Life Sciences Commons^™

Laser-Assisted Single-Molecule Refolding, Rui Zhao

Wayne State University Dissertations

Non-coding RNAs must fold into precise secondary and tertiary structures in order to perform the biological functions. Due to the flexibility of RNA, the RNA folding energy landscape can be rugged and full of local minimum (kinetic trap). To provide a means to study kinetically trapped RNAs, we have developed a new technique combining single-molecule FRET detection with laser induced temperature jump. We have calibrated the magnitude of the temperature jump with 1˚C accuracy using gold micro-size sensor. The accuracy of temperature calibration was confirmed by close agreement between single-molecule and bulk DNA duplex melting experiments.

HIV 1 DIS RNAs …

Prevalence Of Piscine Myocarditis Virus (Pmcv) In Marine Fish Species, Torstein Tengs Dr.

Dr. Torstein Tengs

No abstract.

Optimal Control Of Switched Autonomous Systems In Microbial Fed-Batch Cultures, Chongyang Liu, Enmin Feng

Chongyang Liu

A switched autonomous system is proposed to formulate the fed-batch culture process by taking the switching instants between the feed and batch processes as control variables. To maximize the concentration of 1,3-propanediol (1,3-PD) at the terminal time, an optimal control model subject to our proposed switched autonomous system and continuous state inequality constraints is then presented.Acomputational approach is developed to find the optimal switching instants in two aspects. On the one hand, the constraint transcription and smoothing techniques are applied to dealing with the continuous state inequality constraints; on the other hand, the first and the second derivatives of the …

The Domain Of Images, Chapter 1, In Portuguese, James Elkins

James Elkins

This is the opening chapter of the book "Domain of Images" (Cornell University Press), in Portuguese.

The Stability Of The Extended Model Of Hypothalamic-Pituitary-Adrenal (Hpa) Axis Examined By Stoichiometric Network Analysis, Zeljko D. Cupic

Zeljko D Cupic

No abstract provided.

Predictive Modeling Of The Hypothalamic-Pituitary-Adrenal (Hpa) Axis Response To Acute And Chronic Stress, Zeljko D. Cupic

Zeljko D Cupic

No abstract provided.

The Survival Of The Conformist: Social Pressure And Renewable Resource Management, Alessandro Tavoni

Alessandro Tavoni

This paper examines the role of other-regarding behavior as a mechanism for the establishment and maintenance of cooperation in resource use under variable social and environmental conditions. By coupling resource stock dynamics with social dynamics concerning compliance to a social norm prescribing non-excessive resource extraction in a common 10 pool resource, we show that when reputational considerations matter and a sufficient level of social stigma affects the violators of a norm, sustainable outcomes are achieved. We find large parameter regions where norm-observing and norm-violating types coexist, and analyze to what extent such coexistence depends on the environment.

Creating A Soil Data Base In A Reconnaissance Soil Fertility Ssstudy Of An Encroached Forest Reserve In Northern Nigeria For A Reforestation Programme, F O. Adekayode, Dr. Dipo Theophilus Akomolafe Mbcs, Mncs, Mcpn,

Dr. Dipo Theophilus Akomolafe MBCS, MNCS, MCPN,

The reconnaissance soil fertility study of 10,000 ha partly encroached forest reserve located between latitude 11°47’N and 11°56’N and longitude 4°22’E and 4°32’E in Northern Nigeria was conducted in 2009 to generate a soil fertility data base of the reserve. The tracking of the forest reserve boundary was done using a Garmin 72 model global positioning system (GPS) receiver. The geographic coordinates were input into the computer to generate a digital map of the forest reserve. The entire forest reserve was divided into grids to guide in the location for soil sampling using the GPS/Geographic Information System (GIS) geospatial technique. …

Metalurgia Extractiva Y Política Nacional, Fathi Habashi

Fathi Habashi

Should a country export its mineral wealth in form of concentrates or should it locally treat its ores to produce metals as final products? In the past centuries pyrometallurgy was the only route to extract metals from ores and this required a large capital investment many countries could not afford to raise. This situation encouraged marketing of concentrates. Today, metallurgists have the option to use the hydrometallurgical route to process ores and concentrates at a reasonable capital investment. This opened the way to the possibility of processing ores locally. When need arises to increase production new units can be added …

Adaptive Responses To Flooding Incidents In Ilorin, Kwara State, Nigeria, Habiba I. Jimoh, Kayode A. Iroye

Confluence Journal Environmental Studies (CJES), Kogi State University, Nigeria

Incidents of floods which are mainly caused by changes in landuse is fast becoming a city life experience in Ilorin as in most urban centres in Nigeria causing untold hardships and sometimes loss of lives. This extreme hydro-meteorological event is also being exacerbated by climate change which thus calls for adaptive response by residents towards reducing its risks, hence this study. Data used were generated from direct field measurements and questionnaire administration. Descriptive statistics and cross tabulations were used in analyzing the data. Results obtained indicate that most respondents use a wide range of non-structural adaptive response to flood. The …

An Assessment Of Socio-Economic Impact Of Waste Scavenging As A Means Of Poverty Alleviation In Gwagwalada, Abuja., John Yakubu Magaji, Samuel Panse Dakyes

Confluence Journal Environmental Studies (CJES), Kogi State University, Nigeria

Waste scavengers are usually perceived as being among the poor, and scavenging is considered a marginal activity. They tend to have low incomes, but can obtained decent earning when they are not exploited by middlemen. This study was conducted in Gwagwalada town with the aim of assessing the socio-economic impact of scavenging on the people. A structured questionnaire was constructed to capture the demographic characteristics of the scavengers, their experiences, types of items scavenged, the economic gains and the challenges being faced. The target pollution is waste scavengers and a random sampling technique was adopted in selecting the respondents for …

Generalized Benjamini-Hochberg Procedures Using Spacings, Debashis Ghosh

Debashis Ghosh

For the problem of multiple testing, the Benjamini-Hochberg (B-H) procedure has become a very popular method in applications. We show how the B-H procedure can be interpreted as a test based on the spacings corresponding to the p-value distributions. Using this equivalence, we develop a class of generalized B-H procedures that maintain control of the false discovery rate in finite-samples. We also consider the effect of correlation on the procedure; simulation studies are used to illustrate the methodology.

Software For Assumption Weighting For Meta-Analysis Of Genomic Data, Debashis Ghosh, Yihan Li

Debashis Ghosh

This is the software that accompanies Li and Ghosh, "Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data."

A Causal Framework For Surrogate Endpoints With Semi-Competing Risks Data, Debashis Ghosh

Debashis Ghosh

In this note, we address the problem of surrogacy using a causal modelling framework that differs substantially from the potential outcomes model that pervades the biostatistical literature. The framework comes from econometrics and conceptualizes direct effects of the surrogate endpoint on the true endpoint. While this framework can incorporate the so-called semi-competing risks data structure, we also derive a fundamental non-identifiability result. Relationships to existing causal modelling frameworks are also discussed.

Propensity Score Modelling In Observational Studies Using Dimension Reduction Methods, Debashis Ghosh

Debashis Ghosh

Conditional independence assumptions are very important in causal inference modelling as well as in dimension reduction methodologies. These are two very strikingly different statistical literatures, and we study links between the two in this article. The concept of covariate sufficiency plays an important role, and we provide theoretical justication when dimension reduction and partial least squares methods will allow for valid causal inference to be performed. The methods are illustrated with application to a medical study and to simulated data.

Dead Zones In Porous Catalysts: Concentration Profiles And Efficiency Factors, Roger L. York, Kaitlin M. Bratlie, Lloyd R. Hile, Larry K. Jang

Kaitlin M. Bratlie

This paper examines the conditions under which a dead zone, or a portion of the catalyst devoid of reactant, can form in a porous catalyst in which simultaneous reaction and diffusion are occurring. The condition that allows for the existence of a dead zone is defined by a critical Thiele modulus. When the Thiele modulus - the ratio of chemical reaction to diffusion - is greater than the critical Thiele modulus, a dead zone exists. This dead zone can be mathematically defined by a change of boundary conditions. We examine nth order reactions in isothermal infinite slabs, infinite cylinders, and …

Asymmetry In Chemical Structures And In Life: My Last Two Articles, Otto Vogl

Otto Vogl

No abstract provided.

Measured And Predicted Temporal Changes In Soil Nitrate-N Levels From Late Summer To Early Spring In Montana, Andrew W. Lenssen, Clain Jones, Chengci Chen, Kent Mcvay, Bob Stougaard, Mal Westcott, Joyce Eckhoff, Jennifer Weeding, Mark Greenwood

Andrew W. Lenssen

Most soil sampling is conducted from August to November in Montana because of better soil sampling conditions and because it provides more time for growers to make fertilizer decisions prior to application. Fertilizer guidelines in Montana are based on spring nitrate-N levels in the upper 2 ft because they are more indicative of growing season available N than fall nitrate-N levels. It is not known how much nitrate-N levels change between late summer and spring, nor is it known what factors affect these changes, and large changes could result in either over-application of N fertilizer or sub-optimal yields. A three-year …

Center Of Umass – Industry Research On Polymers: Cumirp: Inception And Founding, Otto Vogl

Otto Vogl

No abstract provided.

Polymer Science And The Arts: Oriental Lacquer, Otto Vogl

Otto Vogl

No abstract provided.

A Primer Of Swarm Equilibria, Andrew J. Bernoff, Chad M. Topaz

Chad M. Topaz

We study equilibrium configurations of swarming biological organisms subject to exogenous and pairwise endogenous forces. Beginning with a discrete dynamical model, we derive a variational description of the corresponding continuum population density. Equilibrium solutions are extrema of an energy functional, and satisfy a Fredholm integral equation. We find conditions for the extrema to be local minimizers, global minimizers, and minimizers with respect to infinitesimal Lagrangian displacements of mass. In one spatial dimension, for a variety of exogenous forces, endogenous forces, and domain configurations, we find exact analytical expressions for the equilibria. These agree closely with numerical simulations of the underlying …

Niche Of Harmful Alga Aureococcus Anophagefferens Revealed Through Ecogenomics, Christopher Gobler, Dianna Berry, Sonya Dyhrman, Steven Wilhelm

Steven Wilhelm

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. …

A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers

Daryl K. Eggers

A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning …

Changes In Apparent Molar Water Volume And Dkp Solubility Yield Insights On The Hofmeister Effect, Daryl K. Eggers, A. Y. Payumo, R. M. Huijon, D. D. Mansfield, L. M. Belk, A. K. Bui, A. E. Knight

Daryl K. Eggers

This study examines the properties of a 4 × 2 matrix of aqueous cations and anions at concentrations up to 8.0 M. The apparent molar water volume, as calculated by subtracting the mass and volume of the ions from the corresponding solution density, was found to exceed the molar volume of ice in many concentrated electrolyte solutions, underscoring the nonideal behavior of these systems. The solvent properties of water were also analyzed by measuring the solubility of diketopiperazine (DKP) in 2.000 M salt solutions prepared from the same ion combinations. Solution rankings for DKP solubility were found to parallel the …

Effects Of Normative Messages On Pro-Environmental Attitudes And Behaviorseffects Of Normative Messages On Pro-Environmental Attitudes And Behaviors, Connor Harron

Occam's Razor

As stated in the fourth assessment report of the Intergovernmental Panel on Climate Change (IPCC), the planet’s climate is warming at an unprecedented rate, and humans are responsible for the large majority of causes creating this situation. If humans are to repair the balance between themselves and nature, then a global environmental movement that includes widespread behavior and attitude reconstruction will have to occur. The current study seeks to build upon past research attempting to promote pro-environmental behavior change in individuals. The author examines the ability of modeling and norms presented in a video format to motivate individuals to change …

Occam's Razor Vol. 1 - Full (2011)

Occam's Razor

No abstract provided.

Ultra-Diffuse Hydrothermal Venting Supports Fe-Oxidizing Bacteria And Massive Umber Deposition At 5000 M Off Hawaii, Katrina J. Edwards, B. T. Glazer, Olivier J. Rouxel, Wolfgang Bach, D. Emerson, Russ E. Davis, Brandy M. Toner, C. S. Chan, B. M. Tebo, Hubert Staudigel, Craig L. Moyer

Biology Faculty and Staff Publications

A novel hydrothermal field has been discovered at the base of Lōihi Seamount, Hawaii, at 5000 mbsl. Geochemical analyses demonstrate that ‘FeMO Deep’, while only 0.2 °C above ambient seawater temperature, derives from a distal, ultra-diffuse hydrothermal source. FeMO Deep is expressed as regional seafloor seepage of gelatinous iron- and silica-rich deposits, pooling between and over basalt pillows, in places over a meter thick. The system is capped by mm to cm thick hydrothermally derived iron-oxyhydroxide- and manganese-oxide-layered crusts. We use molecular analyses (16S rDNA-based) of extant communities combined with fluorescent in situ hybridizations to demonstrate that FeMO Deep deposits …

Computational Methods Of Hidden Markov Models With Respect To Cpg Island Prediction In Dna Sequences, Roberto Angel Ortega

Open Access Theses & Dissertations

Hidden Markov models (HMM's) are a specific case of Markov models where, contrary to Markov chains, the observer is unaware of what state the model was in when the symbol is observed. Like Markov chains, HMM's assume that the future state of a sequence is dependent only on the current state of the sequence. The parameters associated with HMM's are transition and emission probabilities, where transition probabilities are associated with the probability of transitioning from one state to another, and emission probabilities are the probabilities associated with observing a symbol given it came from a specific state.

The structure of …

Abundance And Size Of Quagga Mussels (Dreissena Bugensis) Veligers In Lake Mead, Nevada-Arizona, Shawn Gerstenberger, Sara Ann Mueting, Wai Hing Wong

Environmental & Occupational Health Faculty Publications

The planktonic veligers of the invasive quagga mussel were present year-round from April 2008 to March 2009 in Lake Mead, with high abundance from September to October (>20 veligers/L), whereas the percentage of competent veligers, in terms of the ability to settle, peaked from November 2008 to January 2009 (>60%). The results from this experiment are useful in understanding the life history and population dynamics of quagga mussels in the lower Colorado River Basin.

Quagga Mussels In The Western United States: Monitoring And Management, Wai Hing Wong, Shawn Gerstenberger

Environmental & Occupational Health Faculty Publications

Dreissenid mussels including zebra mussel (Dreissena polymorpha Pallas, 1771), originating from the Ponto-Caspian area, and quagga mussel (Dreissena rostriformis bugensis Andrusov, 1897), originating from the mouths of the Rivers Southern Bug and Dnieper are both species native to Eastern Europe, which were accidently introduced into the Laurentian Great Lakes in North America in the 1980s in ballast water (Carlton 2008; Van der Velde et al 2010). Dreissenid mussels have created severe ecological, recreational and economic impacts on many systems because they are biofoulers and efficient ecological engineers that filter large quantities of water. Examples of these wide-ranging impacts are discussed …