General Research Tool Research Articles

Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry

There has been an almost exponential increase in the use of molecular dynamics simulations in basic research and industry over the last 5 years, with almost a doubling in the number of publications each year. Many of these are focused on neurological membranes, and biological membranes in general, applied to the medical industry. A smaller portion have utilized membrane simulations to answer more basic questions related to the function of specific proteins, chemicals or biological processes. This review covers some newer studies, alongside studies from the last two decades, to determine changes in the field. Some of these are basic, while others are more profound, such as multi-component embedded membrane machinery. It is clear that many facets of the discipline remain the same, while the focus on and uses of the technology are broadening in scope and utilization as a general research tool. Analysis of recent literature provides an overview of the current methodologies, covers some of the recent trends or advances and tries to make predictions of the overall path membrane molecular dynamics will follow in the coming years. In general, the overview presented is geared towards the general scientific community, who may wish to introduce the use of these methodologies in light of these changes, making molecular dynamic simulations more feasible for general scientific or medical research.

Neutron Imaging Facilities in a Global Context

Neutron Imaging (NI) has been developed in the last decades from a film-based inspection method for non-destructive observations towards a powerful research tool with many new and competitive methods. The most important technical step forward has been the introduction and optimization of digital imaging detection systems. In this way, direct quantification of the transmission process became possible—the basis for all advanced methods like tomography, phase-contrast imaging and neutron microscopy. Neutron imaging facilities need to be installed at powerful neutron sources (reactors, spallation sources, other accelerator driven systems). High neutron intensity can be used best for either highest spatial, temporal resolution or best image quality. Since the number of such strong sources is decreasing world-wide due to the age of the reactors, the number of NI facilities is limited. There are a few installations with pioneering new concepts and versatile options on the one hand, but also relatively new sources with only limited performance thus far. It will be a challenge to couple the two parts of the community with the aim to install state-of-the-art equipment at the suitable beam ports and develop NI further towards a general research tool. In addition, sources with lower intensity should be equipped with modern installations in order to perform practical work best.

Fecal Transplants: What Is Being Transferred?

Fecal transplants are increasingly utilized for treatment of recurrent infections (i.e., Clostridium difficile) in the human gut and as a general research tool for gain-of-function experiments (i.e., gavage of fecal pellets) in animal models. Changes observed in the recipient's biology are routinely attributed to bacterial cells in the donor feces (~1011 per gram of human wet stool). Here, we examine the literature and summarize findings on the composition of fecal matter in order to raise cautiously the profile of its multipart nature. In addition to viable bacteria, which may make up a small fraction of total fecal matter, other components in unprocessed human feces include colonocytes (~107 per gram of wet stool), archaea (~108 per gram of wet stool), viruses (~108 per gram of wet stool), fungi (~106 per gram of wet stool), protists, and metabolites. Thus, while speculative at this point and contingent on the transplant procedure and study system, nonbacterial matter could contribute to changes in the recipient's biology. There is a cautious need for continued reductionism to separate out the effects and interactions of each component.

Development of a Field-Deployable Psychomotor Vigilance Test to Monitor Helicopter Pilot Performance.

Flying a helicopter is a complex psychomotor skill. Fatigue is a serious threat to operational safety, particularly for sustained helicopter operations involving high levels of cognitive information processing and sustained time on task. As part of ongoing research into this issue, the object of this study was to develop a field-deployable helicopter-specific psychomotor vigilance test (PVT) for the purpose of daily performance monitoring of pilots. The PVT consists of a laptop computer, a hand-operated joystick, and a set of rudder pedals. Screen-based compensatory tracking task software includes a tracking ball (operated by the joystick) which moves randomly in all directions, and a second tracking ball which moves horizontally (operated by the rudder pedals). The 5-min test requires the pilot to keep both tracking balls centered. This helicopter-specific PVT's portability and integrated data acquisition and storage system enables daily field monitoring of the performance of individual helicopter pilots. The inclusion of a simultaneous foot-operated tracking task ensures divided attention for helicopter pilots as the movement of both tracking balls requires simultaneous inputs. This PVT is quick, economical, easy to use, and specific to the operational flying task. It can be used for performance monitoring purposes, and as a general research tool for investigating the psychomotor demands of helicopter operations. While reliability and validity testing is warranted, data acquired from this test could help further our understanding of the effect of various factors (such as fatigue) on helicopter pilot performance, with the potential of contributing to helicopter operational safety.

Faceted Classification as a General Theory for Knowledge Organization

The Classification Research Group manifesto of 1955, 'Faceted classification as the basis of all information retrieval', has been at least in part achieved, and there is much evidence of faceted classification influencing a whole range of modern information retrieval tools. This paper examines the theory underlying faceted classification, how and why it has been taken up so widely, and what benefits it brings to the activity of knowledge organization. The role of facet analysis as a general research tool is also considered, and how it compares with other content analysis tools as a means of modelling subject domains.

A demonstration of correlation graphs to human body dimensions

A large number of variables and multivariate analyses are required to study complexity. Network analysis is also a valuable complex systems analysis tool. Recently techniques were developed where correlation matrixes are presented as networks, known as correlation graphs. These have been used mainly to study structures in time series data, often in the financial stock markets, and correlation graphs have not been widely adopted. The aim of this paper is to demonstrate correlation graphs as a general research tool by using intuitively understandable data. Correlation graphs of human body shape dimensions were generated and noise reducing techniques are demonstrated. The results support the underlying structures of human biology and gender is distinguished with an accuracy of 89%. Weight plays a vital role and height is more influential in males than in females. With age, males and females become more alike. The potential application of the correlation graphing methodology appears extensive. Key words: Correlation graph, asset graph, multivariate analyses, graph theory, body shape.

A Monte Carlo tool for evaluating VMAT and DIMRT treatment deliveries including planar detectors

The aim of this work is to describe and validate a new general research tool that performs Monte Carlo (MC) simulations for volumetric modulated arc therapy (VMAT) and dynamic intensity modulated radiation therapy (DIMRT), simultaneously tracking dose deposition in both the patient CT geometry and an arbitrary planar detector system. The tool is generalized to handle either entrance or exit detectors and provides the simulated dose for the individual control-points of the time-dependent VMAT and DIMRT deliveries. The MC simulation tool was developed with the EGSnrc radiation transport. For the individual control point simulation, we rotate the patient/phantom volume only (i.e. independent of the gantry and planar detector geometries) using the gantry angle in the treatment planning system (TPS) DICOM RP file such that each control point has its own unique phantom file. After MC simulation, we obtained the total dose to the phantom by summing dose contributions for all control points. Scored dose to the sensitive layer of the planar detector is available for each control point. To validate the tool, three clinical treatment plans were used including VMAT plans for a prostate case and a head-and-neck case, and a DIMRT plan for a head-and-neck case. An electronic portal imaging device operated in ‘movie’ mode was used with the VMAT plans delivered to cylindrical and anthropomorphic phantoms to validate the code using an exit detector. The DIMRT plan was delivered to a novel transmission detector, to validate the code using an entrance detector. The total MC 3D absolute doses in patient/phantom were compared with the TPS doses, while 2D MC doses were compared with planar detector doses for all individual control points, using the gamma evaluation test with 3%/3 mm criteria. The MC 3D absolute doses demonstrated excellent agreement with the TPS doses for all the tested plans, with about 95% of voxels having γ <1 for the plans. For planar dosimetry image comparisons, we defined an acceptable pass rate of >90% of percentage pixels with γ <1. We found that over 90% of control points in the plans passed this criterion. In general, our results indicate that the simulation tool is suitable for accurately calculating both patient/phantom doses and planar doses for VMAT dose delivery. The tool will be valuable to check performance and advance the development of in vivo planar detectors for use in measurement-based VMAT dose verification. In addition, the tool can be useful as an independent research tool for VMAT commissioning of the TPS and delivery system.

Application of the functional-structural tree model LIGNUM to growth simulation of short-rotation eastern cottonwood

The functional-structural tree growth model LIGNUM was developed as a general research tool that can be applied to several tree species. The growth simulation of short-rotation eastern cottonwood (Populus deltoides Bartr. ex Marsh.) inherits the basic LIGNUM modeling concepts including modular tree structure, L-system-based description of structural development, and carbon budget. New developments of LIGNUM model in this study were the incorporation of a biochemically-derived photosynthesis submodel; nested time steps for simulating physiological processes, structural development, and annual biomass production; incorporation of field-measured weather data for modeling the response of physiological processes to environmental variation; and application of a Monte-Carlo voxel space submodel for simulating the stochasticity of tree growth and improving computational efficiency. A specific parameter system was applied for modeling P. deltoides growth in the central Missouri, USA, environment. This adaptation of LIGNUM was applied on modeling growth of P. deltoides in a short-rotation agroforestry practice. The simulated height and biomass growth were close to field observations. Visualization of simulation results closely resembled the trees growing in an open site. The simulated response of tree growth to variations in photon flux input was reasonable. The LIGNUM model may be used as a complement to field studies on P. deltoides in short-rotation forestry and agroforestry.

Dixie Diaspora: An Anthology of Southern Jewish History (review)

Dixie Diaspora: An Anthology of Southern Jewish History, edited by Mark K. Bauman. Tuscaloosa: University of Alabama Press, 2006. 480 pp. $65.00 (c); $35.00 (p). Connoisseurs of the complications of ethnicity, writes Brandeis Professor Stephen J. Whitfield in his 1988 article Braided Identity of Southern Jewry, one of sixteen well-chosen articles by Mark K. Bauman, editor of Dixie Diaspora: An Anthology of Southern Jewish History, can much to meditate in the experience of Southern Jewry. Similarly, historical connoisseurs of American Jewish history, Southern Jewish history as well as numerous other fields of American history in general will find much to meditate upon in this collection of recent, critical historical scholarship by one of the senior and most distinguished scholars of Southern Jewish This anthology, the editor maintains, designed to expose different audiences to the subfield and particularly to the scholarship of the last twenty-five years, and to encourage the integration of southern Jewish history into American, southern, religious, ethnic and Jewish history. At least in this case, the design of the anthology has succeeded both in highlighting the major themes of southern Jewish history and in showcasing many of the new methodological and historiographical approaches employed by contemporary critical scholars. Selection, Bauman further explains, was based on methodological innovation, how well articles opened discussion of key themes, and how well they complemented one another. Moreover, the editor notes that rather than chronology, the articles are organized topically to provide a clearer understanding of contemporary debates and questions. Five topics in all are used as major rubrics for Dixie Diaspora, including I. Jews and Judaism; II. Small-Town Jewish Life; III. Business and Governance; IV. Interaction; and V Identity. With respect to chronology, Dixie Diaspora includes articles from the Colonial period to the present A brief Introduction to the entire book as well as Introductions to each of the anthology's five sections provide helpful conceptual frameworks for the book's readers. An excellent Bibliographical Essay offers a virtual tour of the secondary literature of the southern Jewish experience. The book's only flaw is the absence of a topical index which would have increased its utility as a general research tool. In addition to articles by Bauman and Whitfield, articles by Leonard R. Rogoff (The Racial Place of the Southern Jew), Deborah R. Weiner (Appalachian Jewish Women), Lee Shai Weissbach (East European Jews in the South), and Gary P. Zola (Southern Rabbis) are representative of the book's depth and scope. …

Analysis of microbial components using LC-IR.

Characterization of bacteria is currently an important research area in the medical, military, food, and agricultural sciences. In recent years, FT-IR has found an application as a microbiological detection method and as a general research tool. When coupled with a liquid chromatographic system, a new facet of research has evolved. By utilizing the separation ability of typical liquid chromatography systems, matrix elimination is possible, therefore allowing for clean spectra of cellular components. Information about the compositional makeup of various bacteria enhances the overall understanding of biology at the cellular level, provides a quantification of the chemistry of cellular processes, and can be used as a general identification tool. Both whole cells and lysed Escherichia coli cells were investigated in the present study. The cellular components consisting of proteins, glycoproteins, phospholipids, fatty amides and acids, and genomic materials were separated, isolated, and identified by FT-IR.

Web-based surveys for corporate information gathering: A bias-reducing design framework

The cost effectiveness of Internet-based communications in the ever more fully networked business environment continues to drive the use of Web surveys for corporate information gathering. However, simply applying traditional survey techniques to the Web can result in significant shortcomings in the data so gathered. Recent research has been directed at these issues, within the context of Web surveys as a general research tool. We discuss the application of that research to the narrower organizational context. This article synthesizes from the literature on Web-based surveying and from the authors' own experiences. It suggests a design framework for managers and communications professionals interested in increasing the statistical validity of Web surveys deployed in an organizational context. The results of a recent organizational Web survey developed and administered within the framework guidelines support the efficacy of the framework.

超流動衝撃波管装置の開発及びその動作特性試験結果

The superfluid shock-tube facility has been developed as a versatile tool for general research of low-temperature thermo-fluid dynamic phenomena. The shock tube was designed to be operated with the He II-filled test section immersed in superfluid helium. A gasdynamic shock wave impinging onto a He II-free surface generates a transmitted compression shock wave (of first sound origin) and thermal shock wave (of second sound origin) as the genuine temperature wave in He II. The target physical phenomena in the He II are measured using pressure transducers and superconductive temperature sensors, by applying a laser beam refraction method and with the aid of some optical visualization methods. In this study, the general superfluid thermodynamic performance of shock waves in the facility is investigated to verify the validity of the facility under a wide range of experimental conditions.

TPS: A theorem-proving system for classical type theory

This is description of TPS, a theorem-proving system for classical type theory (Church's typed λ-calculus). TPS has been designed to be a general research tool for manipulating wffs of first- and higher-order logic, and searching for proofs of such wffs interactively or automatically, or in a combination of these modes. An important feature of TPS is the ability to translate between expansion proofs and natural deduction proofs. Examples of theorems that TPS can prove completely automatically are given to illustrate certain aspects of TPS's behavior and problems of theorem proving in higher-order logic.

Sub-ambient measurement of platelet function: the requirements for modification of a standard platelet aggregometer.

This methodological report documents the electro-mechanical modifications that were applied to a commercially available aggregometer, in order to achieve direct platelet aggregation measurement at sub-ambient temperatures. This development provides a facility, not previously available, for examining certain aspects of platelet physiology at any desired temperature. This innovation was primarily developed for investigating optimum storage parameters for platelets, as they apply to clinical blood transfusion practice. However, a wider scope of application is envisaged, including its use as both a general research tool, and eventually as an additional component of clinical measurement in the routine coagulation laboratory. Some illustrative data is briefly provided.

OR Practice—Solving Complex Chemical Equilibria Using a Geometric-Programming Based Technique

Determining the composition of a chemical system at equilibrium is an important problem that arises in many fields of science and engineering. For complex equilibria, the use of a digital computer is required. The chemist often finds the use of current computer codes an inefficient and frustrating experience. This paper presents a globally convergent algorithm for the solution of chemical equilibrium problems. This algorithm has been made both efficient and easy to use and is now employed successfully by chemists on important problems. It is based on the application of geometric programming principles to solve systems of nonlinear equations. Although presented in a form that can be quickly understood by the practitioner, the methodology is mathematically rigorous. Computer programs that require no familiarity with the details of the methodology were developed and extensively tested. These programs can be used as general research tools for investigating the solution of nonlinear equations in areas other than chemistry.

Ion Implantation in Metals

The purpose of this chapter is to give an overview of ion implantation in metals. This field has expanded into many areas; however, most of the work may be categorized into one of two areas. The first, and the major emphasis of this chapter, is the use of ion implantation to modify the properties of materials. This use of implantation is proving to be a valuable tool in developing our understanding of the microscopic basis of materials' properties. In addition, there is the potential of tailoring surface properties of metal components for specialized applications. The second major area is the use of ion implantation as a general research tool. This controlled introduction of elements and defects provides a method to explore kinetics and equilibria in metal alloying reactions, to investigate the formation of new phases, and to simulate radiation effects relevant to nuclear reactor environments. Current uses of ion implantation extend from research laboratory studies of metastable phase formation to production line fabrication of integrated circuits. This widespread application of ion implantation stems from several advantages' of the process. The number of ions implanted can be controlled by counting the charge each ion brings to the surface. In addition the penetration depth can be independently controlled by varying the energy of the incident beam. Thus the composition as a function of depth can be tailored over a wide range. Finally, pure beams of any atomic number can be implanted into almost any solid, opening an almost endless range of material combinations that can be explored. These advantages lead to extreme control and versatility of the process. There are a number of special features of ion-implanted materials. First,

The assessment of a plasma melatonin assay using gas chromatography negative ion chemical ionization mass spectrometry.

It has been shown that negative ion chemical ionization can increase the sensitivity of the mass spectrometric assay of the pineal hormone melatonin. However, it is an exacting assay requiring extensive sample preparation which precludes its use as a general research tool. We have investigated different derivatizing reagents and reaction conditions to demonstrate that a simple negative ion chemical ionization assay can be developed which will measure low picogram or even femtogram levels of the hormone in samples where the data have been ambiguous.