bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluid dynamics as a branch of physics
Authors: Lighthill M. J.
Published: January 2009

I must confess that I have never traveled 5000 miles before to make an after-dinner speech, and I feel warmly appreciative about your having thought of me, 5000 miles away, when you were planning this occasion. To be sure, I know that the difference between an after-dinner speech and any other kind of speech is just a trifle less marked in these longitudes than it is around the meridian of Greenwich, where one can rely on an audience half-seas-over in port and brandy instead of just recovering from the martinis. I was greatly impressed, for example, once at Brown University when a very good dinner indeed was fitted in as a sort of filling in a sandwich between two thick and stodgy talks in a certain adjoining lecture room on “Sound Generated Aerodynamically” and “Shock Wave Boundary Layer Interaction”. The audience stayed awake manfully, even in the inner viscous layers, and no snores were generated, aerodynamically or otherwise.
Correction
Authors: DeWitt Cecile
Published: January 2009

The following items were omitted in the announcement of the session of the Summer School for Theoretical Physics of the University of Grenoble at Les Houches (Physics Today, January 1962, p. 88):

1. A course on “The Sun, Earth Storms and Radiation Belts” will be given by Prof. S. Chapman.

2. A course on “General Circulation and Tides in the Atmosphere” will be given by Prof. G. MacDonald.

3. A limited number of NSF travel grants will be available for US citizens admitted to the Summer School.
Horizons in physics: Cryogenics
Authors: Daunt John G.
Published: January 2009

The present activity in low-temperature physics research, together with the current rapid application of the results of this research to commercial and military uses, is on a far grander and, we may hope, on an equally significant scale as that occurring in that great period at the turn of the century which saw the birth of cryogenics. In the space of little over a decade at that time, the first major achievements in the production of low temperatures were realized, namely the liquefaction of air, hydrogen, and helium; new laboratories dedicated for the first time to low-temperature research were established and through their work the frontiers of our physical knowledge were handsomely enlarged, especially concerning the early foundations of quantum theory. As if this were not enough, this early period saw the beginning of cryogenic engineering on a substantial scale in the almost immediate application of air liquefaction to the separation and production of liquid oxygen and liquid nitrogen. This application of cryogenics, as we are now well aware, was destined to grow into a major industry, separating and supplying not only oxygen and nitrogen but also other gases and products. It is not my purpose to dwell on the many significant contributions which this industry makes to our complex society. I only wish to note how immediate were the uses it made, and still makes, of frontier knowledge in research.
A lawyer's history lesson
Authors: Moe Henry Allen
Published: January 2009

Within the month—this month—one of your many eminent members, Dr. Lee DuBridge, published an article which begins like this: “The fact that social and natural scientists seem to have so little to say to each other is one of the tragedies of modern times.”
The man-made chemical elements beyond uranium
Authors: Seaborg Glenn T.
Published: January 2009

An exciting branch of science, which started as recently as World War II and has a clearly discernible future of great promise, is that of the “transuranium elements”. These are the man-made chemical elements with atomic numbers greater than that of the heaviest natural element, uranium, which has the atomic number 92.
We're only one fourth the way to our goal…
Authors: Klopsteg Paul E.
Published: January 2009

The response from about ten percent of our 16 000 members of the American Institute of Physics must be encouraging to every physicist who takes pride in his profession. Members who have received and read the communications from the Institute regarding the badly needed Development Fund will recall that the Committee is asking only $150000 from the total individual membership and the other $350000 from industries and other sources. The encouragement comes out of the following breakdown of gifts received from individuals up to March 8, 1957.
Data-type abstracts
Authors: Way Katharine
Published: January 2009

The recent increase in new research results in physics hardly needs to be pointed out to those in the field. When single issues of The Physical Review number from 300 to 500 pages in spite of the fact that several new journals have been recently started, the physicist who is trying to “keep up” feels pretty much overwhelmed. How can he read, analyze, digest, and assimilate all the new information that might be helpful to him in his own researches or as a teacher?
Excerpts from a Russian diary
Authors: Alvarez Luis W.
Published: January 2009

I left Los Angeles at midnight on Friday the 11th of May. I was the second through passenger by Scandinavian Airlines (SAS) over the polar route direct to Moscow. Murray Gell-Mann, who attended the conference, was the first such passenger and had his picture taken boarding the plane the day before. We first landed at Winnipeg and then flew over Hudson Bay and Baffin Island and landed in western Greenland, at South Stromfjord, just above the Arctic Circle. (From here on, I'll take it directly from my diary.)
Do technical reports become published papers?
Authors: Gray Dwight E. , Rosenborg Staffan
Published: January 2009

Since World War II the technical report has come to occupy a position of considerable importance among media in which results of scientific research first appear. The estimated 50 000 or more documents of this kind which are issued each year—particularly by laboratories engaged in defense-related research—constitute the first appearance in print of much of the newest and most important scientific information being developed today. Almost half of these reports carry no security classification. Yet, for the most part they are not covered by the standard abstracting and indexing services. This is partly because the enormous complexity of the scientific report picture would make systematic coverage very difficult and partly because it would be almost impossible to assure readers of the abstracts of access to the parent reports.
Further excerpts from a Russian diary
Authors: Alvarez Luis W.
Published: January 2009

Sunday. We had a most amazing tour of the Kremlin today. None of our interpreters had ever been inside the Kremlin walls before, although it is possible to get tickets which allow Russians to go inside. But such tickets do not permit anyone into the buildings and rooms we visited. The normal visitor can only walk in certain places, and look inside the churches. We started our tour by entering the northeast gate under the famous clock tower, the Big Ben of Russia. We watched the changing of the guard at the Lenin-Stalin mausoleum at 10 AM and followed the men as they goose-stepped their way to the northeast gate of the Kremlin. We were taken to the large building where Lenin lived and worked. We passed down a long corridor, which reminded me of the corridor outside the Chiefs of Staff offices in the Pentagon Building. I translated one of the names on the impressive big doors as Mikoyan. We were surprised to find one of the offices open and noticed maps of Russia hanging on the wall. We soon found out, when we were taken inside, that this had been Lenin's private office where he did all his work. The office was arranged exactly as it was when he left. (He was sick for several months in 1923 and died in the spring of 1924.) This room is one of the sacred shrines of Communism and our interpreters were absolutely bug-eyed to find themselves there. Lenin worked at a small desk, sitting in a straight chair. The desk butted up against a felt covered table surrounded by large stuffed leather easy chairs. The table and chairs were for the visitors and government officials who came to talk with him. The room was roughly square and about twenty or twenty-five feet on a side. The wall behind Lenin's chair was covered with bookshelves which were filled with books in Russian, French, German, and English. Lenin read all these languages and was apparently a rather scholarly man. His private apartment, just down the hall, also was filled with books—the guide said there were 20 000 books in Lenin's private study and 2000 in his office. We walked around the room and examined the various objects on the tables. I had the feeling that Lenin might show up at any minute—the room was in such a natural state. There was a large oil painting of Karl Marx on the wall, facing Lenin as he sat at his desk. The maps had been marked by Lenin, and the calendars on the desk and on the wall were opened to a day in 1923.
Corrections to the American Institute of Physics Handbook
Authors: Gray Dwight E.
Published: January 2009

Handbooks as a group possess one unfortunate combination of characteristics. On the one hand, the very nature of their function makes errors and inconsistencies more serious in handbooks than in many other types of publication. On the other, because handbook content is so largely tabular and composed of relatively unrelated sections, mistakes are not as obvious from the context as in publications with greater over-all continuity of thought; thus errors are not as readily recognized in manuscript and proof. In the American Institute of Physics Handbook, avoidance of errors and achievement of complete consistency were further complicated by the magnitude of the copy (some 3500–4000 manuscript pages) and the fact that, to speed publication, production was begun on some parts before the entire manuscript had been completed.
The APS-AAPT Joint Committee for Cooperation with Secondary School Science Teaching
Authors: Jauch J. M.
Published: January 2009

The unsatisfactory state of science education in our secondary schools has been the subject of numerous studies and articles in various journals. It is now generally recognized that effective action must be taken if we are to meet the growing demand for physicists in education, in industry, and in the defense program.
Energy as an ultimate raw material
Authors: Weinberg Alvin M.
Published: January 2009

My purpose in these remarks is to speculate on the role of energy in the “Asymptotic State of Humanity”—that is, the state toward which we are moving, inexorably, because man's urge to multiply is limitless whereas his resources are finite. In my talk I draw very heavily from many authors, in particular, Palmer Putnam, Hans Thirring and, above all, Harrison Brown, who has given much ingenious thought to the matters which I discuss. I choose to dwell on energy; first, because as physicists our basic subject of study is energy; and, second, because the character of the asymptotic state of mankind—whether it will be a bare existence or a passably abundant life—will depend centrally on our capturing an inexhaustible energy supply, either by learning how to burn the seas (fusion) or to burn the rocks (fission) or to trap the sun's energy in a practical way.
Frequency control symposium
Authors: Guttwein G. K. , Plotkin H. H.
Published: January 2009

On May 12, 13, and 14, 1959, the Thirteenth Annual Frequency Control Symposium sponsored by the Frequency Control Division of the US Army Signal Research and Development Laboratory was held at Asbury Park, New Jersey. Besides 700 participants of industrial, educational, and governmental organizations from the US, the Symposium was attended by a sizeable number of engineers and physicists from foreign countries, many of them participating actively in the discussions. Representatives of Canada, England, the Netherlands, West Germany, and Japan also presented papers. The Symposium covered the physical and technical aspects of frequency control with a high degree of completeness. Subjects under discussion ranged from a consideration of how the aging of the universe may affect gravitational and atomic time scales to a report on a mechanized plant for producing quartz crystals.
Physics in engineering education 1958
Authors: Seeger R. J. , Weber E.
Published: January 2009

About three years ago a “Progress Report on Physics in Engineering Education” ended with the hope that “through pioneering and experimental, cooperative planning physicists and engineers will now enter enthusiastically and adventurously a new era in the teaching of Physics and in the teaching of Engineering”. This hope was the result of a report of the Committee on Evaluation of Engineering Education by the American Society for Engineering Education in June 1955. At its June 1958 meeting, E. Weber, Chairman of the Follow-up Committee (ad hoc) on Evaluation of Engineering Education, made a more detailed report of the engineering sciences, which had been merely mentioned in the original report. It consisted of a number of individual reports of special committees, varying from the presentation of broad principles to detailed courses. The subjects were:

Mechanics of Solids

Mechanics of Fluids

Transfer and Rate Processes

Thermodynamics

Electrical Sciences

Nature and Properties of Materials

Engineering Analysis and Design
The 11th Annual Gaseous Electronics Conference
Authors: Rose David J.
Published: January 2009

The Eleventh Annual Gaseous Electronics Conference was held at the Barbizon-Plaza Hotel, New York City, from Wednesday, October 22 through Saturday, October 25, 1958. The conference was sponsored jointly by the Division of Electron Physics of the American Physical Society and by the Bell Telephone Laboratories, Inc. On Thursday, October 23, sessions were held at the Laboratories' Murray Hill location.
The physicist and the National Defense Education Act of 1958
Authors: Overbeck C. J.
Published: January 2009

For many years the college faculty has expressed a dissatisfaction with the scholastic background of college students. An unusual opportunity is presented to physicists now to help improve the science education of the youth of this country. This new opportunity is embodied in Title III of the National Defense Education Act of 1958. Our national security is so dependent on the upgrading of science education that it is imperative to respond fully to the provisions of this Act.
Lattice defects in noble metals
Authors: Sosin A. , Brinkman J. A. , Meechan C. J.
Published: January 2009

On October 16–17, 1958, an international roundtable meeting on “Lattice Defects in the Noble Metals” was held at the laboratory of Atomics International in Canoga Park, California. The meeting was sponsored by the Metallurgy and Materials Branch of the Division of Research, US Atomic Energy Commission, and was chaired by Dr. George Vineyard of the Brookhaven National Laboratory.
The “Little Geneva” Conference
Authors: Schmitt Roland W. , Marcus Paul M.
Published: January 2009

Almost simultaneously with the Second Atoms for Peace Conference in Geneva, Switzerland, a much smaller international group of physicists gathered in Geneva, New York, August 25 to 29, 1958. This group of about 125 scientists met to discuss the “Electronic Properties of Metals at Low Temperatures”, a topic narrow enough to hold the number of participants to manageable size, but broad enough to evoke lively interest.
Lattice vibrations
Authors: Cole H.
Published: January 2009

If you believe in atoms, and believe that atoms bind themselves together to form solids, and are willing to grant that these binding forces are not so strong but that the atoms may vibrate one against the other, then you have a mechanism that can be used to explain many of the properties of solids. In fact this mechanism is very basic to our description of the solid state. Without these atomic oscillations, or lattice vibrations, we would be hard put to explain, say, normal electrical resistance; yet without this mechanism, apparently superconductivity also would be virtually impossible. Luckily, though, many of the things of interest in solid-state physics can be decoupled for the purpose of significant study from the details of the vibrating lattice, although few explanations, indeed, are offered without acknowledging the existence of this large reservoir of lattice interactions. This basic importance of the mechanism leads to an extremely rich historical background on the subject; the number of brilliant, and modest, lights in physics illuminating the theory of these vibrations being great, and growing still.
Power sources
Authors: Moncrief John L.
Published: January 2009

The Thirteenth Annual Power Sources Conference was held April 28–30, 1959, at the Shelbourne Hotel in Atlantic City. What was once a yearly review of progress made in the electrochemical field has been expanded over the past few years to cover all energy sources, power conversion systems, and power control devices which may find application in military programs. The sponsor of the conference, the Power Sources Division of the US Army Signal Research and Development Laboratory, Fort Monmouth, N.J., recognized that such an exchange of information is a practical necessity for specialists in the various fields.
The Varenna Conference on Simple Liquids
Authors: Mayer Joseph E.
Published: January 2009

An international conference on the condensed state of simple systems was held at Varenna sul Lago di Como, Italy, on the 11th to the 14th of September, 1957. The subject of discussion concerned primarily simple liquids and the melting of crystals. The meeting was at the invitation of the Italian Physical Society and was held in the charming Villa Monastero on the shores of Lake Como. Approximately eighty scientists from over eleven different countries attended. Both experimental papers and theoretical papers on statistical mechanical theory composed the formal part of the program.
Fluctuations in solids
Authors: Brophy James J.
Published: January 2009

There are an ever increasing number of topical technical conferences which supplement the general meetings of the various scientific societies. These gatherings, usually devoted to one quite specific research area, provide an opportunity for those scientists actively working in the field to concentrate on their specialty. However, they also increase the number of conferences one feels obliged to attend in order to keep abreast of current activities. That such meetings fulfill a purpose is attested to by the fact that many have grown over the years into formal conferences with attendances of several hundred.
Enhanced synchronizability in scale-free networks
Authors: Chen Maoyin , Shang Yun , Zhou Changsong , Wu Ye , Kurths Jürgen
Published: January 2009

We introduce a modified dynamical optimization coupling scheme to enhance the synchronizability in the scale-free networks as well as to keep uniform and converging intensities during the transition to synchronization. Further, the size of networks that can be synchronizable exceeds by several orders of magnitude the size of unweighted networks.
On the maximum entropy principle and the minimization of the Fisher information in Tsallis statistics
Authors: Furuichi Shigeru
Published: January 2009

We give a new proof of the theorems on the maximum entropy principle in Tsallis statistics. That is, we show that the q-canonical distribution attains the maximum value of the Tsallis entropy, subject to the constraint on the q-expectation value, and the q-Gaussian distribution attains the maximum value of the Tsallis entropy, subject to the constraint on the q-variance, as applications of the non-negativity of the Tsallis relative entropy, without using the Lagrange multipliers method. In addition, we define a q-Fisher information and then prove a q-Cramér–Rao inequality that the q-Gaussian distribution with special q-variances attains the minimum value of the q-Fisher information.
Evolution of surface potential barrier for negative-electron-affinity GaAs photocathodes
Authors: Zou Jijun , Chang Benkang , Yang Zhi , Zhang Yijun , Qiao Jianliang
Published: January 2009

The evolution of surface potential barrier for reflection-mode GaAs photocathodes in an ultrahigh vacuum system has been investigated by using spectral response and angle-dependent x-ray photoelectron spectroscopy (ADXPS) measurements at room temperature. The escape probabilities of electrons emitted into vacuum are obtained as a function of the incident electron energy, surface barrier height, and thickness. Based on the new escape probability expressions, we obtain the surface barrier parameters of the reflection-mode negative-electron-affinity (NEA) cathodes from the fit of the spectral response curves by using quantum-efficiency equations. These parameters reveal the evolution of the NEA cathode surface during the degradation process. In addition, the surface layer structure of both the freshly activated and degraded cathodes is calculated from the ADXPS spectra. The calculated results are in fair agreement with the fitted barrier parameters.
Electronic and optical properties of InGaN quantum dot based light emitters for solid state lighting
Authors: Wu Yuh-Renn , Lin Yih-Yin , Huang Hung-Hsun , Singh Jasprit
Published: January 2009

In this paper, we have made a systematic study of the electronic and optical properties of InGaN based quantum dot light emitters. The valence force field model and 6×6k⋅p method have been applied to study the band structures in InGaN or InN quantum dot devices. Piezoelectric and spontaneous polarization effects are included. A comparison with InGaN quantum wells shows that InGaN quantum dots can provide better electron-hole overlap and reduce radiative lifetime. We also find that variation in dot sizes can lead to emission spectrum that can cover the whole visible light range. For high carrier density injection conditions, a self-consistent method for solving quantum dot devices is applied for better estimation of device performance. Consequences of variations in dot sizes, shapes, and composition have been studied in this paper. The results suggest that InGaN quantum dots would have superior performance in white light emitters.
Tuning the Er3+ sensitization by Si nanoparticles in nanostructured as-grown Al2O3 films
Authors: Núñez-Sánchez S. , Serna R. , López J. García , Petford-Long A. K. , Tanase M. , Kabius B.
Published: January 2009

Nanostructured films consisting of single Si nanoparticles (NPs) and Er3+ ions layers separated by nanometer-scale Al2O3 layers of controlled thickness have been prepared in order to tune the energy transfer between Si NPs and Er3+ ions. The amorphous Si NPs with an effective diameter of ∼4.5 nm are formed during growth and are able to sensitize the Er3+ ions efficiently with no postannealing treatments. The characteristic distance for energy transfer from Si NPs to Er3+ ions in Al2O3 is found to be in the 1 nm range. It is shown that in the nanostructured films, it is possible to achieve an optimized configuration in which almost all the Er3+ ions have the potential to be excited by the Si NPs. This result stresses the importance of controlling the dopant distribution at the nanoscale to achieve improved device performance.
Investigations on magnetic and magnetocaloric properties of the intermetallic compound TbAgAl
Authors: Singh Niraj K. , Kumar Pramod , Suresh K. G. , Nigam A. K.
Published: January 2009

Magnetic and magnetocaloric properties of the intermetallic compound TbAgAl have been investigated. Temperature dependence of magnetization data revealed that TbAgAl exhibits magnetic ordering at 59 K and possesses competing ferromagnetic-antiferromagnetic interactions, which leads to the formation of Griffiths-like phase. The field dependence of magnetization data shows the existence of a metamagnetic-like transition at a critical field of 10 kOe. Unusually potent relaxation effects are seen in the time dependence of magnetization data in the ordered phase. The presence of spin-glass-like state is found to affect magnetocaloric properties of this compound.
Operation and performance analyses of 350 and 700 MHz low-/high-temperature superconductor nuclear magnetic resonance magnets: A march toward operating frequencies above 1 GHz
Authors: Hahn Seungyong , Bascuñán Juan , Lee Haigun , Bobrov Emanuel S. , Kim Wooseok , Ahn Min Cheol , Iwasa Yukikazu
Published: January 2009

Since 2000, a three-phase program with a final goal to complete a 1 GHz high-resolution low-/high-temperature superconductor (LTS/HTS) nuclear magnetic resonance (NMR) magnet has been conducted at the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology (MIT). In a LTS/HTS magnet assembly, a HTS insert is placed in the cold bore of a LTS background magnet. To date, two LTS/HTS magnets have been designed, constructed, and tested: a 350 MHz (LH350) in phase 1 and a 700 MHz (LH700) in phase 2. The program’s target has recently been upgraded from the original goal of 1 GHz to a new goal of 1.3 GHz. In this paper, we present extensive performance analyses of the two LTS/HTS NMR magnets. Spatial homogeneity and temporal stability of LH350 and LH700, examined with harmonic analysis, and four key issues that became evident in the operation of these two magnets are discussed: (1) field constant reduction, (2) “large” residual Z1 gradient and its temporal decay, (3) large one-periodic tesseral field gradients, and (4) screening-current-induced field in the HTS inserts.
Dependence of memory margin of Cap-less memory cells on top Si thickness
Authors: Choi Ki-Ryoung , Lee Choong-Hyun , Kim Seong-Je , Enomoto Hirofumi , Shim Tae-Hun , Cho Won-Ju , Park Jea-Gun
Published: January 2009

We investigated the dependence of Cap-less memory on top of silicon with a thickness between 15.5 and 72.3 nm. It was confirmed that the memory margin depends on the impact ionization rate associated with the increased conduction current density and the decreased lateral electric field as the top silicon thickness increases. In particular, we observed that the maximum memory margin is 61 μA at a 45 nm top silicon thickness, where the impact ionization rate is maximized. Consequently, we obtained the optimal top silicon thickness of 45 nm for Cap-less memory cells operating in fully depleted silicon-on-insulator n-metal-oxide-semiconductor field-effect transistors.
A radio frequency device for measurement of minute dielectric property changes in microfluidic channels
Authors: Song Chunrong , Wang Pingshan
Published: January 2009

We demonstrate a sensitive radio frequency (rf) device to detect small dielectric property changes in microfluidic channel. The device consists of an on-chip Wilkinson power divider and a rat-race hybrid, which are built with planar microstrip lines and thin film chip resistors. Interference is used to cancel parasitic background signals. As a result, the measurement sensitivity is improved by more than 20 dB compared with conventional transmission lines. Compared with an ultrasensitive slot antenna/cuvette assembly [K. M. Taylor and D. W. van der Weide, IEEE Trans. Microwave Theory Tech. 53, 1576 (2005)], the proposed rf device is two times more sensitive.
Open circuit voltage enhancement due to reduced dark current in small molecule photovoltaic cells
Authors: Li Ning , Lassiter Brian E. , Lunt Richard R. , Wei Guodan , Forrest Stephen R.
Published: January 2009

We demonstrate high open circuit voltage photovoltaic cells achieved by reducing the electron leakage current through the introduction of both organic and inorganic electron blocking layers between the donor layer and the anode contact. As an example, the blocking layers reduce the dark current in tin (II) phthalocyanine (SnPc)∕C60 solar cells with response across the visible and near infrared spectral region up to a wavelength of 1000nm, is decreased by two orders of magnitude compared to cells lacking the layers, resulting in a doubling of the open circuit voltage. The structure: indium tin oxide/electron blocker/SnPc (100Å)∕C60 (400Å)/bathocuproine (100Å)∕Al, has a power conversion efficiency of (2.1±0.1)% at 1sun, standard AM1.5G solar illumination. This work demonstrates the importance of reducing dark current to achieve high organic thin film photovoltaic cell efficiencies.
Institutions and the Provision of Local Services in Mexico
Authors: Silva-Ochoa Esteban
Published: January 2009

The growing relevance of local governments in the provision of public services and the implementation of development policies increasingly require an attentive analysis of the determinants of governments' performance at this scale. Among these determinants I analyze the impact of institutional factors in the provision of public goods at the municipal level in Mexico, and more specifically: the institutional capacity (a skilled bureaucracy and local budgets), institutional thickness (civic engagement, corruption), and region size (surface area and population) in the provision of education (literacy), health (child mortality), and housing (electricity, water, and sewerage supply). The results highlight the importance of institutional capacity at the local level, as well as the size of subnational units in the provision of public goods, but there are mixed findings regarding the level of institutional thickness.
agr
receptor mutants reveal distinct modes of inhibition by staphylococcal autoinducing peptides
Authors: Geisinger Edward , Muir Tom W. , Novick Richard P.
Published: January 2009

Through the
agr
quorum-sensing system, staphylococci secrete unique autoinducing peptides (AIPs) and detect their concentration via the AgrC transmembrane receptor, coordinating local bacterial population density with global changes in gene expression. Unique AIP and AgrC variants exist within and between species, and although autologous interactions lead to
agr
activation, heterologous interactions usually lead to cross-inhibition, resulting in natural quorum-sensing interference. To gain insight into the mechanisms responsible for these phenomena at the level of the receptor, we used random mutagenesis to isolate variants of
Staphylococcus aureus
AgrC-I with constitutive activity. Constitutive mutations in the sensor domain of the receptor were localized to the last transmembrane helix, whereas those in the histidine kinase domain were mostly clustered to a region near the phosphorylation site histidine. Analysis of these mutants with a range of noncognate AIPs revealed that inhibition is manifested by inverse agonism in certain heterologous pairings and by neutral antagonism in others. In addition, we isolated and characterized an AgrC sensor domain mutant with dramatically broadened activation specificity and reduced sensitivity to inhibition, identifying a single amino acid as a critical determinant of ligand-mediated inhibition. These results suggest that certain noncognate AIPs stabilize an inhibitory receptor conformation that may be a critical feature of the ligand–receptor interaction not initially appreciated in previous analyses of
agr
inhibition.
Signaling gradients in cascades of two-state reaction-diffusion systems
Authors: Berezhkovskii Alexander M. , Coppey Mathieu , Shvartsman Stanislav Y.
Published: January 2009

Biological networks frequently use cascades, generally defined as chain-like arrangements of similar modules. Spatially lumped cascades can serve as noise filters, time-delay, or thresholding elements. The operation and functional capabilities of spatially distributed cascades are much less understood. Motivated by studies of pattern formation in the early
Drosophila
embryo, we analyze cascades of 2-state reaction-diffusion systems. At each stage within such as a cascade, a diffusible particle is reversibly bound by immobile traps and can be annihilated in both mobile and immobile states. When trapped, these particles drive the next stage by converting mobile particles of a different type from a passive to active form. The cascade initiated by injection of mobile particles into the first stage. We derive analytical expressions for the steady-state concentration profiles of mobile and immobile particles and analyze how the output of a cascade is controlled by properties of the constituent stages.
Reconnection and merging of positive streamers in air
Authors: Nijdam S , Geurts C G C , van Veldhuizen E M , Ebert U
Published: January 2009

Pictures show that streamer or sprite discharge channels emerging from the same electrode sometimes seem to reconnect or merge though their heads carry electric charge of the same polarity; one might therefore suspect that reconnections are an artefact of the two-dimensional projection in the pictures. Here we use stereo photography to investigate the full three-dimensional structure of such events. We analyse reconnection, possibly an electrostatic effect in which a late thin streamer reconnects to an earlier thick streamer channel, and merging, a suggested photoionization effect in which two simultaneously propagating streamer heads merge into one new streamer. We use four different anode geometries (one tip, two tips, two asymmetric protrusions in a plate and a wire), placed 40 mm above a flat cathode plate in ambient air. A positive high voltage pulse is applied to the anode, creating a positive corona discharge. This discharge is studied with a fast ICCD camera, in many cases combined with optics to enable stereoscopic imaging. We find that reconnections as defined above occur frequently. Merging on the other hand was only observed at a pressure of 25 mbar and a tip separation of 2 mm, i.e. for a reduced tip distance ofp·d= 50 µm bar. In this case the full width at half maximum of the streamer channel is more than 10 times as large as the tip separation. At higher pressures or with a wire anode, merging was not observed.
MSMAD: a computationally efficient method for the analysis of noisy array CGH data
Authors: Budinska Eva , Gelnarova Eva , Schimek Michael G.
Published: January 2009

Motivation: Genome analysis has become one of the most important tools for understanding the complex process of cancerogenesis. With increasing resolution of CGH arrays, the demand for computationally efficient algorithms arises, which are effective in the detection of aberrations even in very noisy data.

Results: We developed a rather simple, non-parametric technique of high computational efficiency for CGH array analysis that adopts a median absolute deviation concept for breakpoint detection, comprising median smoothing for pre-processing. The resulting algorithm has the potential to outperform any single smoothing approach as well as several recently proposed segmentation techniques. We show its performance through the application of simulated and real datasets in comparison to three other methods for array CGH analysis.

Implementation: Our approach is implemented in the R-language and environment for statistical computing (version 2.6.1 for Windows, R-project, 2007). The code is available at: http://www.iba.muni.cz/~budinska/msmad.html

Contact:  budinska@iba.muni.cz

Supplementary information:  Supplementary data are available at Bioinformatics online.
The pathologist’s approach to small airways disease
Authors: Rice Alexandra , Nicholson Andrew G
Published: January 2009

The small airways constitute a significant compartment of the lung, and diseases therein are not uncommon, occurring in a wide variety of diseases, either as a primary bronchiolar disorder or as a component of local or systemic disease affecting multiple anatomical compartments. Unlike the idiopathic interstitial pneumonias, there is as yet no consensus classification system for bronchiolar disorders, and a multidisciplinary approach to their classification is discussed. Whereas some conditions show relatively characteristic histological features, others show non‐specific or subtle changes that rely on a combination of clinical, radiological and pathological information for accurate final diagnosis. Furthermore, certain diseases of the small airways have been better characterized recently, and several provisional new entities have also been described, some of these being reviewed here.
Pulmonary adenocarcinomas: classification and reporting
Authors: Kerr Keith M
Published: January 2009

Pulmonary adenocarcinoma is the most common, and the most diverse form of primary lung carcinoma. The histological complexity of these tumours poses problems for pathologists. The current WHO classification of pulmonary adenocarcinoma does not adequately address a number of clinically relevant, biological factors. The accurate diagnosis of adenocarcinoma on small biopsy specimens, accounting for most diagnoses of this disease, is challenged by the absence of tumour architecture in most samples. Tumours showing a pure bronchioloalveolar (BAC) pattern are now best regarded as adenocarcinoma‐in‐situ; yet invasive adenocarcinomas may also show elements with the BAC pattern, dictating a better prognosis but biologically not necessarily in‐situ disease. Multifocal BAC‐pattern adenocarcinoma still poses considerable conceptual and diagnostic problems. In small tumours the papillary pattern, especially when micropapillary, confers a poor prognosis but this is not reflected in larger tumours. In early tumours of predominantly BAC (in‐situ) pattern, the identification of invasion is particularly difficult, yet minor degrees of infiltration seem not to degrade prognosis. It may therefore be possible to define a minimally invasive category of adenocarcinoma. Consequently, there are a number of issues to consider when reporting this tumour type, depending on the nature of the diagnostic specimen. The rapid emergence of chemotherapeutic agents with histology‐specific efficacy will increase the need for more accurate and specific diagnosis of adenocarcinoma on small samples. Immunohistochemistry may help suggest this diagnosis when the features are non‐specific but immunohistochemical findings are not diagnostic of this form of lung cancer. The emerging clinical and prognostic relevance of a number of histological features in these complex tumours strengthens the argument in favour of including quantitative detail of pattern sub‐types in reports on resected tumours.
Reporting lung cancer pathology specimens. Impact of the anticipated 7th Edition TNM Classification based on recommendations of the IASLC Staging Committee
Authors: Travis William D
Published: January 2009

Led by the International Association for the Study of Lung Cancer (IASLC), there are currently several major international collaborative projects underway that will have a significant impact on the future reporting of lung cancer pathology. In particular, the IASLC Staging Committee has just completed an analysis of >100 000 lung cancer cases, providing the basis for proposed revisions of the current TNM staging classification. The purpose of this review is not to provide a comprehensive document on recommendations for specimen processing, but rather to discuss how the anticipated changes in the 7th edition TNM will impact on specimen processing, specifically looking at tumour size, how to deal with multiple tumours and visceral pleural invasion. TNM staging of carcinoid tumours and small cell carcinoma is also discussed.
Advances in the understanding and classification of pulmonary hypertension
Authors: Stewart Susan , Rassl Doris
Published: January 2009

Pulmonary hypertension has a complex pathobiology and the term pulmonary arterial hypertension (PAH) includes a variety of pulmonary hypertensive diseases that have different aetiologies, but which may have a similar clinical presentation and, in some cases, the same response to medical treatment. More recent classifications have been based on aetiology, functional data and clinical presentation, but morphometric studies have shown differences in the distribution and prevalence of vascular changes amongst cases of PAH of different aetiologies. Recent advances in the understanding of some aspects of the genetic and molecular mechanisms, together with detailed descriptions of the histopathological findings in PAH cases of different aetiologies, should contribute to a better understanding of the relationships of the various subsets of the disease, the prognostic implications and possible treatment options.
The challenge of classifying poorly differentiated tumours in the lung
Authors: Wallace William A H
Published: January 2009

The lung is a common site for primary carcinomas as well as a wide range of metastatic carcinomas and other rarer primary and secondary tumours that clinically and radiologically may mimic lung cancer. The World Health Organization classification of lung tumours is based on the morphological appearances in resected specimens. This provides a widely applicable system for classification, which, although complex, can be applied universally. The vast majority of patients with lung cancer, however, do not have their tumours resected, and the application of the same classification system to small biopsy specimens is problematic due in large part to sampling. Recognition of this has led to the widespread use of the term ‘non‐small cell carcinoma’. Future developments in our understanding of lung cancer and the development of novel targeted therapies may mean that in the future classification will become based more on the molecular features of tumours that predict response to therapies and prognosis rather than simple morphology. The predictive validity of such an approach using small biopsy or cytology specimens, however, still requires to be established. The problem of tumour heterogeneity, which is problematic for morphological classification, may also pose similar challenges for molecular approaches.
Complex pattern of genome size variation in a polymorphic member of the Asteraceae
Authors: Slovák Marek , Vít Petr , Urfus Tomáš , Suda Jan
Published: January 2009

Aim  Although divergences in nuclear DNA content among different species within a genus are widely acknowledged, intraspecific variation is still a somewhat controversial issue. The aim of this study was to assess genome size variation in the polymorphic species Picris hieracioides L. (Asteraceae) and to search for potential interpretations of the size heterogeneity.

Location  Europe.

Methods  The genome sizes of 179 plants of P. hieracioides collected from 54 populations distributed across 10 European countries were determined by propidium iodide flow cytometry. Differences in nuclear DNA content were confirmed in simultaneous analyses.

Results  2C‐values (population means) at the diploid level varied from 2.26 to 3.11 pg, spanning a 1.37‐fold range. The variation persisted even after splitting the whole data set into two recently distinguished morphotypes (i.e. the ‘Lower altitude’ type and the ‘Higher altitude’ type) that possess significantly different nuclear DNA contents. Cluster analysis revealed the presence of three major groups according to genome size, which exhibited a particular geographical pattern. Generally, the genome size of both morphotypes increased significantly from south‐west to north‐east. A new cytotype, DNA triploid, was found for the first time.

Main conclusions  High intraspecific variation in the amount of nuclear DNA in P. hieracioides correlates with the extensive morphological variation found within the taxon. Despite the complex pattern that was presented, genome size variants were non‐randomly distributed and reflected palaeovegetation history. We suggest that the complex evolutionary history of P. hieracioides (e.g. the existence of several cryptic lineages with different levels of cross‐interactions) is the most plausible explanation for the observed heterogeneity in genome size.
Dynamics of core and occasional species in the marine plankton: tintinnid ciliates in the north‐west Mediterranean Sea
Authors: Dolan John R. , Ritchie Mark E. , Tunin‐Ley Alina , Pizay Marie‐Dominique
Published: January 2009

Aim  To assess short‐term variability in the community composition and community structure of tintinnid ciliates, herbivores of the microzooplankton.

Location  North‐west Mediterranean Sea.

Methods  We sampled on 18 dates over a 4‐week period in 2004 at an open‐water site. Species were classified as ‘core species’, found on every date, or ‘occasional species’, absent on one or more dates. Species abundance distributions of the entire community, and separately the core and occasional species, were compared with geometric, log‐series and log‐normal distributions. Core and occasional species were compared in terms of the shell or lorica oral diameter (LOD), analogous to gape size.

Results  We found 11 core and 49 occasional species. Diversity metrics were stable compared with shifts in abundances. Core species accounted for the majority of individuals in all samples. On each date, 9–22 occasional species, representing 10–15% of the population, were found. Species richness of the occasionals was positively related to population size. The identities of the occasional species found were unrelated to the time between sampling. The species abundance distribution of the occasional population was best fit by a log‐series distribution, while that of the core species was best fit by a log‐normal distribution. The species abundance distribution of the entire community was best fit by a log‐series distribution. Most of the occasional species had LODs distinct from that of a core species and occupied size classes left empty by the core population. However, the most abundant and frequent of the occasional species had a LOD similar to that of a core species.

Main conclusions  Among tintinnids, which are planktonic protists, occasional species have a species abundance distribution pattern distinct from that of core species. Occasional species appeared to be composed of two groups, one of relatively abundant species and similar to core species, and a second group of ephemeral species with morphologies distinct from core species. The existence of two categories of occasional or rare species may be common: (1) those similar to, and thus perhaps able to replace, dominant species in the absence of a change in the environment; and (2) those distinct from dominant species and requiring different conditions to prosper.
Narrative and learning with Web 2.0 technologies: towards a research agenda
Authors: Pachler N. , Daly C.
Published: January 2009

Abstract  This paper investigates the impact of Web. 2.0 technologies on the ways learning can be conceived of as a narrative process within contemporary contexts, using blogs as an illustrative example. It is premised on the concept of narrative as a way in which individuals represent and organize experience in order to learn from it and make it shareable with others within social contexts. The first part of the paper offers a theoretical analysis of the role of narrative in the social construction of knowledge by the ways it enables users of Web 2.0 technologies to participate meaningfully in the exchange of experiences and ideas. The second part of the paper offers a ‘situated’ analysis of the narrative practices engaged with by users of blogs. A ‘narrative trail’ is used to provide a contextualized instance of the narrative practices which are involved. The paper concludes by examining the research issues which are raised and suggests a research agenda which is needed to explore Web 2.0 technologies as social utilities affecting knowledge production, in which the adaptation of narrative theory is a central feature.