Life Sciences Commons^™

Computing Inconsistency Measure Based On Paraconsistent Semantics, Pascal Hitzler, Yue Ma, Guilin Qi

Computer Science and Engineering Faculty Publications

Measuring inconsistency in knowledge bases has been recognized as an important problem in several research areas. Many methods have been proposed to solve this problem and a main class of them is based on some kind of paraconsistent semantics. However, existing methods suffer from two limitations: (i) they are mostly restricted to propositional knowledge bases; (ii) very few of them discuss computational aspects of computing inconsistency measures. In this article, we try to solve these two limitations by exploring algorithms for computing an inconsistency measure of first-order knowledge bases. After introducing a four-valued semantics for first-order logic, we define an …

Afghan Genetic Mysteries, Bernard Dupaigne

Human Biology Open Access Pre-Prints

Letter To The Editor

Population Status, Habitat Dependence, And Reproductive Ecology Of Bahama Orioles: A Critically Endangered Synanthropic Species, Melissa R. Price, Valerie A. Lee, William K. Hayes

Faculty Works

Recent elevation of critically endangered Bahama Orioles (Icterus northropi) to species status prompted us to evaluate their population status, habitat use, and breeding ecology. From surveys, we estimated that at least 141 to 254 individuals remain globally, with 90 to 162, 24 to 44, and 27 to 48 individuals remaining on North Andros Island, Mangrove Cay, and South Andros Island, The Bahamas, respectively. Orioles were observed nesting exclusively in anthropogenic habitat (residential and agricultural land), but home ranges also included nearby pine forest and coppice (dry broadleaf forest). Most nests (40 of 46, or 87%) were in nonnative coconut palm …

Fuel Poverty, Older People And Cold Weather: An All-Island Analysis, Patrick J. Goodman, Helen Helen Mcavoy, Noëlle Cotter, Eugene Monahan,, Eimear Barrett, Stephen Browne, Ariana Zeka

Reports

The research presented in this report is the culmination of 18 months of work which has been funded by The Centre for Ageing Research and Development in Ireland (CARDI). The research is concerned with older people and how they cope with cold weather, and whether they are able to keep sufficiently warm in winter. This report is structured into a number of distinct chapters, with each chapter dealing with a specific aspect of the fuel poverty issue.

The Y-Str Genetic Diversity Of An Idaho Basque Population, With Comparison To European Basques And Us Caucasians, Josu Zubizarreta, Michael C. Davis, Greg Hampikian

Human Biology Open Access Pre-Prints

Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). A total of 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a US Caucasian population. The haplotype diversity …

A Non-Invasive Assay For Monitoring Stress Responses: A Comparison Between Wild And Captive-Reared Rainbowfish (Melanoteania Duboulayi), Amina Zuberi, Sinan Ali, Culum Brown

Aquaculture Collection

The stress response of wild and captive reared rainbowfish (Melanoteania duboulayi) following chasing by a simulated predator was examined. Cortisol release rate was monitored using a flow through system by measuring water borne hormone levels. Tests using known cortisol concentrations revealed that the technique yielded 95% of the cortisol present in the water. Cortisol release rates increased several fold in both populations after being chased but peaked at different time periods. Wild fish showed a typical stress response with release rate rising to (2.29±0.22 ng g⁻¹ h⁻¹) 2 h after exposure followed by rapid recovery. The captive-reared …

Animal Pain: What It Is And Why It Matters, Bernard E. Rollin

Animal Welfare Collection

The basis of having a direct moral obligation to an entity is that what we do to that entity matters to it. The ability to experience pain is a sufficient condition for a being to be morally considerable. But the ability to feel pain is not a necessary condition for moral considerability. Organisms could have possibly evolved so as to be motivated to flee danger or injury or to eat or drink not by pain, but by ‘‘pangs of pleasure’’ that increase as one fills the relevant need or escapes the harm. In such a world, ‘‘mattering’’ would be positive, …

Lessons From Chimpanzee-Based Research On Human Disease: The Implications Of Genetic Differences, Jarrod Bailey

Laboratory Experiments Collection

Assertions that the use of chimpanzees to investigate human diseases is valid scientifically are frequently based on a reported 98–99% genetic similarity between the species. Critical analyses of the relevance of chimpanzee studies to human biology, however, indicate that this genetic similarity does not result in sufficient physiological similarity for the chimpanzee to constitute a good model for research, and furthermore, that chimpanzee data do not translate well to progress in clinical practice for humans. Leading examples include the minimal citations of chimpanzee research that is relevant to human medicine, the highly different pathology of HIV/AIDS and hepatitis C virus …

How To Control Texture In Cultured Dairy, Phillip S. Tong

Dairy Science

No abstract provided.

Uses Of Genomic Predictions In Commercial Beef Cattle Operations, Matt Miller

Dairy Science

This paper aimed to achieve two different objectives. The first objective of this study was to identify and explain the genetic gain achieved in commercial beef cattle operations with the use of genomic predictions versus the use of visual appraisal and EPDs. The second goal of this paper was to develop a method to easily explain genomic predictions and their practical applications on commercial beef operations to a lay audience, specifically to ranchers. In order to accomplish these objectives, I evaluated three of the most common selection methods used by producers today. These included visual appraisal, expected progeny differences (EPDs), …

Utilizing Fishermen Knowledge And Expertise: Keys To Success For Collaborative Fisheries Research, Noëlle Yochum, Richard M. Starr, Dean Wendt

Biological Sciences

Collaborative fisheries research provides a mechanism for integrating the unique knowledge, experience, and skills of fishermen and scientists. It is a joint intellectual endeavor that begins with the inception of a project and continues until its final stages, with each group having mutual investment in—and ownership of— the project. Collaborative fisheries research promotes communication and trust among fishermen, scientists, and managers and can provide much-needed scientifically valid data for fisheries management. It can enhance federal and state management data collection programs, which span broad sections of coastline, by increasing the ability to detect changes in local metapopulations that may be …

Suppression Of Phospholipase Dγs Confers Increased Aluminum Resistance In Arabidopsis Thaliana, Xuemin Wang, Jian Zhao, Cunxi Wang, Mohamed Bedair, Ruth Welti, Lloyd Sumner, Ivan Baxter

Biology Department Faculty Works

Aluminum (Al) toxicity is the major stress in acidic soil that comprises about 50% of the world's arable land. The complex molecular mechanisms of Al toxicity have yet to be fully determined. As a barrier to Al entrance, plant cell membranes play essential roles in plant interaction with Al, and lipid composition and membrane integrity change significantly under Al stress. Here, we show that phospholipase Dγs (PLDγs) are induced by Al stress and contribute to Al-induced membrane lipid alterations. RNAi suppression of PLDγ resulted in a decrease in both PLDγ1 and PLDγ2 expression and an increase in Al resistance. Genetic …

Land Systems Of The Kimberley Region, Western Australia, A L. Payne, N Schoknecht

Technical Bulletins

The Land Systems of the Kimberley Region Report describes and maps the landscapes, soils and vegetation of the Kimberley region. This report is a consolidation of surveys carried out by different organisations, across different areas of the Kimberley, since the 1940s. The Kimberley region, as defined in this bulletin, covers 330 070km². The report categorises the Kimberley region into 111 land systems. Under each land system, the report identifies the vulnerabilities of those areas, and provides recommendations on how to achieve sustainable use. The report also publishes pasture types for the entire region and the grazing potential for each pasture, …

Bacterial Interactions Of Inoculated Price's Potato Bean (Apios Priceana): A Biological Study, Rhonda Walker

Masters Theses & Specialist Projects

Apios priceana is a native endangered species plant found in the Southeast United States. It is characterized as a leguminous species that bears wisteria like clusters with pea like flowers, a large tuberous root and four to six inch long seed pods. It is believed the Native Americans and early European settlers relied on this species as a source of protein and utilized the seeds for cultivation of the tuberous “potato” which formed. Apios priceana contains an average of 13% fiber, 6.9% protein, 71% carbohydrate and 9 of the 11 essential amino acids needed in human diets (Walter et al.,1986). …

Groundwater Chemistry Of The Weaber Plain: Preliminary Results, Adam Lillicrap, Paul Raper, Richard J. George Dr, D L. Bennett

Resource management technical reports

In 2008, the Ord Irrigation Expansion Project was approved by the Western Australian Government to develop irrigated agriculture on the Weaber Plain. Construction of the M2 supply channel connecting the ORIA and the Weaber Plain, and the final period of irrigation design, environmental management and related approval processes, commenced later in 2009. This process followed a protracted period of public and private industry planning and environmental assessment (Kinhill 2000). This report summarises an analysis of groundwater salinity trends on the Ivanhoe and Weaber plains and the preliminary results of an intensive water-quality sampling program carried out in 2010 as part …

Stock Assessment For The Shark Bay Scallop Fishery, Mervi Kangas, Errol Brown, Marie Shanks, Arani Chandrapavan, Adrian Thomson

Fisheries Research Reports

The Shark Bay scallop fishery is based on a single species Amusium balloti and is the most valuable scallop fishery (AUD 10-57 million) in Western Australia. This species is short-lived, has fast growth and highly variable recruitment which is primarily environmentally driven. The scallop fishery consists of two classes of licences, A and B. There are fourteen Licensed Fishing Boats with A Class licences that target scallops and account for approximately 70% of the catch. There are twenty-seven Class B licences, which primarily fish for prawns (in the Shark Bay Prawn Managed Fishery) with scallops a secondary target species. Restructuring …

Sagestep News, Winter 2011, No. 14, Sagestep

Newsletters

Seasonal newsletter of SageSTEP.

Sagestep News, Fall 2011, No. 16, Sagestep

Newsletters

Seasonal newsletter of SageSTEP.

A Comparison Of Current Anuran Monitoring Methods With Emphasis On The Accuracy Of Automatic Vocalization Detection Software, Jacob Douglas Eldridge

Masters Theses & Specialist Projects

Currently, a variety of methods are available to monitor anurans, and little standardization of methods exists. New methods to monitor anurans have become available over the past twenty years, including PVC pipe arrays used for tree frog capture and Automated Digital Recording Systems (ADRS) used to remotely monitor calling activity. In addition to ADRS, machine-learning computer software, automated vocalization recognition software (AVRS), has been developed to automatically detect vocalizations within digital sound recordings. The use of a combination of ADRS and AVRS shows the promise to reduce the number of people, time, and resources needed for an effective call survey …

Genotypic And Phenotypic Variation In Pseudomonas Aeruginosa Reveals Signatures Of Secondary Infection And Mutator Activity In Certain Cystic Fibrosis Patients With Chronic Lung Infections, Ashley E. Warren, Carla M. Boulianne-Larsen, Christine B. Chandler, Kami Chiotti, Evgueny Kroll, Scott R. Miller, Francois Taddei, Isabelle Sermet-Gaudelus, Agnes Ferroni, Kathleen Mcinnerney, Michael J. Franklin, Frank Rosenzweig

Biological Sciences Faculty Publications

Evolutionary adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung is limited by genetic variation, which depends on rates of horizontal gene transfer and mutation supply. Because each may increase following secondary infection or mutator emergence, we sought to ascertain the incidence of secondary infection and genetic variability in populations containing or lacking mutators. Forty-nine strains collected over 3 years from 16 patients were phenotyped for antibiotic resistance and mutator status and were genotyped by repetitive-sequence PCR (rep-PCR), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Though phenotypic and genetic polymorphisms were widespread and clustered more strongly within than …

Lack Of Fire Has Limited Physiological Impact On Old-Growth Ponderosa Pine In Dry Montane Forests Of North-Central Idaho, Eric Keeling, Anna Sala, Thomas H. Deluca

Biological Sciences Faculty Publications

Reduced frequency of fire in historically fire-adapted ecosystems may have adverse effects on ecosystem structure, function, and resilience. Lack of fire increases stand density and promotes successional replacement of seral dominant trees by late-successional, more shade-tolerant species. These changes are thought to increase competition for limited resources among trees and to increase physiological stress of dominant, fire-adapted species. However, there has been little effort to directly investigate effects of lack of fire on the physiological status of old trees, especially in unlogged, protected forests. At four remote sites in the Selway-Bitterroot region of Idaho, we tested whether the physiological status …

Evolution Of Coordinated Mutagenesis And Somatic Hypermutation In Vh5, Barbara E. Wright, Karen H. Schmidt, Aaron T. Hunt, Dennis K. Reschke, Michael F. Minnick

Biological Sciences Faculty Publications

The VH5 human antibody gene was analyzed using a computer program (mfg) which simulates transcription, to better understand transcription-driven mutagenesis events that occur during "phase 1" of somatic hypermutation. Results show that the great majority of mutations in the non-transcribed strand occur within loops of two predicted high-stability stem-loop structures, termed SLSs 14.9 and 13.9. In fact, 89% of the 2505 mutations reported are within the encoded complementarity-determining region (CDR) and occur in loops of these high-stability structures. In vitro studies were also done and verified the existence of SLS 14.9. Following the formation of SLSs 14.9 and 13.9, a …

Skeletal Muscle Function, Morphology, And Biochemistry In Ts65dn Mice: A Model Of Down Syndrome, Patrick Michael Cowley

Exercise Science - Dissertations

A common clinical observation of persons with Down syndrome at all developmental stages is hypotonia and generalized muscle weakness. The cause of muscle weakness in Down syndrome is not known and there is an immediate need to establish an acceptable animal model to explore the muscle dysfunction that is widely reported in the human population. Using a combination of functional, histological, and biochemical analyses this dissertation provides the initial characterization of skeletal muscle from the Ts65Dn mouse, a model of Down syndrome. The experiments revealed that Ts65Dn muscle over-expresses SOD1 protein but this did not lead to oxidative stress. Ts65Dn …

A General Target For Mvps: Unsupported And Unnecessary, Curtis H. Flather, Gregory D. Hayward, Steven R. Beissinger, Philip A. Stephens

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

In a recent article in TREE [1], we reviewed evidence for a consistent standardized estimate of minimum viable populations (MVPs) across taxa [2–4] and found that the universal MVP of 5000 adults advocated by Traill et al. [5] was unsupported by reanalyses of their data. We identified shortcomings in the original analyses, and found substantial uncertainty in standardized MVP estimates, both within populations of the same species and among species. We concluded that neither data nor theory supported a generally applicable MVP.

No evidence refuting the technical problems that we identified in their original analyzes was presented by Brook …

Antitrypanosomal Activities And Cytotoxicity Of Some Novel Imido-Substituted 1,4-Naphthoquinone Derivatives, Clarence Lee

Department of Biology Faculty Publications

The antitrypanosomal activities, cytotoxicity, and selectivity indices of eleven imido-substituted 1,4-naphthoquinone derivatives and nifurtimox have been studied. Compared to nifurtimox (IC(50) = 10.67 μM), all the imido-naphthoquinone analogs (IMDNQ1-IMDNQ11) are more potent on Trypanosoma cruzi with IC50 values ranging from 0.7 μM to 6.1 μM (p < 0.05). Studies of the cytotoxic activities of these compounds on a Balb/C 3T3 mouse fibroblast cell line revealed that four of these compounds, IMDNQ1, IMDNQ2, IMDNQ3, and IMDNQ10 displayed selectivity indices of 60.25, 53.97, 31.83, and 275.3, respectively, rendering them significantly (p < 0.05) more selective in inhibiting the parasite growth than nifurtimox (selectivity index = 10.86).

Antitrypanosomal Activities And Cytotoxicity Of Some Novel Imido-Substituted 1,4-Naphthoquinone Derivatives, Franklin Ampy

Department of Biology Faculty Publications

The antitrypanosomal activities, cytotoxicity, and selectivity indices of eleven imido-substituted 1,4-naphthoquinone derivatives and nifurtimox have been studied. Compared to nifurtimox (IC(50) = 10.67 μM), all the imido-naphthoquinone analogs (IMDNQ1-IMDNQ11) are more potent on Trypanosoma cruzi with IC50 values ranging from 0.7 μM to 6.1 μM (p < 0.05). Studies of the cytotoxic activities of these compounds on a Balb/C 3T3 mouse fibroblast cell line revealed that four of these compounds, IMDNQ1, IMDNQ2, IMDNQ3, and IMDNQ10 displayed selectivity indices of 60.25, 53.97, 31.83, and 275.3, respectively, rendering them significantly (p < 0.05) more selective in inhibiting the parasite growth than nifurtimox (selectivity index = 10.86).

Worldwide Distribution Of Allelic Variation At The Progesterone Receptor Locus And The Incidence Of Female Reproductive Cancers, Fatimah Linda Collier Jackson

Department of Biology Faculty Publications

Global patterns of the incidence of cancer are often attributed to environmental and lifestyle differences between regions. Less attention has been given to global patterns of allelic variation of genes that may contribute to the risk of developing cancer.We genotyped samples from 21 populations for four variants of the progesterone receptor (PR) gene. One is an Alu insertion in intron 7 which defines the PROGINS haplotype. The others include a promoter region SNP 331+ G/A (rs10895068), a haplotype defining T/C substitution in intron 6 (rs561650), and an A/T substitution (rs608995) in the 3' untranslated region of the gene. All variants …

Gene Expression And Physiological Analyses To Study Metabolic Shifts In Medicago Truncatula Subjected To Biotic Stresses, Michelle Ryan Martin

Graduate Theses and Dissertations

Plants are frequently under attack from pests and deploy various defense mechanisms to fight off predators. Many plant defenses are induced following herbivory or pathogen infection. An investment in defense could potentially lead to a diversion of metabolic resources away from primary metabolism, including reduction in plant commitment to photosynthesis. In this thesis, changes in expression levels of representative genes for primary and secondary metabolism were studied using real-time polymerase chain reaction (PCR) in Medicago truncatula Gaertner subjected to beet armyworm (Spodoptera exigua H¨¹bner) damage or Phoma medicaginis Malbr. & Roum. infection. Photosynthetic yield was also measured using chlorophyll fluorescence …

Hands-On Labs (Hol): Using Technology And Web-Based Resources To Transform A Traditional Lab-Based Biology Course Into A Distance Learning (Dl) Hybrid Course, Across Schools At Pace University., Erica Kipp

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Diversification Or Cotton Recovery In The Malian Cotton Zone: Effects On Households And Women, Jeanne Yekeleya Coulibaly

INTSORMIL Scientific Publications

This dissertation investigates income diversification alternatives from the cotton economy and compares those initiatives with present policy measures to restore the cotton sector in Mali. It also derives the welfare implications for women of these various policy measures.

During the decade preceding 2011, farmers’ incomes in the cotton zone of Mali have been significantly affected by the downturn of the cotton economy explained by many factors including the low farm gate cotton price, the declining cotton yields and soil fertility concerns. In 2011, the Malian government substantially increased the farm gate cotton price as a result of the world cotton …