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A New Histone Structure Which Binds DNA at Its Eight Subunit N-Termini  [PDF]
Ken Biegeleisen
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102386
Abstract: A new model for the nucleosome is presented. The histone octamer core is unchanged, but the location of the DNA is different. Since the highest number, and highest concentration of positively- charged amino acid residues is located not in the “superhelical ramp” of the octamer core, but rather in the domain of the eight histone subunit N-termini collectively, the DNA is therefore placed there. The role models for the protein and DNA structures in the N-terminal domain are taken from the comparable role models for protein and DNA in the protamine-DNA complex in sperm cells. The histone subunit N-termini are each modeled as beta-strands, with psi/phi values of approximately /﹣130.5° respectively, which gives a straight chain. The DNA is modeled according to the “straight ladder” model of Tai Te Wu. Each DNA phosphate group is bound to a lysine or arginine residue of histone by a 3 A salt bridge. The new model lends itself so readily to further models of higher-order chromatin structure that the problem shifts entirely, from one of deducing any higher-order structure at all, to one of distinguishing between several models which compete for our attention.
The Probable Structure of “Form IV” (Alkali-Denatured Circular DNA)  [PDF]
Ken Biegeleisen
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1103114
Abstract:
A detailed molecular model for alkali-denatured duplex circular DNA (“Form IV”) is proposed. The illustrative biological example used is the replicative form of fx174, a 5 kb duplex circular chromosome. The model explains all of Form IV’s known and peculiar features. In a sedimentation coefficient vs. pH titration, Form IV begins to appear at pH 12.3, at which point it can be persuasively argued that no further supertwists can be added to the already-highly-supertwisted chromosome. Therefore a new structure must appear. The sedimentation coefficient s then undergoes a massive, but initially reversible increase as the pH is raised further, culminating at pH 12.8 with a 250% increase. This degree of compactness can only be explained by a 4-stranded tetraplex structure, consisting of a pair of duplexes whose base pairs are mutually intercalated. Above pH 12.8, the structural changes become irreversible, suggesting a further conformational change. It is proposed that this involves an axial rotation of the component duplex strands, so that the bases now stack on the outside, and the phosphate groups lie in the core, where they bond ionically by means of salt bridges. When the irreversibly denatured compact structure is neutralized at moderate-to-high salt concentrations, a third novel structure appears, which has a sedimentation coefficient midway between the native 21 s and the denatured 50 s. It is proposed that this is a hybrid structure; part tetraplex, part duplex. To return to a fully-duplex form, it is necessary to both neutralize the solution, and also to greatly reduce the ionic strength, i.e., to the range 0.001-0.01 M. Since the DNA, under those conditions, cannot possibly have normal complementary base-pairing, the duplex structure must either be tautomerically base-paired, or else stabilized solely by base-stacking, with no base-pairing at all.
Is “Time” Speeding up?  [PDF]
Ken Biegeleisen
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1103196
Abstract:
This article considers the possibility that there might be a plausible scientific explanation for the 900-year lifespans of the characters in the beginning of the biblical book of Genesis. The explanation is based upon the hypothesis that there may be two different forms of “time”. The first form would be “astronomical” time, which is based upon the quasi-perpetual rotational and revolutionary motions of heavenly bodies. The rates of these processes, which ideally consume no energy, have been, to a first approximation, relatively invariant, at least within the brief temporal framework of recorded human history. The second form of time would be “thermodynamic” time, the measurement of which is based upon the movements of clocks, whose reported rates of passage of time are linked inextricably to a decrease in the free energy of the system. This second form of time is the form generally employed to measure the rates of progress of physical phenomena, such as chemical reactions. If the underlying rate of passage of thermodynamic time had changed at some point in history, both the chemical reactions and the clocks used to measure their progress, would have changed together, which change might therefore have gone unnoticed. The effects of a changing thermodynamic clock on human perception of the world, and upon the perceived speed of light, are discussed.
Methods for Non-Destructively Separating or Reannealing the Strands of Circular Duplex DNA Chromosomes  [PDF]
Ken Biegeleisen
Open Access Library Journal (OALib Journal) , 2017, DOI: 10.4236/oalib.1103353
Abstract:
Although it is not widely-known, the strands of circular duplex plasmid and viral chromosomes have been non-destructively separated, and the separated strands have been reconstituted to yield a new duplex structure with all the properties of the native chromosome restored. This suggests a paranemic structure for the DNA, that is, a structure whose strands are not topologically linked by plectonemic (i.e., Watson-Crick) twists. The reason that these phenomena are largely unknown to the general scientific public is that they were either published in obscure journals, or not published at all. Moreover, the methods employed to obtain these results were very difficult, time-consuming and expensive, wherefore they are not likely to be repeated anytime soon. Since these phenomena would be of great interest to the general scientific public, the experiments therefore need to be repeated, but in a way that is easy, fast and inexpensive to perform, so that the results may be readily reproduced in other laboratories. Two such experiments are described herein.
Evolution and the Prevention of Violent Crime  [PDF]
Jason Roach, Ken Pease
Psychology (PSYCH) , 2011, DOI: 10.4236/psych.2011.24062
Abstract: This paper suggests how violence prevention can be better informed by embracing an evolutionary approach to understanding and preventing violent crime. Here, ethical crime control through an evolutionary lens is considered and speculation is offered as to what an evolution-evidenced crime reduction programme might look like. The paper begins with an outline of the current landscape of crime prevention scholarship within criminology and presents some possible points of contact with actual or possible violence reduction practice, including child homicide and violence against women. The paper concludes with suggestions for an ethical research agenda for reducing violence, whereby it is hoped that an audience of open-minded criminologists and diverse students of evolution may lend a hand in increasing the sophistication of the criminological study of violence prevention.
International Outsourcing and Long-Run Growth in a Variety Expansion Model  [PDF]
Ken-ichi Hashimoto
Theoretical Economics Letters (TEL) , 2012, DOI: 10.4236/tel.2012.24072
Abstract: We develop a North-South trade model including the opportunity for outsourcing in a variety expansion framework and derive the effect of an increase in outsourcing on long-run growth. We find that the effect of increased outsourcing on the growth rate of product variety is contingent on the labor size of the Northern and Southern economy. In particular, if the relative labor size of South to North is smaller, outsourcing the production of intermediate goods to Southern economy can have negative effects on economic growth.
A Neural Network and Expert Systems Based Model for Measuring Business Effectiveness of Information Technology Investment  [PDF]
Mahmud Mavaahebi, Ken Nagasaka
American Journal of Industrial and Business Management (AJIBM) , 2013, DOI: 10.4236/ajibm.2013.32030
Abstract:

Today’s indispensable bound between Information Technology (IT) and Business bears heavy expectations on IT to enable firms achieve their strategic business goals and drive competitiveness [1] and revenue growth via offered Technology Solutions and Services. To assess achievement level associated with such expectations, mechanisms must exist for determining the relationship between Organization’s Technology investments and services provided by IT, enabling quantification of effectiveness. In spite of many methods and tools on the market for measuring the Return On Investment (ROI) [2], Net Present Values (NPV), etc., and various studies that have been conducted toward measuring IT’s Business effectiveness, the result has been mostly qualitative, speculative and hypothetical. A mechanism does not seem to exist for measuring [3] quantitatively the effectiveness of incurred technology investment in an organization by leveraging such concepts as Neural Nets or Fuzzy Logic. While Neural Network has been providing possibilities for solving problems in various fields such as Medicine, Engineering, Finance, Economics, etc., [4] its capabilities do not appear to have been explored adequately in the field of Information Technology. Hence, a research is being conducted to develop a Neural Nets/Expert Systems model that can identify within a firm the correlation between IT cost factors, IT services, percentage of utilized services by Business Functions and their associative technology costs inline with the percentage of contributions made by each Function toward achieving Business Objectives. Once developed, the model can calculate Yielded Unit Costs of IT Services and Business Objectives for comparison with their respective optimized unit costs to determine effectiveness and impact that Technology investment has caused on achieving Objectives during a given fiscal period. Neural Network’s modeling is used for developing patterns and quantifying correlations between various layers based on past experiences. Additionally, the model can more accurately forecast required Technology investment for an upcoming fiscal period.

Protecting Water Quality and Public Health Using a Smart Grid  [PDF]
Ken Thompson, Raja Kadiyala
Computational Water, Energy, and Environmental Engineering (CWEEE) , 2013, DOI: 10.4236/cweee.2013.22B013
Abstract: After the attacks on September 11, 2001 and the follow-up risk assessments by utilities across the United States, securing the water distribution system against malevolent attack became a strategic goal for the U.S. Environmental Protection Agency. Following 3 years of development work on a Contamination Warning System (CWS) at the Greater Cincinnati Water Works, four major cities across the United States were selected to enhance the CWS development conducted by the USEPA. One of the major efforts undertaken was to develop a process to seamlessly process “Big Data” sets in real time from different sources (online water quality monitoring, consumer complaints, enhanced security, public health surveillance, and sampling and analysis) and graphically display actionable information for operators to evaluate and respond to appropriately. The most significant finding that arose from the development and implementation of the “dashboard” were the dual benefits observed by all four utilities: the ability to enhance their operations and improve the regulatory compliance of their water distribution systems. Challenge: While most of the utilities had systems in place for SCADA, Work Order Management, Laboratory Management, 311 Call Center Management, Hydraulic Models, Public Health Monitoring, and GIS, these systems were not integrated, resulting in duplicate data entry, which made it difficult to trace back to a “single source of truth.” Each one of these data sources can produce a wealth of raw data. For most utilities, very little of this data is being translated into actionable information as utilities cannot overwhelm their staffs with manually processing the mountains of data generated. Instead, utilities prefer to provide their staffs with actionable information that is easily understood and provides the basis for rapid decision-making. Smart grid systems were developed so utilities can essentially find the actionable needle in the haystack of data. Utilities can then focus on rapidly evaluating the new information, compare it known activities occurring in the system, and identify the correct level of response required. Solution: CH2M HILL was engaged to design, implement, integrate, and deploy a unified spatial dashboard/smart grid system. This system included the processes, technology, automation, and governance necessary to link together the disparate systems in real time and fuse these data streams to the GIS. The overall solution mapped the business process involved with the data collection, the information flow requirements, and the system and
Genetic and health issues emerging from sperm donation—The experiences and views of donors  [PDF]
Ken Daniels, Wendy Kramer
Advances in Reproductive Sciences (ARSci) , 2013, DOI: 10.4236/arsci.2013.13003
Abstract: 164 previous sperm donors completed an online survey regarding health and genetic experiences and views. Results highlight that donors desire to act responsibly with recruiting facilities is not always possible. Objective: Obtaining the views and experiences of sperm donors regarding health and genetic matters. Design: Online survey. Setting: Not applicable. Participants: 164 previous sperm donors. Interventions: Not applicable. Main outcome measures: Views and experiences on health and genetic issues. Results: A variety of approaches are adopted by recruiting facilities in regard to selection and post-donation factors. The vast majority of donors said they had not been contacted by the facility they donated at to update their medical information, while almost one quarter of donors indicated that a health or genetic risk factor had occurred. A great majority of donors felt that they had not received any education or counselling on the potential curiosities of donor conceived people. Donors sought to be honest and open with staff but often found there were difficulties in doing so. Conclusions: Overall, donors indicate that they see donating as involving responsibilities to the offspring and families. The study highlights however that their ability to act responsibly is limited by some of the interactions or lack of them with the facilities where they donated. Implications for recruiting facilities need to be considered.
Oxygen Isotope Study of Silica Sinter from the Osorezan Geothermal Field, Northeast Japan  [PDF]
Ken-ichiro Hayashi
International Journal of Geosciences (IJG) , 2013, DOI: 10.4236/ijg.2013.410141
Abstract:

Silica sinter developed on the northern shore of Lake Usoriyama in the Osorezan geothermal field was examined for the occurrence, texture, crystallinity of silica minerals, and the concentrations of trace elements and oxygen isotopes. The silica sinter consists of a thick eastern mound (layer A) and a thin western part (layer B). Most of the silica sinter is composed of alternating bands of thin layers of silica minerals with colors varying from white to yellow and reddish gray. There is a unique stromatolitic texture, an aggregate of stratified concentric layers that extends upward and is red to reddish gray in color in the middle of layer A. Silica minerals, mainly opal-A and opal-CT, dominate the mineralogical constituents of the sinter. The δ18O of the silica mineral in layer A varies between 13‰ and 26‰, while layer B has higher values, between 19‰ and 33‰. The hydrothermal fluid from which the silica sinter precipitated is dominated by meteoric water is similar to present-day hot spring water.

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