Showing papers by "Mississippi State University published in 2013"

The importance of correcting for sampling bias in MaxEnt species distribution models

Abstract: Aim Advancement in ecological methods predicting species distributions is a crucial precondition for deriving sound management actions. Maximum entropy (MaxEnt) models are a popular tool to predict species distributions, as they are considered able to cope well with sparse, irregularly sampled data and minor location errors. Although a fundamental assumption of MaxEnt is that the entire area of interest has been systematically sampled, in practice, MaxEnt models are usually built from occurrence records that are spatially biased towards better-surveyed areas. Two common, yet not compared, strategies to cope with uneven sampling effort are spatial filtering of occurrence data and background manipulation using environmental data with the same spatial bias as occurrence data. We tested these strategies using simulated data and a recently collated dataset on Malay civet Viverra tangalunga in Borneo. Location Borneo, Southeast Asia. Methods We collated 504 occurrence records of Malay civets from Borneo of which 291 records were from 2001 to 2011 and used them in the MaxEnt analysis (baseline scenario) together with 25 environmental input variables. We simulated datasets for two virtual species (similar to a range-restricted highland and a lowland species) using the same number of records for model building. As occurrence records were biased towards north-eastern Borneo, we investigated the efficacy of spatial filtering versus background manipulation to reduce overprediction or underprediction in specific areas. Results Spatial filtering minimized omission errors (false negatives) and commission errors (false positives). We recommend that when sample size is insufficient to allow spatial filtering, manipulation of the background dataset is preferable to not correcting for sampling bias, although predictions were comparatively weak and commission errors increased. Main Conclusions We conclude that a substantial improvement in the quality of model predictions can be achieved if uneven sampling effort is taken into account, thereby improving the efficacy of species conservation planning.

Gene ontology annotations and resources

Abstract: The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

Prescribed fire in North American forests and woodlands: history, current practice, and challenges

Abstract: Whether ignited by lightning or by Native Americans, fire once shaped many North American ecosystems. Euro-American settlement and 20th-century fire suppression practices drastically altered historic fire regimes, leading to excessive fuel accumulation and uncharacteristically severe wildfires in some areas and diminished flammability resulting from shifts to more fire-sensitive forest species in others. Prescribed fire is a valuable tool for fuel management and ecosystem restoration, but the practice is fraught with controversy and uncertainty. Here, we summarize fire use in the forests and woodlands of North America and the current state of the practice, and explore challenges associated with the use of prescribed fire. Although new scientific knowledge has reduced barriers to prescribed burning, societal aversion to risk often trumps known, long-term ecological benefits. Broader implementation of prescribed burning and strategic management of wildfires in fire-dependent ecosystems will require improved integration of science, policy, and management, and greater societal acceptance through education and public involvement in land-management issues.

Beyond deterrence: an expanded view of employee computer abuse

Abstract: Recent academic investigations of computer security policy violations have largely focused on nonmalicious noncompliance due to poor training, low employee motivation, weak affective commitment, or individual oversight. Established theoretical foundations applied to this domain have related to protection motivation, deterrence, planned behavior, self-efficacy, individual adoption factors, organizational commitment, and other individual cognitive factors. But another class of violation demands greater research emphasis: the intentional commission of computer security policy violation, or insider computer abuse. Whether motivated by greed, disgruntlement, or other psychological processes, this act has the greatest potential for loss and damage to the employer. We argue the focus must include not only the act and its immediate antecedents of intention (to commit computer abuse) and deterrence (of the crime), but also phenomena which temporally precede these areas. Specifically, we assert the need to consider the thought processes of the potential offender and how these are influenced by the organizational context, prior to deterrence. We believe the interplay between thought processes and this context may significantly impact the efficacy of IS security controls, specifically deterrence safeguards. Through this focus, we extend the Straub and Welke (1998) security action cycle framework and propose three areas worthy of empirical investigation--techniques of neutralization (rationalization), expressive/instrumental criminal motivations, and disgruntlement as a result of perceptions of organizational injustice--and propose questions for future research in these areas.

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

Abstract: Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

Increased cancer burden among pesticide applicators and others due to pesticide exposure.

Abstract: A growing number of well-designed epidemiological and molecular studies provide substantial evidence that the pesticides used in agricultural, commercial, and home and garden applications are associated with excess cancer risk. This risk is associated both with those applying the pesticide and, under some conditions, those who are simply bystanders to the application. In this article, the epidemiological, molecular biology, and toxicological evidence emerging from recent literature assessing the link between specific pesticides and several cancers including prostate cancer, non-Hodgkin lymphoma, leukemia, multiple myeloma, and breast cancer are integrated. Although the review is not exhaustive in its scope or depth, the literature does strongly suggest that the public health problem is real. If we are to avoid the introduction of harmful chemicals into the environment in the future, the integrated efforts of molecular biology, pesticide toxicology, and epidemiology are needed to help identify the human carcinogens and thereby improve our understanding of human carcinogenicity and reduce cancer risk. CA Cancer J Clin 2013;63:120–142. V C 2013 American Cancer Society.*

Nematode effector proteins: an emerging paradigm of parasitism

Abstract: Phytonematodes use a stylet and secreted effectors to modify host cells and ingest nutrients to support their growth and development. The molecular function of nematode effectors is currently the subject of intense investigation. In this review, we summarize our current understanding of nematode effectors, with a particular focus on proteinaceous stylet-secreted effectors of sedentary endoparasitic phytonematodes, for which a wealth of information has surfaced in the past 10 yr. We provide an update on the effector repertoires of several of the most economically important genera of phytonematodes and discuss current approaches to dissecting their function. Lastly, we highlight the latest breakthroughs in effector discovery that promise to shed new light on effector diversity and function across the phylum Nematoda.

Integrated Optimal Formation Control of Multiple Unmanned Aerial Vehicles

Abstract: In this paper, we investigate the formation control of multiple unmanned aerial vehicles (UAVs), specifically unmanned aircraft, in an obstacle-laden environment. The main contribution of this paper is to integrate the formation control, trajectory tracking, and obstacle/collision avoidance into one unified optimal control framework. A nonquadratic avoidance cost is innovatively constructed via an inverse optimal control approach, which leads to an analytical, distributed, and optimal formation control law. The stability and optimality of the closed-loop system are proven. In addition, the proposed optimal control law is dependent only on the information from the local neighbors, rather than all UAVs' information. Simulation of multiple UAVs' formation flying demonstrates the effectiveness of the integrated optimal control design with desired behaviors including formation flying, trajectory tracking, and obstacle/collision avoidance.

Draft genome sequence of the Tibetan antelope

Abstract: The Tibetan antelope (Pantholops hodgsonii) is endemic to the extremely inhospitable highaltitude environment of the Qinghai-Tibetan Plateau, a region that has a low partial pressure of oxygen and high ultraviolet radiation. Here we generate a draft genome of this artiodactyl and use it to detect the potential genetic bases of highland adaptation. Compared with other plain-dwelling mammals, the genome of the Tibetan antelope shows signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission. Both the highland American pika, and the Tibetan antelope have signals of positive selection for genes involved in DNA repair and the production of ATPase. Genes associated with hypoxia seem to have experienced convergent evolution. Thus, our study suggests that common genetic mechanisms might have been utilized to enable high-altitude

Cardiovascular Reactivity, Stress, and Physical Activity

Abstract: Psychological stress has been proposed as a major contributor to the progression of cardiovascular disease (CVD). Acute mental stress can activate the sympathetic-adrenal-medullary (SAM) axis, eliciting the release of catecholamines (NE and EPI) resulting in the elevation of heart rate (HR) and blood pressure (BP). Combined stress (psychological and physical) can exacerbate these cardiovascular responses, which may partially contribute to the elevated risk of CVD and increased proportionate mortality risks experienced by some occupations (e.g., firefighting and law enforcement). Studies have supported the benefits of physical activity on physiological and psychological health, including the cardiovascular response to acute stress. Aerobically trained individuals exhibit lower sympathetic nervous system (e.g., HR) reactivity and enhanced cardiovascular efficiency (e.g., lower vascular reactivity and decreased recovery time) in response to physical and/or psychological stress. In addition, resistance training has been demonstrated to attenuate cardiovascular responses and improve mental health. This review will examine stress-induced cardiovascular reactivity and plausible explanations for how exercise training and physical fitness (aerobic and resistance exercise) can attenuate cardiovascular responses to stress. This enhanced functionality may facilitate a reduction in the incidence of stroke and myocardial infarction. Finally, this review will also address the interaction of obesity and physical activity on cardiovascular reactivity and CVD.

A Review of Technology-Based Interventions to Teach Academic Skills to Students with Autism Spectrum Disorder

Abstract: A comprehensive review of the literature was conducted for articles published between 1993 and 2012 to determine the degree to which technology-based interventions can be considered an evidence-based practice to teach academic skills to individuals with Autism Spectrum Disorder (ASD). Criteria developed by Horner et al. (Except Child 71:165–178, 2005) and Gersten et al. (Except Child 71:149–164, 2005) were used to determine the quality of single-subject research studies and group experimental research studies respectively. A total of 25 studies met inclusion criteria. Of these studies, only three single-subject studies and no group studies met criteria for quality or acceptable studies. Taken together, the results suggest that practitioners should use caution when teaching academic skills to individuals with ASD using technology-based interventions. Limitations and directions for future research are discussed.

Is breath acetone a biomarker of diabetes? A historical review on breath acetone measurements.

Abstract: Since the ancient discovery of the 'sweet odor' in human breath gas, pursuits of the breath analysis-based disease diagnostics have never stopped. Actually, the 'smell' of the breath, as one of three key disease diagnostic techniques, has been used in Eastern-Medicine for more than three thousand years. With advancement of measuring technologies in sensitivity and selectivity, more specific breath gas species have been identified and established as a biomarker of a particular disease. Acetone is one of the breath gases and its concentration in exhaled breath can now be determined with high accuracy using various techniques and methods. With the worldwide prevalence of diabetes that is typically diagnosed through blood testing, human desire to achieve non-blood based diabetic diagnostics and monitoring has never been quenched. Questions, such as is breath acetone a biomarker of diabetes and how is the breath acetone related to the blood glucose (BG) level (the golden criterion currently used in clinic for diabetes diagnostic, monitoring, and management), remain to be answered. A majority of current research efforts in breath acetone measurements and its technology developments focus on addressing the first question. The effort to tackle the second question has begun recently. The earliest breath acetone measurement in clearly defined diabetic patients was reported more than 60 years ago. For more than a half-century, as reviewed in this paper, there have been more than 41 independent studies of breath acetone using various techniques and methods, and more than 3211 human subjects, including 1581 healthy people, 242 Type 1 diabetic patients, 384 Type 2 diabetic patients, 174 unspecified diabetic patients, and 830 non-diabetic patients or healthy subjects who are under various physiological conditions, have been used in the studies. The results of the breath acetone measurements collected in this review support that many conditions might cause changes to breath acetone concentrations; however, the results from the six independent studies using clearly-defined Type 1 and Type 2 diabetic patients unanimously support that an elevated mean breath acetone concentration exists in Type 1 diabetes. Note that there is some overlap between the ranges of breath acetone concentration in individual T1D patients and healthy subjects; this reminds one to be careful when using an acetone breath test on T1D diagnostics. Comparatively, it is too early to draw a general conclusion on the relationship between a breath acetone level and a BG level from the very limited data in the literature.

A STELLA Model to Estimate Soil CO 2 Emissions from a Short-Rotation Woody Crop

Abstract: The potential for climatic factors as well as soil–plant–climate interactions to change as a result of rising levels of atmospheric CO2 concentration is an issue of increasing international environmental concern. Agricultural and forest practices and managements may be important contributors to mitigating elevated atmospheric CO2 concentrations. A computer model was developed using the Structural Thinking and Experiential Learning Laboratory with Animation (STELLA) software for soil CO2 emissions from a short-rotation woody crop as affected by soil water and temperature regimes, root and microbial respiration, and surficial processes such as rainfall, irrigation, and evapotranspiration. The resulting model was validated with good agreement between the model predictions and the experimental measurements prior to its applications. Two scenarios were then chosen to estimate both diurnal and annual soil CO2 emissions from a 1-ha mature cottonwood plantation as affected by soil temperature, soil (i.e., root and microbial) respiration, and irrigation. The simulation resulted in typical diurnal soil respiration and CO2 emission patterns, with increases from morning to early afternoon and decreases from early afternoon to midnight. This pattern was driven by diurnal soil temperature variations, indicating that soil temperature was the main influence on soil respiration and CO2 efflux into the atmosphere. Our simulations further revealed that the average seasonal soil respiration rate in summer was 1.6 times larger than in winter, whereas the average seasonal CO2 emission rate in summer was 1.77 times larger than in winter. Characteristic annual variation patterns for soil respiration and CO2 emission also were modeled, with both increasing from January 1 through June 30 followed by steady declines from September 1 through December 31. These results suggest that the STELLA model developed is a useful tool for estimating soil CO2 emission from a short-rotation woody crop plantation.

Microwave energy potential for biodiesel production

Abstract: Microwave energy based chemical synthesis has several merits and is important from both scientific and engineering standpoints. Microwaves have been applied in numerous inorganic and organic chemical syntheses; perhaps, from the time their ability to work as heat source was discovered. Recent laboratory scale microwave applications in biodiesel production proved the potential of the technology to achieve superior results over conventional techniques. Short reaction time, cleaner reaction products, and reduced separation-purification times are the key observations reported by many researchers. Energy utilization and specific energy requirements for microwave based biodiesel synthesis are reportedly better than conventional techniques. Microwaves can be very well utilized in feedstock preparation, extraction and transesterification stages of the biodiesel production process. Although microwave technology has advanced in other food, pharmaceutical and polymer chemistry related research and industry, it has yet to prove its potential in the biodiesel industry at large scale applications. This paper reviews principles and practices of microwave energy technology as applied in biodiesel feedstock preparation and processing. Analysis of laboratory scale studies, potential design and operation challenges for developing large scale biodiesel production systems are discussed in detail.

Only If It Is Convenient Understanding How Convenience Influences Self-Service Technology Evaluation

Abstract: Self-service technologies (SSTs) can help firms reduce labor costs while providing more channel options, but customers must be convinced of their value before foregoing a full service alternative. ...

Removal of Molecular Adsorbates on Gold Nanoparticles Using Sodium Borohydride in Water

Abstract: The mechanism of sodium borohydride removal of organothiols from gold nanoparticles (AuNPs) was studied using an experimental investigation and computational modeling. Organothiols and other AuNP surface adsorbates such as thiophene, adenine, rhodamine, small anions (Br– and I–), and a polymer (PVP, poly(N-vinylpyrrolidone)) can all be rapidly and completely removed from the AuNP surfaces. A computational study showed that hydride derived from sodium borohydride has a higher binding affinity to AuNPs than organothiols. Thus, it can displace organothiols and all the other adsorbates tested from AuNPs. Sodium borohydride may be used as a hazard-free, general-purpose detergent that should find utility in a variety of AuNP applications including catalysis, biosensing, surface enhanced Raman spectroscopy, and AuNP recycle and reuse.

An Adaptive Particle Swarm Optimization With Multiple Adaptive Methods

Abstract: Particle swarm optimization (PSO) has attracted much attention and has been applied to many scientific and engineering applications in the last decade. Most recently, an intelligent augmented particle swarm optimization with multiple adaptive methods (PSO-MAM) was proposed and was demonstrated to be effective for diverse functions. However, inherited from PSO, the performance of PSO-MAM heavily depends on the settings of three parameters: the two learning factors and the inertia weight. In this paper, we propose a parameter control mechanism to adaptively change the parameters and thus improve the robustness of PSO-MAM. A new method, adaptive PSO-MAM (APSO-MAM) is developed that is expected to be more robust than PSO-MAM. We comprehensively evaluate the performance of APSO-MAM by comparing it with PSO-MAM and several state-of-the-art PSO algorithms and evolutionary algorithms. The proposed parameter control method is also compared with several existing parameter control methods. The experimental results demonstrate that APSO-MAM outperforms the compared PSO algorithms and evolutionary algorithms, and is more robust than PSO-MAM.

Exploring Traditional and Emerging Parallel Programming Models Using a Proxy Application

Abstract: Parallel machines are becoming more complex with increasing core counts and more heterogeneous architectures. However, the commonly used parallel programming models, C/C++ with MPI and/or OpenMP, make it difficult to write source code that is easily tuned for many targets. Newer language approaches attempt to ease this burden by providing optimization features such as automatic load balancing, overlap of computation and communication, message-driven execution, and implicit data layout optimizations. In this paper, we compare several implementations of LULESH, a proxy application for shock hydrodynamics, to determine strengths and weaknesses of different programming models for parallel computation. We focus on four traditional (OpenMP, MPI, MPI+OpenMP, CUDA) and four emerging (Chapel, Charm++, Liszt, Loci) programming models. In evaluating these models, we focus on programmer productivity, performance and ease of applying optimizations.

Racist comments at online news sites: a methodological dilemma for discourse analysis

Abstract: In 2004, awash with the hope for a public sphere reinvigorated by the popular internet, the online arms of many U.S. newspapers opened their websites for comments. Now, nine years into this experiment, many newspapers have abandoned the practice of allowing comments. Online news sites have adopted a variety of strategies to deal with offensive comments, including turning “comments off,” not archiving comments, and adopting aggressive comment moderation policies. These strategies present researchers who wish to understand how racism operates in the new public sphere of mainstream news sites with a set of methodological dilemmas. In this article we (1) lay out the methodological pitfalls for the systematic investigation of the prevalent pattern of racism in online comments in the public sphere and (2) suggest steps by which scholars may deal with these methodological intricacies. We conclude by pointing to the broader implications of online content moderation.

Composite Properties of High-Strength, High-Ductility Concrete

Abstract: A new fiber-reinforced cementitious composite—high-strength, high-ductility concrete (HSHDC)—has been developed at the University of Michigan, Ann Arbor, in collaboration with the U.S. Army Engineer Research and Development Center, Vicksburg, MS. The micromechanics-based design of HSHDC resulted in a unique combination of ultra-high compressive strength (166 MPa [24 ksi]), tensile ductility (3.4%), and high specific energy absorption under direct tension (greater than 300 kJ/m3 [6270 lb-ft/ft3]). The material design approach and mechanical property characterization of HSHDC under direct tension, split tension, third-point flexure, and uniaxial compression loading, along with its density and fresh properties, are reported in this paper.

Effect of different C/N ratios on carotenoid and lipid production by Rhodotorula glutinis.

Abstract: Due to the increasing demand for sustainable biofuels, microbial oils as feedstock for the transesterification into biodiesel have gained scientific and commercial interest. Also, microbial carotenoids have a considerable market potential as natural colorants. The carbon to nitrogen (C/N) ratio of the respective cultivation media is one of the most important parameters that influence the production of microbial lipids and carotenoids. Thus, in the present experiment, the influence of different C/N ratios, initial glucose loadings, and ammonium concentrations of the cultivation medium on microbial cell growth and lipid and carotenoid production by the oleaginous red yeast Rhodotorula glutinis has been assessed. As a general trend, both lipid and carotenoid production increased at high C/N ratios. It was shown that not only the final C/N ratio but also the respectively applied initial carbon and nitrogen contents influenced the observed parameters. The lipid yield was not affected by different ammonium contents, while the carotenoid production significantly decreased both at low and high levels of ammonium supply. A glucose-based increase from C/N 70 to 120 did not lead to an increased lipid production, while carotenoid synthesis was positively affected. Generally, it can be asserted that lipid and carotenoid synthesis are stimulated at higher C/N ratios.

Modeling Cyber-Physical Vulnerability of the Smart Grid With Incomplete Information

Abstract: This paper addresses the attack modeling using vulnerability of information, communication and electric grid network. Vulnerability of electric grid with incomplete information has been analyzed using graph theory based approach. Vulnerability of information and communication (cyber) network has been modeled utilizing concepts of discovery, access, feasibility, communication speed and detection threat. Common attack vector based on vulnerability of cyber and physical system have been utilized to operate breakers associated with generating resources to model aurora-like event. Real time simulations for modified IEEE 14 bus test case system and graph theory analysis for IEEE 118 bus system have been presented. Test case results show the possible impact on smart grid caused by integrated cyber-physical attack.