Pattern matching is the process of comparing two objects to see if they are similar to each other. Objects can be physical objects, situations, facts or events. The criteria of matching can be exact or partial. Traditional pattern matching systems rely on exact matches, in which a small set of...
Multimedia networking is one of the most exciting developments in today's Internet. Streaming technology; which allows the player to start playing audio/video data immediately instead of waiting for the entire file to be downloaded, presents an attractive vehicle for the distribution of multimedia content over the Internet. However, transmitting real-time...
The Structural Active-Object System (SAOS) approach allows rapid development of various concurrent systems by structural and hierarchical object composition (SHOC). We implemented, as a SAOS program, a graphical editing and simulation program for automatic guided vehicle (AGV) systems, which carry around parts in automated factories. It is difficult to predict...
Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has...
Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has...
Programming style is important for program understanding in programming tasks such as maintenance. testing, and debugging. The goal of programming style is to improve the readability of the source program without adversely affecting its performance.
Critique is a FORTRAN source program style critic which analyzes the source program and outputs...
Hayes, in his Naive Physics Manifesto, identified two alternate ontologies for reasoning about liquids, an ontology based on the notion of a contained substance and one based on the notion of a molecular collection. Qualitative Process theory, proposed by Forbus, lends itself easily to encoding the contained substance ontology. It...
In this report, we describe an implementation of a prototype information resources management system for the synthesis and integration project of the forest response program using a 4GL application development system ACCELL. Our system is called Prototype Virtual Data Management System (PVDMS). ACCELL is a software package that combines a...
With sequential computing technology reaching its speed limits, parallel processing is emerging as the key to very-high-speed computation. However, developing a parallel program is by no means a simple task; neither is analyzing the performance of parallel programs.
C* is a high-level data-parallel language that hides explicit message passing and...
The reaction of fluid or gas flowing around an obstacle is a common engineering problem. Computer simulations are often used to measure and visualize the physical processes involved. In this report, we will discuss a parallel implementation of a simulation using the Smooth Particle Hydrodynamics (SPH) approach to fluid flow....
An execution of a database system is considered correct if its net effect is as if transactions were executed serially, and such an execution is called serializable. In this short paper we show that the serializability test problem can be reduced to a simple pebbling problem. Our characterization is intuitive...
In this report, we present future projections of climate and climate-related natural hazards in Benton County for the 2020s (2010–2039) and 2050s (2040–2069) relative to the 1971–2000 historical baseline. The projections are based on multiple global climate models for both a lower greenhouse gas emissions scenario (RCP 4.5) and a...
Modular construction methods have recently gained interest due to the advantages offered in terms of safety, quality, and productivity for projects. In this method, a significant portion of the construction is performed off-site in factories where modular components are built in different workstations, assembled on the production line, and shipped...
Ice-free cryopreservation, known as vitrification, is an appealing approach for banking of adherent cells and tissues because it prevents dissociation and morphological damage that may result from ice crystal formation. However, current vitrification methods are often limited by the cytotoxicity of the concentrated cryoprotective agent (CPA) solutions that are required...
Organic agriculture requires cultivars that can adapt to organic crop management systems without the use of synthetic
pesticides as well as genotypes with improved nutritional value. The aim of this study encompassing 16 experiments was to
compare 23 broccoli cultivars for the content of phytochemicals associated with health promotion grown...
Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale’s Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the...
Meniscal tears are a common cause of stifle lameness in dogs. Use of autologous
synoviocytes from the affected stifle is an attractive cell source for tissue engineering
replacement fibrocartilage. However, the diseased state of these cells may impede
in vitro fibrocartilage formation. Synoviocytes from 12 osteoarthritic (“oaTSB”) and
6 normal...
The genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. Here, to test this hypothesis,...
Background: We present a model for reporting accelerometer paradata (process-related data produced from survey administration) collected in the International Study of Childhood Obesity Lifestyle and the Environment (ISCOLE), a multi-national investigation of >7000 children (averaging 10.5 years of age) sampled from 12 different developed and developing countries and five continents....
Background: High birthweight is an established risk factor for childhood leukaemia.
Its association with other childhood cancers is less clear, with studies hampered by low
case numbers. Methods: We used two large independent datasets to explore risk associations between
birthweight and all subtypes of childhood cancer. Data for 16 554...
Bayesian networks are probabilistic models that represent complex distributions in a modular way and have become very popular in many fields. There are many methods to build Bayesian networks from a random sample of independent and identically distributed observations. However, many observational studies are designed using some form of clustered...
Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly...
This paper reviews the current progress in mathematical modeling of
anti-reflective subwavelength structures. Methods covered include effective medium
theory (EMT), finite-difference time-domain (FDTD), transfer matrix method (TMM), the
Fourier modal method (FMM)/rigorous coupled-wave analysis (RCWA) and the finite
element method (FEM). Time-based solutions to Maxwell’s equations, such as FDTD,
have...
Case control studies of nonagenarians and centenarians provide evidence that long‐lived individuals do not
differ in the rate of disease associated variants compared to population controls. These results suggest that an enrichment
of novel protective variants, rather than a lack of disease associated variants, determine the genetic predisposition to
exceptionally...
Fungal hyphae are among the most highly polarized cells. Hyphal polarized
growth is supported by tip-directed transport of secretory vesicles, which accumulate temporarily
in a stratified manner in an apical vesicle cluster, the Spitzenkörper. The exocyst complex
is required for tethering of secretory vesicles to the apical plasma membrane. We...
Understanding how intra-specific differences in plant traits mediate vulnerability to herbivores of relevant habitat-forming plants is vital to attain a better knowledge on the drivers of the structure and functioning of ecosystems. Such studies, however, are rare in seagrass-mesograzer systems despite the increasingly recognized relevance of mesograzers as seagrass consumers....
Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day marine currents on the extant patterns of genetic diversity in the...
Methane (CH₄) is a valuable fuel, constituting 70–95% of natural gas, and a potent
greenhouse gas. Release of CH₄ into the atmosphere contributes to climate change.
Biological CH₄ production or methanogenesis is mostly performed by methanogens, a
group of strictly anaerobic archaea. The direct substrates for methanogenesis are H₂
plus...
Anthropogenic and natural stressors often interact to affect organisms. Amphibian populations are undergoing unprecedented declines and extinctions with pesticides and emerging infectious diseases implicated as causal factors. Although these factors often co-occur, their effects on amphibians are usually examined in isolation. We hypothesized that exposure of larval and metamorphic amphibians...
Understanding the causes and consequences of rapid environmental change is an essential scientific frontier, particularly given the threat of climate-and land use-induced changes in disturbance regimes. In western North America, recent widespread insect outbreaks and wildfires have sparked acute concerns about potential insect-fire interactions. Although previous research shows that insect...
Graduate teaching assistants (GTAs) in science, technology, engineering, and mathematics (STEM)
have a large impact on undergraduate instruction but are often poorly prepared to teach. Teaching
self-efficacy, an instructor’s belief in his or her ability to teach specific student populations a specific
subject, is an important predictor of teaching skill...
BACKGROUND: Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can
be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA
methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations
in virtually any blood sample including...
Background:
Neisseria gonorrhoeae (GC) is a Gram-negative pathogen that most commonly infects mucosal surfaces, causing sexually transmitted urethritis in men and endocervicitis in women. Serious complications associated with these infections are frequent and include pelvic inflammatory disease, ectopic pregnancy, and infertility. The incidence of gonorrhea cases remains high globally while...
Histone deacetylase (HDAC) inhibitors are undergoing clinical trials as anticancer agents, but some exhibit resistance mechanisms
linked to anti-apoptotic Bcl-2 functions, such as BH3-only protein silencing. HDAC inhibitors that reactivate BH3-only family
members might offer an improved therapeutic approach. We show here that a novel seleno-α-keto acid triggers global histone...
Coastal wetland plants are adapted to varying degrees of inundation. However, functional relationships between inundation and productivity are poorly characterized for most species. Determining species-specific tolerances to inundation is necessary to evaluate sea-level rise (SLR) effects on future marsh plant community composition, quantify organic matter inputs to marsh accretion, and...
Antisense oligonucleotide (AO)-mediated exon-skipping therapeutics shows great promise in correcting frame-disrupting mutations in the DMD gene for Duchenne muscular dystrophy. However, insufficient systemic delivery limits clinical adoption. Previously, we showed that a glucose/fructose mixture augmented AO delivery to muscle in mdx mice. Here, we evaluated if fructose alone could enhance...
Meta-analyses of field studies have shown that biomass, density, species richness, and size of organisms protected by no-take marine reserves generally increase over time. The magnitude and timing of changes in these response variables, however, vary greatly and depend upon the taxonomic groups protected, size and type of reserve, oceanographic...
Background: Nonalcoholic steatohepatitis (NASH) is a progressive form of nonalcoholic fatty liver disease and a risk
factor for cirrhosis, hepatocellular carcinoma and liver failure. Previously, we reported that dietary docosahexaenoic
acid (DHA, 22:6,n-3) was more effective than eicosapentaenoic acid (EPA, 20:5,n-3) at reversing western diet (WD)
induced NASH in LDLR-/-...
Ligand activation of the aryl hydrocarbon (AHR) has profound effects upon the immunological status of the gastrointestinal tract, establishing and maintaining signaling networks, which facilitate host-microbe homeostasis at the mucosal interface. However, the identity of the ligand(s) responsible for such AHR-mediated activation within the gut remains to be firmly established....
We apply GENMOM, a coupled atmosphere–ocean climate model, to simulate eight equilibrium time
slices at 3000-year intervals for the past 21,000 years forced
by changes in Earth–Sun geometry, atmospheric greenhouse
gases (GHGs), continental ice sheets, and sea level. Simulated
global cooling during the Last Glacial Maximum
(LGM) is 3.8°C and...
Background: Recent interest in reference-free deconvolution of DNA methylation data has led to several supervised methods, but these methods do not easily permit the interpretation of underlying cell types.
Results: We propose a simple method for reference-free deconvolution that provides both proportions of putative cell types defined by their underlying...
To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found...
Rapamycin (Rapa) and dietary restriction (DR) have consistently
been shown to increase lifespan. To investigate whether Rapa
and DR affect similar pathways in mice, we compared the effects
of feeding mice ad libitum (AL), Rapa, DR, or a combination of
Rapa and DR (Rapa + DR) on the transcriptome and...
Marine sponges are vital components of benthic and coral reef ecosystems, providing
shelter and nutrition for many organisms. In addition, sponges act as an essential carbon
and nutrient link between the pelagic and benthic environment by filtering large quantities
of seawater. Many sponge species harbor a diverse microbial community (including...
Background: Theobroma cacao L., the source of cocoa, is a crop of significant economic value around the world. To facilitate the study of gene function in cacao we have developed a rapid Agrobacterium-mediated transient genetic transformation protocol. Here we present a detailed methodology for our transformation assay, as well as...
The Lena River in central Siberia is one of the
major pathways translocating terrestrial organic matter (OM)
from its vast catchment area to the coastal zone of the Laptev
Sea and the Arctic Ocean. The permafrost soils of its far
south-stretching catchment, which store huge amounts of
OM, will most...
For decades, the bio-duck sound has been recorded in the Southern Ocean,
but the animal producing it has remained a mystery. Heard mainly during
austral winter in the Southern Ocean, this ubiquitous sound has been
recorded in Antarctic waters and contemporaneously off the Australian
west coast. Here, we present conclusive...