A six degrees of freedom femtosecond laser system for fabrication of small-scale mechanical property specimens.

We present the details of a novel ultra-short pulsed laser machining workstation that has been employed for high-throughput laser machining of small-scale mechanical property specimens. This system employs a six degrees of freedom hexapod positioning stage capable of macroscopic movements at high positional accuracy. We developed a methodology that uses quantitative image analysis to measure key parameters required to minimize the hexapod positioning and rotational error.

Remote Monitoring of Canine Patients Treated for Pruritus during the COVID-19 Pandemic in Florida Using a 3-D Accelerometer.

The medical management of chronic canine pruritic dermatologic conditions is challenging and often frustrating. This is a report that shows one way of aiding the management of pruritic dogs using a remote monitoring device. It is often difficult for veterinarians to get dog owners to return to the clinic once a dog is treated.

A review of ecosystem services from edge-of-field practices in tile-drained agricultural systems in the United States Corn Belt Region.

Edge-of-field management practices that reduce nutrient pollution from tile drainage while contributing habitat and other ecosystem services are needed to enhance agricultural systems in the US Corn Belt Region. In this review, we identified edge-of-field and catchment scale agricultural conservation practices for intercepting and treating tile drainage. The reviewed conservation practices were (1) controlled drainage, also known as drainage water management (USDA-NRCS Code 554); (2) drainage water recycling (USDA-NRCS Code 447); (3) denitrifying bioreactors (USDA-NRCS Code 605); (4) saturated buffers (USDA-NRCS Code 604); and (5) constructed or restored wetlands designed for water quality improvement (USDA-NRCS Code 656) herein referred to as water quality wetlands.

Potential of water quality wetlands to mitigate habitat losses from agricultural drainage modernization.

Given widespread biodiversity declines, a growing global human population, and demands to improve water quality, there is an immediate need to explore land management solutions that support multiple ecosystem services. Agricultural water quality wetlands designed to provide both water quality benefits and wetland and grassland habitat are an emerging restoration solution that may reverse habitat declines in intensive agricultural areas. Installation of water quality wetlands in the Upper Midwest, USA, when considered alongside the repair and modification of aging agricultural tile drainage infrastructure, is a likely scenario that may mitigate nutrient pollution exported from agricultural systems and improve crop yields.

Integration of SWAT and HSPF for Simulation of Sediment Sources in Legacy Sediment-Impacted Agricultural Watersheds.

A total maximum daily load for the Chesapeake Bay requires reduction in pollutant load from sources within the Bay watersheds. The Conestoga River watershed has been identified as a major source of sediment load to the Bay. Upland loads of sediment from agriculture are a concern; however, a large proportion of the sediment load in the Conestoga River has been linked to scour of legacy sediment associated with historic millpond sites.

Scientific integrity issues in Environmental Toxicology and Chemistry: Improving research reproducibility, credibility, and transparency.

High-profile reports of detrimental scientific practices leading to retractions in the scientific literature contribute to lack of trust in scientific experts. Although the bulk of these have been in the literature of other disciplines, environmental toxicology and chemistry are not free from problems. While we believe that egregious misconduct such as fraud, fabrication of data, or plagiarism is rare, scientific integrity is much broader than the absence of misconduct.

Breast Reconstruction Among Commercially Insured Women With Breast Cancer in the United States.

Introduction: This study evaluated trends related to breast reconstruction and the factors associated with reconstruction.

Methods: Women with breast cancer aged 19 to 64 years who underwent a mastectomy procedure between July 1, 2011, and September 30, 2014, were identified from the MarketScan Commercial Claims and Encounters Database. The first date of surgical procedure during this period was defined as the index date.

Using ecological production functions to link ecological processes to ecosystem services.

Ecological production functions (EPFs) link ecosystems, stressors, and management actions to ecosystem services (ES) production. Although EPFs are acknowledged as being essential to improve environmental management, their use in ecological risk assessment has received relatively little attention. Ecological production functions may be defined as usable expressions (i.

Role of DNA Methylation in Modulating Transcription Factor Occupancy.

Although DNA methylation is commonly invoked as a mechanism for transcriptional repression, the extent to which it actively silences transcription factor (TF) occupancy sites in vivo is unknown. To study the role of DNA methylation in the active modulation of TF binding, we quantified the effect of DNA methylation depletion on the genomic occupancy patterns of CTCF, an abundant TF with known methylation sensitivity that is capable of autonomous binding to its target sites in chromatin. Here, we show that the vast majority (>98.

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.

Background: The brain, spinal cord, and neural retina comprise the central nervous system (CNS) of vertebrates. Understanding the regulatory mechanisms that underlie the enormous cell-type diversity of the CNS is a significant challenge. Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues.

Integrative analysis of 111 reference human epigenomes.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements.

Topologically associating domains are stable units of replication-timing regulation.

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs).

Conservation of trans-acting circuitry during mammalian regulatory evolution.

The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining ∼8.6 million transcription factor (TF) occupancy sites at nucleotide resolution.

A comparative encyclopedia of DNA elements in the mouse genome.

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.

Genome-scale mapping of DNase I hypersensitivity.

DNase I-seq is a global and high-resolution method that uses the nonspecific endonuclease DNase I to map chromatin accessibility. These accessible regions, designated as DNase I hypersensitive sites (DHSs), define the regulatory features, (e.g.

Widespread plasticity in CTCF occupancy linked to DNA methylation.

CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome-wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines.

Systematic localization of common disease-associated variation in regulatory DNA.

Genome-wide association studies have identified many noncoding variants associated with common diseases and traits. We show that these variants are concentrated in regulatory DNA marked by deoxyribonuclease I (DNase I) hypersensitive sites (DHSs). Eighty-eight percent of such DHSs are active during fetal development and are enriched in variants associated with gestational exposure-related phenotypes.

An expansive human regulatory lexicon encoded in transcription factor footprints.

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements.

The accessible chromatin landscape of the human genome.

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

Background: The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology.

Results: We used in vivo DNaseI sensitivity to map the locations of regulatory elements, and explore the changing chromatin landscape during the first 11 hours of Drosophila embryonic development.

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains.

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.

Faithful transmission of genetic material to daughter cells involves a characteristic temporal order of DNA replication, which may play a significant role in the inheritance of epigenetic states. We developed a genome-scale approach--Repli Seq--to map temporally ordered replicating DNA using massively parallel sequencing and applied it to study regional variation in human DNA replication time across multiple human cell types. The method requires as few as 8,000 cytometry-fractionated cells for a single analysis, and provides high-resolution DNA replication patterns with respect to both cell-cycle time and genomic position.

Meta-analysis of nitrogen removal in riparian buffers.

Riparian buffers, the vegetated region adjacent to streams and wetlands, are thought to be effective at intercepting and reducing nitrogen loads entering water bodies. Riparian buffer width is thought to be positively related to nitrogen removal effectiveness by influencing nitrogen retention or removal. We surveyed the scientific literature containing data on riparian buffers and nitrogen concentration in streams and groundwater to identify trends between nitrogen removal effectiveness and buffer width, hydrological flow path, and vegetative cover.