follows: demonstrating c-Kit myocardial biology through combined studies of both human and murine cardiac cells; advancing understanding of c-Kit myocardial biology through creation and characterization of a novel, inducible transgenic c-Kit reporter mouse model that overcomes limitations inherent to knock-in reporter models; and providing perspective to reconcile disparate viewpoints on c-Kit biology in the myocardium.

Median regression spline modeling of longitudinal FEV1 measurements in cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) patients.

Rationale: Clinical phenotyping, therapeutic investigations as well as genomic, airway secretion metabolomic and metagenomic investigations can benefit from robust, nonlinear modeling of FEV1 in individual subjects. We demonstrate the utility of measuring FEV1 dynamics in representative cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) populations.

Methods: Individual FEV1 data from CF and COPD subjects were modeled by estimating median regression splines and their predicted first and second derivatives.

Meta-mass shift chemical profiling of metabolomes from coral reefs.

Untargeted metabolomics of environmental samples routinely detects thousands of small molecules, the vast majority of which cannot be identified. Meta-mass shift chemical (MeMSChem) profiling was developed to identify mass differences between related molecules using molecular networks. This approach illuminates metabolome-wide relationships between molecules and the putative chemical groups that differentiate them (e.

Characterizing Lung Disease in Cystic Fibrosis with Magnetic Resonance Imaging and Airway Physiology.

Translational investigations in cystic fibrosis (CF) have a need for improved quantitative and longitudinal measures of disease status. To establish a non-invasive quantitative MRI technique to monitor lung health in patients with CF and correlate MR metrics with airway physiology as measured by multiple breath washout (MBW). Data were collected in 12 CF patients and 12 healthy controls.

Discovery of Novel HIV-1 Integrase Inhibitors Using QSAR-Based Virtual Screening of the NCI Open Database.

Background: Quantitative structure-activity relationship (QSAR) models can be used as a predictive tool for virtual screening of chemical libraries to identify novel drug candidates. The aims of this paper were to report the results of a study performed for descriptor selection, QSAR model development, and virtual screening for identifying novel HIV-1 integrase inhibitor drug candidates.

Methods: First, three evolutionary algorithms were compared for descriptor selection: differential evolution-binary particle swarm optimization (DE-BPSO), binary particle swarm optimization, and genetic algorithms.

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins.

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical.

Diagnostic classification of intrinsic functional connectivity highlights somatosensory, default mode, and visual regions in autism.

Despite consensus on the neurological nature of autism spectrum disorders (ASD), brain biomarkers remain unknown and diagnosis continues to be based on behavioral criteria. Growing evidence suggests that brain abnormalities in ASD occur at the level of interconnected networks; however, previous attempts using functional connectivity data for diagnostic classification have reached only moderate accuracy. We selected 252 low-motion resting-state functional MRI (rs-fMRI) scans from the Autism Brain Imaging Data Exchange (ABIDE) including typically developing (TD) and ASD participants (n = 126 each), matched for age, non-verbal IQ, and head motion.

Multidimensional clinical phenotyping of an adult cystic fibrosis patient population.

Background: Cystic Fibrosis (CF) is a multi-systemic disease resulting from mutations in the Cystic Fibrosis Transmembrane Regulator (CFTR) gene and has major manifestations in the sino-pulmonary, and gastro-intestinal tracts. Clinical phenotypes were generated using 26 common clinical variables to generate classes that overlapped quantiles of lung function and were based on multiple aspects of CF systemic disease.

Methods: The variables included age, gender, CFTR mutations, FEV1% predicted, FVC% predicted, height, weight, Brasfield chest xray score, pancreatic sufficiency status and clinical microbiology results.

Multivariate analysis of functional metagenomes.

Metagenomics is a primary tool for the description of microbial and viral communities. The sheer magnitude of the data generated in each metagenome makes identifying key differences in the function and taxonomy between communities difficult to elucidate. Here we discuss the application of seven different data mining and statistical analyses by comparing and contrasting the metabolic functions of 212 microbial metagenomes within and between 10 environments.

Applying Shannon's information theory to bacterial and phage genomes and metagenomes.

All sequence data contain inherent information that can be measured by Shannon's uncertainty theory. Such measurement is valuable in evaluating large data sets, such as metagenomic libraries, to prioritize their analysis and annotation, thus saving computational resources. Here, Shannon's index of complete phage and bacterial genomes was examined.

PHACTS, a computational approach to classifying the lifestyle of phages.

Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques.

Computational analysis of HIV-1 protease protein binding pockets.

Mutations that arise in HIV-1 protease after exposure to various HIV-1 protease inhibitors have proved to be a difficult aspect in the treatment of HIV. Mutations in the binding pocket of the protease can prevent the protease inhibitor from binding to the protein effectively. In the present study, the crystal structures of 68 HIV-1 proteases complexed with one of the nine FDA approved protease inhibitors from the Protein Data Bank (PDB) were analyzed by (a) identifying the mutational changes with the aid of a developed mutation map and (b) correlating the structure of the binding pockets with the complexed inhibitors.

Transcatheter and transapical aortic valve replacement.

Minimally invasive valve replacement is limited to bioprosthetic aortic and pulmonary valves for use in very specific populations of patients. Replacement via trans-catheter and transapical techniques should be used only in patients in whom traditional surgical replacement is deemed an unacceptable risk. Nursing management will focus heavily on care for comorbid conditions because of the high-risk nature of the patients in whom these valves will initially be implanted.