bluuebunny/crossref_metadata_2025 huggingface dataset:
Probing the mechanical stability of proteins using the atomic force microscope
Authors: Brockwell D.J.
Published: January 2008

The mechanical strength of single protein molecules can be investigated by using the atomic force microscope. By applying this technique to a wide range of proteins, it appears that the type of secondary structure and its orientation relative to the extension points are important determinants of mechanical strength. Unlike chemical denaturants, force acts locally and the mechanical strength of a protein may thus appear to be mechanically weak or strong by simply varying the region of the landscape through which the protein is unfolded. Similarly, the effect of ligand binding on the mechanical resistance of a protein may also depend on the relative locations of the binding site and force application. Mechanical deformation may thus facilitate the degradation or remodelling of thermodynamically stable proteins and their complexes in vivo.
Advances in the design of new epoxy supports for enzyme immobilization–stabilization
Authors: Mateo C. , Grazú V. , Pessela B.C.C. , Montes T. , Palomo J.M. , Torres R. , López-Gallego F. , Fernández-Lafuente R. , Guisán J.M.
Published: January 2008

Multipoint covalent immobilization of enzymes (through very short spacer arms) on support surfaces promotes a very interesting ‘rigidification’ of protein molecules. In this case, the relative positions of each residue of the enzyme involved in the immobilization process have to be preserved unchanged during any conformational change induced on the immobilized enzyme by any distorting agent (heat, organic solvents etc.). In this way, multipoint covalent immobilization should induce a very strong stabilization of immobilized enzymes. Epoxy-activated supports are able to chemically react with all nucleophile groups placed on the protein surface: lysine, histidine, cysteine, tyrosine etc. Besides, epoxy groups are very stable. This allows the performance of very long enzyme–support reactions, enabling us to get very intense multipoint covalent attachment. In this way, these epoxy supports seem to be very suitable to stabilize industrial enzymes by multipoint covalent attachment. However, epoxy groups exhibit a low intermolecular reactivity towards nucleophiles and hence the enzymes are not able to directly react with the epoxy supports. Thus a rapid physical adsorption of enzymes on the supports becomes a first step, followed by an additional rapid ‘intramolecular’ reaction between the already adsorbed enzyme and the activated support. In this situation, a suitable first orientation of the enzyme on the support (e.g. through regions that are very rich in nucleophiles) is obviously necessary to get a very intense additional multipoint covalent immobilization. The preparation of different ‘generations’ of epoxy supports and the design of different protocols to fully control the first interaction between enzymes and epoxy supports will be reviewed in this paper. Finally, the possibilities of a directed immobilization of mutated enzymes (change of an amino acid by cysteine on specific points of the protein surface) on tailor-made disulfide-epoxy supports will be discussed as an almost-ideal procedure to achieve very intense and very efficient rigidification of a desired region of industrial enzymes.
Structural stability of an enzyme biocatalyst
Authors: Dalby P.A. , Aucamp J.P. , George R. , Martinez-Torres R.J.
Published: January 2008

TK (transketolase) undergoes inactivation during biocatalytic processes due to oxidation, substrate and product inhibition, reactivity of aldehyde substrates, irreversible inactivation at low pH, and dissociation of cofactors. However, the contribution of protein denaturation to each of these mechanisms is not fully understood. The urea-induced reversible denaturations of the apo- and holo-enzyme forms of the homodimeric Escherichia coli TK have been characterized, along with the reconstitution of holo-TK from the apoenzyme and cofactors. An unusual cofactor-bound yet inactive intermediate occurs on both the reconstitution and holo-TK denaturation pathways. The denaturation pathways of the holo- and apoenzymes converge at a second intermediate consisting of a partially denatured apo-homodimer. Preliminary investigation of the denaturation under oxidizing conditions reveals further complexity in the mechanisms of enzyme deactivation that occur under biocatalytic conditions.
Immobilization of thermophilic enzymes in miniaturized flow reactors
Authors: Hickey A.M. , Marle L. , McCreedy T. , Watts P. , Greenway G.M. , Littlechild J.A.
Published: January 2008

The exploitation of enzymes for biotransformation reactions for the production of new and safer drug intermediates has been the focus of much research. While a number of enzymes are commercially available, their use in an industrial setting is often limited to reactions that are cost-effective and they are rarely investigated further. However, the development of miniaturized flow reactor technology has meant that the cost of such research, once considered cost- and time-inefficient, would be much less prohibitive. The use of miniaturized flow reactors for enzyme screening offers a number of advantages over batch enzyme assay systems. Since the assay is performed on a miniaturized scale, enzyme, substrate and cofactor quantities are significantly reduced, thus reducing the cost of laboratory-scale investigations. Since flow reactors use microfluidic systems, where the substrate and products flow out of the system, the problems of substrate inhibition and product inhibition encountered by some enzymes are avoided. Quite often, enzymes fulfil a single-use function in biotransformation processes; however, enzyme immobilization allows enzyme reuse and often helps to increase enzyme stability. We have used an aminoacylase enzyme with potential use for industrial biotransformation reactions and have successfully immobilized it in miniaturized flow reactors. This L-aminoacylase is from the thermophilic archaeon Thermococcus litoralis. Two approaches to enzyme immobilization have been examined, both involving enzyme cross-linking. The first reactor type has used monoliths, to which the enzyme was attached, and the second contained previously cross-linked enzyme trapped using frits, in the microfluidic channels. Two different microreactor designs were used in the investigation: microreactor chips for the monoliths and capillary flow reactors for the cross-linked enzyme. These systems allowed passage of the substrate and product through the system while retaining the aminoacylase enzyme performing the catalytic conversion. The enzyme has been successfully immobilized and used to produce stable biocatalytic microreactors that can be used repeatedly over a period of several months.
The amazing diversity of cap-independent translation elements in the 3′-untranslated regions of plant viral RNAs
Authors: Miller W.A. , Wang Z. , Treder K.
Published: January 2008

Many plant viral RNAs lack the 5′-cap structure that is required on all host mRNAs for interacting with essential translation initiation factors. Instead, uncapped viral RNAs take over the host translation machinery by harbouring sequences that functionally replace the 5′-cap. Recent reports reveal at least eight different classes of CITE (cap-independent translation element) located in the 3′-UTRs (untranslated regions) of various viruses. We describe how the structure and behaviour of each class of element differs from the other classes, suggesting that they recruit translation factors and, ultimately, the ribosome by diverse mechanisms. These results greatly expand our understanding of ways in which mRNAs can recruit ribosomes, and they provide insight into the regulation of virus gene expression.
Riboregulators in plant development
Authors: Laporte P. , Merchan F. , Amor B.B. , Wirth S. , Crespi M.
Published: January 2008

npcRNA (non-protein-coding RNAs) are an emerging class of regulators, so-called riboregulators, and include a large diversity of small RNAs [miRNAs (microRNAs)/siRNAs (small interfering RNAs)] that are involved in various developmental processes in plants and animals. In addition, several other npcRNAs encompassing various transcript sizes (up to several kilobases) have been identified using different genomic approaches. Much less is known about the mechanism of action of these other classes of riboregulators also present in the cell. The organogenesis of nitrogen-fixing nodules in legume plants is initiated in specific root cortical cells that express the npcRNA MtENOD40 (Medicago truncatula early nodulin 40). We have identified a novel RBP (RNA-binding protein), MtRBP1 (M. truncatula RBP 1), which interacts with the MtENOD40 RNA, and is exported into the cytoplasm during legume nodule development in the region expressing MtENOD40. A direct involvement of the MtENOD40 RNA in the relocalization of this RBP into cytoplasmic granules could be demonstrated, revealing a new RNA function in the cell. To extend these results, we searched for npcRNAs in the model plant Arabidopsis thaliana whose genome is completely known. We have identified 86 novel npcRNAs from which 27 corresponded to antisense RNAs of known coding regions. Using a dedicated ‘macroarray’ containing these npcRNAs and a collection of RBPs, we characterized their regulation in different tissues and plants subjected to environmental stresses. Most of the npcRNAs showed high variations in gene expression in contrast with the RBP genes. Recent large-scale analysis of the sRNA component of the transcriptome revealed an enormous diversity of siRNAs/miRNAs in the Arabidopsis genome. Bioinformatic analysis revealed that 34 large npcRNAs are precursors of siRNAs/miRNAs. npcRNAs, which are a sensitive component of the transcriptome, may reveal novel riboregulatory mechanisms involved in post-transcriptional control of differentiation or environmental responses.
Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles
Authors: Delannoy E. , Stanley W.A. , Bond C.S. , Small I.D.
Published: January 2008

PPR (pentatricopeptide repeat) genes form a large family particularly prevalent in higher plants and targeted to organelles. They are involved in many post-transcriptional processes such as splicing, editing, processing and translation. Current data suggest that PPR proteins are involved in targeting effectors to the correct sites on the correct transcripts but the molecular mechanisms for RNA binding and effector recruitment by PPR proteins are not understood yet.
Images within the Precarity Movement in Italy
Authors: Mattoni Alice , Doerr Nicole
Published: January 2008

The recent cycle of social struggles against precarity in Italy has been characterized by an extensive use of images representing precarious workers. This contribution explores this in the case of the Euro Mayday Parade (EMP) protest campaign. The subversion of existing popular culture traditions was the main objective of the activists’ newly created icons such as San Precario, Serpica Naro and other visual tools. The visual work on gender in the EMP seemed to fill a gap between theoretical work on the feminization of affective and immaterial labour and the less predominant presence of gender. Visual icons seem to have been at least as successful as text messages in publicizing the precarity discourse and their production deserves further attention.
Voicing the Non-Place: Precarious Theatre in a Women's Prison
Authors: Poole Susanna
Published: January 2008

Based on the personal experience of the author, who is involved in theatre projects with women convicts, the article moves across issues of detention, migration, and precarity. Foucault's concept of governmentality is instrumental in describing the arbitrary exercise of power on incarcerated people and their precarious living conditions. Life in jail is especially uncertain for clandestine migrants. In the article, recollections from the rehearsals of the show / racconti del corpo (Tales of the body) alternate with images and quotes from the play, poems by women convicts, and reflections on detention as the ultimate condition of precarity for migrant women.
Female Literature of Migration in Italy
Authors: Curti Lidia
Published: January 2008

Starting symbolically from a place of transit and mobility such as the Galleria in Naples, I look at the pace of immigration movements to Italy from both ex-colonial territories and other countries. Precarity characterizes the migrant condition in Italy: entrance and stay permits; work and housing, which are difficult to obtain and always temporary; bureaucratic control is severe and the right to citizenship is distant. The collective amnesia of the colonial enterprise obscures the fact that at least some of the guests of today were the hosts of yesterday. I analyse these, and other aspects, in the literature of migration that in recent decades has emerged in Italy, focusing on women's writing and confronting the problem of how long it will take for this literature to receive recognition in the Italian literary canon. In women's narratives, precarity emerges in the journey of emigration, described as a real odyssey; in tensions over identity and language; in contrasting cultures of departure and cultures of destination; in the problematic concept of ‘home’. Racial and gender differences subsumed in the colour of skin are a recurrent motif. For women, hardships may be more deeply felt: isolation and loneliness is augmented by the distance from children and family; the relationship between past and present more troublesome as it often leads to a double oppression. independence is more fiercely fought for in the affirmation of identity. Finally, I show that, alongside conditions of isolation and despair, strength and hope in the new life emerge from these writings, touching on the importance of writing in Italian and on the motives leading to this choice.
The Body, Sexuality and Precarity
Authors: Giuliani Gaia
Published: January 2008

The focus group held in Bologna on 2 October 2005 revolved around the relationships between ‘body’, ‘sexuality’ and ‘precarity’, which are concepts at the heart of the reflections and political agenda of the feminist and Gay, Lesbian, Bisexual, Transgender and Queer (GLBTQ) movements in Italy.
A Snapshot of Precariousness: Voices, Perspectives, Dialogues
Authors: Sconvegno  , Galetto Manuela , Lasala Chiara , Magaraggia Sveva , Martucci Chiara , Onori Elisabetta , Pozzi Francesca
Published: January 2008

This collectively written article aims to offer a bird's eye view of the Italian debates about precarity in employment and life, as captured in discussions among participants in a focus group held in Milan in 2006. The chief topics that emerged from this discussion include the feminization of labour, feminist practices and methodologies, representation/participation, and guaranteed income. Here, we give as much space as possible to the diverse voices of participants and their strategies for transformation.
Comparing Different Generations of Feminists: Precariousness versus Corporations?
Authors: Di Cori Paola
Published: January 2008

This article focuses on the gap and conflicts in Italy between the so-called ‘historical feminists’ of the 1960s and 1970s, and the generation of young women who entered the public and political arena from 1990 onwards. It discusses the absence of a critical and self-critical perspective within the Italian historical feminist tradition, the various political conflicts that emerged before and during the Berlusconi right-wing government at the beginning of 2000 and the absence of an active visible presence of young women in the media and in politics.
Physics News in 1985
Authors: Schewe Phillip F.
Published: January 2008

The American Institute of Physics is a not-for-profit membership corporation chartered in New York State in 1931 for the purpose of promoting the advancement and diffusion of the knowledge of physics and its application to human welfare. Leading societies in the field of physics and astronomy are its members. AIP's activities include providing services to its Member Societies in the publishing, fiscal, and educational areas, as well as other services which can best be performed by one operating agency rather than dispersed among the constituent societies.
Currents in Normal-Metal Rings Exhibit Aharonov–Bohm Effect
Authors: Schwarzschild Bertram
Published: January 2008

Ever since Yakir Aharonov and David Bohm pointed out, in 1959, that electrons propagating around a magnetic field through a field-free vacuum should exhibit a quite surprising interference effect, its experimental and theoretical investigation has been contributing to our understanding of the fundamental character of the quantum theory. The recent appearance of this Aharonov–Bohm effect in a rather different context may eventually have a profound effect on our view of the solid state on a “mesoscopic” scale—between the microscopic and the truly macroscopic.
Measuring the Hubble Constant
Authors: Schechter Bruce
Published: January 2008

Hubble's celebrated constant, which relates the recessional velocities of galaxies to their distances, is perhaps the most important number in extragalactic astronomy. Using it, along with their favorite models, astronomers and cosmologists derive the age of the universe, estimate its size, calculate the luminosity of quasars and much more. Unfortunately, astronomers are far from agreeing on a value for Hubble's constant. Some believe that H0 is about 50 km/sec Mpc; others think it is closer to 100 km/sec Mpc. Depending on the details of the cosmological model chosen, this can lead to a discrepancy of a factor of 2—ten billion years or so—in the age of the universe.
Superconducting-Cavity Progress Spurs New CEBAF Design
Authors: Schwarzschild Bertram
Published: January 2008

What is the best way to provide nuclear physicists with continuous beams of 4-GeV electrons? Three years ago the pulse-stretcher-ring concept embodied in the winning SURA design for the Continuous Electron Beam Accelerator Facility appeared to be the optimal solution (PHYSICS TODAY, July 1983, page 57). But while construction of CEBAF has not yet begun, accelerator technology has not stood still. In the light of recent progress in the development of superconducting rf cavities, a review of CEBAF technology initiated last summer by Hermann Grunder, the project's new director, has concluded that a superconducting-linac design should now replace the original pulse-stretcher-ring concept (see page 51). Looking toward the beginning of construction in fiscal 1987, DOE in December directed CEBAF to prepare a conceptual design for such a machine.
Redshift Surveys of Galaxies Find a Bubbly Universe
Authors: Schwarzschild Bertram
Published: January 2008

“The distribution of galaxies in [our] redshift survey is like a slice through the suds in the kitchen sink.” With this deceptively mundane metaphor, a report in the 1 March issue of Astrophysical Letters presents us with an astonishing new view of structure in the cosmos on the largest scale we know about. The authors, Valerie de Lapparent, Margaret Geller and John Huchra of the Harvard-Smithsonian Center for Astrophysics, conclude from a complete compilation of the redshifts of the 1100 brightest galaxies in an extensive strip of sky near our galactic north pole that the galaxies are sharply concentrated at the surfaces of contiguous, bubblelike structures with diameters as large as 50 megaparsecs (150 million light years).
Conversion in Matter May Account for Missing Solar Neutrinos
Authors: Schwarzschild Bertram
Published: January 2008

In 1938 Hans Bethe propounded the nuclear-fusion sequences we confidently assume to describe the energy sources of the Sun. Almost a halfcentury later, a 24 March Physical Review Letter by this same Hans Bethe takes a swipe at the one conspicuous fly remaining in the ointment of the “standard solar model” that has grown up around his seminal explanation of what makes the stars shine.
Consider Graduate-Student Life
Authors: Whitman Llyod J.
Published: January 2008

Beyond the general feeling that “students should live only as well as I did when I was in school,” the physics community apparently gives little consideration to graduatestudent life. As chairman of the physicsgraduate-student organization at Cornell University, I recently completed a survey of the living expenses of physics graduate students at Cornell. This survey was the latest in a series conducted annually to monitor how well salaries for teaching and research assistants keep up with the cost of living. While preparing my report I found that there seems to be no way of determining whether such support is adequate other than comparing the value of the support from year to year. Through discussions with administrators, faculty and other graduate students it became apparent that departments give little thought to what kind of life graduate students lead.
Women Graduate Students
Authors: Dresselhaus Mildred S.
Published: January 2008

When I started teaching solid-state-physics courses at MIT, nearly 20 years ago, there were very few women at MIT and very few women students in my classes. It was unusual for women students to ask questions in class or to participate in class discussions. As the number of women students increased, they participated more and more, and in very recent years their class participation has become essentially indistinguishable from that of the men. A turning point appeared to occur when the number of women reached a “critical mass” of about 10–15% of the students in a class. But in some other physics courses at MIT the critical mass hasn't been reached.
Reanalysis of Old Eötvös Data Suggests 5th Force…To Some
Authors: Schwarzschild Bertram
Published: January 2008

Newton's gravitational constant has been with us for three centuries. Yet despite our long and intimate acquaintance, we know this fundamental constant of nature to little better than a part per thousand. Astronomical data are of scant use, because they always involve G multiplied by the mass of the Earth or some celestial body, and our knowledge of the mean density of such bodies is even more uncertain. Our best knowledge of G comes from modern variants of the classic Cavendish experiment, measuring the horizontal force between test bodies at distances up to a few meters in the laboratory.
Ozone Hole Attributed to Solar Maximum
Authors: Schwarzschild Bertram
Published: January 2008

In the 20 September issue of the Journal of Geophysical Research, Linwood Callis (NASA) and Murali Natarajan (SASC Technologies) suggest that the recently hyperactive Sun, rather than manmade pollution, bears primary responsibility for the mysterious and troubling “ozone hole” that has for several years been appearing every October over the South Pole. They point out that 1979–80 witnessed one of the most intense solar maxima in centuries. This, they argue, would account for the striking increase in the level of “odd-nitrogen compounds”—various oxides of nitrogen—observed in the stratosphere between 1979 and 1984. Produced in an atmospheric layer above the stratosphere with the aid of sunlight and solar wind, these molecules can participate catalytically in the destruction of ozone.
Reports on Subfields of Physics: Gravitation, Cosmology and Cosmic-Ray Physics
Authors: Schechter Bruce
Published: January 2008

In 1982 the Astronomy Survey Committee, under the direction of George Field, published Astronomy and Astrophysics in the 1980s (see PHYSICS TODAY, April 1982, page 96, and November 1982, page 25), a report similar in purpose to the current Brinkman report. Gravitation, cosmology and cosmic-ray physics were then, properly, considered as subfields of astrophysics. But these three fields, because they are concerned with the nature of the fundamental forces and constituents of matter, are also of direct interest to physicists. For this reason one volume of the Brinkman report is devoted to recounting the achievements in and identifying goals for the related fields of gravitation, cosmology and cosmic-ray physics.
Physics and Psychic Research in Victorian and Edwardian England
Authors: Oppenheim Janet
Published: January 2008

Scientists in industrialized England commanded public respect, even veneration. Their widely publicized discoveries promised to elucidate the mysteries of nature, to harness natural forces for human purposes, to increase productivity in fields and factories and to improve the odds in the struggle against disease. The scientific method itself was celebrated as the surest means of attaining truth.
The Sentiment of the Unity of Physics
Authors: Wilson Robert R.
Published: January 2008

We discuss the unity of physics with a kind of nostalgia, for our field today is so patently diverse. We hear this diversity in the cacophony of our meeting halls, in the differing languages of theorists and experimenters, of rheologists and astrophysicists. The sheer numbers of physicists and of the papers we publish—one every few minutes—overwhelm us. Diversity has even been institutionalized: Our American Physical Society is now organized into a dozen disparate divisions, and physicists have organized many physics societies outside APS. One would expect one of the clearest expressions of the unity of physics to lie in the teaching of physics, but even that enterprise has its separate American Association of Physics Teachers. And didn't we establish the American Institute of Physics, of which APS is but one of ten members, because of the need for unity in physics?
Scientific Approaches to Science Education
Authors: Reif Frederick
Published: January 2008

Our traditional approaches to science and mathematics education are based largely on intuitive notions and are, in some ways, rather unscientific. Whereas we usually tackle problems in science and engineering through the systematic use of fundamental principles, we often approach problems in science teaching by the seat of our pants, without deeper analysis. While we make great efforts in physics to understand the mechanisms that underlie observed phenomena, we are often content to consider scientists and students as “black boxes” whose internal intellectual functioning can be left largely unexamined in spite of its importance for teaching.
High-Field Superconductivity
Authors: Larbalestier David , Fisk Gene , Montgomery Bruce , Hawksworth David
Published: January 2008

One does not often read original research communications that are 50 or 75 years old. Preparing an article to commemorate the 75th anniversary of the discovery of superconductivity seemed to be an appropriate occasion for reading some of Heike Kamerlingh Onnes's original articles. Two years after his discovery, Onnes made a report to the third International Conference of Refrigeration in 1913. He reviewed the recent research of his Leiden group. This article is quite astonishing, and only extensive quotations can convey the breadth of Onnes's conception of the possibilities of the superconducting state. Onnes commences his description of the superconducting state by describing his initial 1911 experiments on mercury, but he proceeds rapidly to sketch whole segments of the technology of superconducting magnets:

Mercury has passed into a new state, which on account of its extraordinary electrical properties may be called the superconductive state…. The behavior of metals in this state gives rise to new fundamental questions as to the mechanism of electrical conductivity.

It is therefore of great importance that tin and lead were found to become superconductive also. Tin has its step-down point at 3.8 K, a somewhat lower temperature than the vanishing point of mercury. The vanishing point of lead may be put at 6 K. Tin and lead being easily workable metals, we can now contemplate all kinds of electrical experiments with apparatus without resistance….
SQUIDs, Brains and Gravity Waves
Authors: Clarke John
Published: January 2008

▸ A lonely instrument in Baja California records tiny fluctuations in the Earth's magnetic field, giving valuable information on the location of geothermal energy.

▸ An extremely quiet amplifier detects electrical noise generated by the fluctuating spins in a collection of chlorine nuclei—the first observation of nuclear-spin noise.

▸ Superconducting gradiometers in liquid helium measure tiny fluctuating magnetic fields emanating from the human brain (see figure 1), pinpointing the source of the electrical discharge associated with focal epilepsy.

▸ An aluminum bar weighing 4800 kg and cooled to 4.2 K rests in a vacuum chamber at Stanford University, working as the world's most sensitive monitor of gravitational radiation.
Metal-Semiconductor Interfaces
Authors: Weaver John H.
Published: January 2008

In my view of the evolution of solidstate physics, the 1970s were the decade of bulk phenomena. We made enormous strides in understanding crystals—we mapped their energy bands, developed clever computational schemes and became experimentally and theoretically adept at characterizing solid crystals. At the same time, we developed the tools to study surfaces, and we continue to make amazing progress in this area, as Shuk Y. Tong explained in a recent article (PHYSICS TODAY, August 1984, page 50).
Reviving the Spirit of Enterprise: Role of the Federal Labs
Authors: Blanchard Paul A. , McDonald Frank B.
Published: January 2008

About 400 research facilities officially classified as Federal laboratories employ nearly 185 000 of the nation's scientists and engineers and account for roughly $18 billion per year—a third of all Federal R&D funding in fiscal 1985. Most of this support went to a relatively few large centers devoted to energy and weapons research, highenergy physics experiments, medical programs and space science and exploration. Besides the multipurpose national labs such as Sandia, Argonne, Los Alamos and the National Bureau of Standards, which perform a broad range of R&D activities, the full roster includes a diversity of installations, including the Boll Weevil Research Laboratory; the National Radio Astronomy Observatory; the Insect Attractant, Behavior and Basic Biology Center; the FBI Laboratory; and even the National Zoo. Despite the contributions of the Federal labs, how they can enrich the nation's R&D enterprise with “public technology” has been a subject of concern in Washington for decades.
Special Issue: The Science of VLSI
Authors: Armstrong John A.
Published: January 2008

The emergence of silicon-based very-large-scale integration is one of the major technological events of our time. This development was fueled in large measure by previously obtained scientific knowledge, but the devices of modern microelectronics in turn have made possible dramatic advances in all fields of science. Physics (and the physical sciences generally) has played an important part in this story. As this special issue of PHYSICS TODAY shows, very important contributions are still being made; more are needed to support continued progress in VLSI.
Interconnections in VLSI
Authors: Ghate Prabhakar B.
Published: January 2008

For more than a decade after the invention of the transistor in 1948, all semiconductor circuits consisted of discrete devices either connected by wires or mounted on printed circuit boards. Such circuits offered tremendous advantages over the vacuum-tube circuits that they replaced: less power consumption, higher speed, higher reliability, lower cost, less weight and smaller size. In 1958–59, a major technological breakthrough led to the realization of all these advantages for a second time: Working independently, Jack S. Kilby, an engineer at Texas Instruments, and Robert N. Noyce, a scientist at Fairchild, showed how one could form interconnected transistors, diodes, resistors, capacitors and other active and passive components on a single piece of silicon. The resulting “integrated circuits” have revolutionized electronics ranging from radio to computers, and a decade ago these circuits surpassed discrete devices in use by the microelectronics industry. In recognition of their invention, the National Academy of Sciences inducted Kilby and Noyce into the National Inventor's Hall of Fame in 1982 and 1983, respectively.
Reflections on the 1974 APS Energy Study
Authors: Socolow Robert H.
Published: January 2008

We physicists who worked together on the 1974 American Physical Society summer study entitled Efficient Use of Energy: A Physics Perspective believed we were doing something important in questioning two beliefs strongly held by most people involved in problems of energy supply. One of the beliefs that we challenged concerned how energy relates to wellbeing, namely that only by ever greater use of energy can society achieve greater well-being. The other concerned how physicists relate to energy: that it is appropriate for physicists to work on problems of energy supply, but inappropriate for us to work on problems of energy use. The shared goal of the participants in the 1974 APS summer study was to overturn both of these majority positions—by creating counterexamples. In the first instance our counterexamples would be analyses that demonstrated the emptiness of the connection between various aspects of wellbeing—personal mobility and light to read by, for example—and the level of energy use required to achieve them (see figure 1). In the second instance our counterexamples would be ourselves.
The Inner Logic of the Coase Theorem and a Coasian Planning Research Agenda
Authors: Lai Lawrence W C , Hung Connie W Y
Published: January 2008

This paper is an original attempt to explore the inner logic of and apply the Coase Theorem—specifically the corollary of the invariant version of the Coase Theorem (CIT) and the extension of the corollary of the optimality version of the Coase Theorem (COTE)—to empirical planning research. This attempt hinges critically upon seven theoretical propositions developed on the basis of seven law and policy relevant determining variables that are manifestations of ways of ‘assignment of rights and liabilities’ for the application of CIT (COTE). This is preceded by an examination of the meaning of seven allocative outcomes or determined variables pertaining to the theorem component ‘resource allocation would (under CIT not) be identical’. A 7 × 7 matrix (with forty-nine cells, each defining a specific research arena) is constructed, and relevant literature is surveyed to map the landscape of Coasian planning research as a step to building a transaction-cost-based research agenda. An example of empirically refutable planning hypotheses is given to demonstrate the usefulness of the propositions and to obtain a glimpse of the applicability of the agenda.
Using the ART-MMAP Neural Network to Model and Predict Urban Growth: A Spatiotemporal Data Mining Approach
Authors: Liu Weiguo , Seto Karen C
Published: January 2008

Predicting patterns of urban growth will be a major challenge for policy makers and environmental scientists in the 21st century. How cities grow—their shape and size—will have enormous implications for environmental sustainability and infrastructure needs. This paper presents a spatiotemporal ART-MMAP neural method to simulate and predict urban growth. Factors that affect urban growth—that is, transportation routes, land use, and topography—were directly used as inputs to the neural network model for model calibration. The calibrated network was then applied to a study site—St Louis, Missouri—to predict future urban growth and to examine future land development scenarios. This paper also introduces an effective and straightforward method for model validation and accuracy assessment, the prediction error matrix, which has been used in the pattern recognition field for several decades. In order to assess the performance of the neural network model, an in-depth accuracy assessment was conducted in which the model results were compared against a null model, an alternative naïve model, and two random models. The neural network model consistently outperformed the naïve model and two random models, and produced similar or better results than the null model. Furthermore, we evaluated the models' performance at different spatial resolutions. The prediction accuracy increases when spatial resolution becomes coarser. One particularly interesting result is that when the results are aggregated to 1 km spatial resolution, there is 100% accuracy of urban growth predicted by the neural network model versus actual urban growth.
The Contribution of Ecological Footprinting to Planning Policy Development: Using REAP to Evaluate Policies for Sustainable Housing Construction
Authors: Nye Michael , Rydin Yvonne
Published: January 2008

The complexity of the sustainable-development policy goal is such that policy makers are searching for tools to enable them to evaluate and develop policy directions. To date, ecological footprinting has been used mainly for raising awareness of environmental impacts but it also has considerable potential as a policy tool, enabling policy makers in their strategic work. The paper presents an application of a specific ecological footprinting development, the REAP (Resource and Energy Analysis Programme) tool, to a current policy issue, the promotion of sustainable construction. Using the London Plan of the Greater London Authority as a case study, it considers the strengths and weaknesses of this approach and how it can contribute to policy development.
Monitoring Eye Movements to Investigate the Picture Superiority Effect in Spatial Memory
Authors: Cattaneo Zaira , Rosen Mitchell , Vecchi Tomaso , Pelz Jeff B
Published: January 2008

Spatial memory is usually better for iconic than for verbal material. Our aim was to assess whether such effect is related to the way iconic and verbal targets are viewed when people have to memorize their locations. Eye movements were recorded while participants memorized the locations of images or words. Images received fewer, but longer, gazes than words. Longer gazes on images might reflect greater attention devoted to images due to their higher sensorial distinctiveness and/or generation with images of an additional phonological code beyond the visual code immediately available. We found that words were scanned mainly from left to right while a more heterogeneous scanning strategy characterized encoding of images. This suggests that iconic configurations tend to be maintained as global integrated representations in which all the item/location pairs are simultaneously present whilst verbal configurations are maintained through more sequential processes.
Investigating the Effects of Inversion on Configural Processing with an Audiovisual Temporal-Order Judgment Task
Authors: Vatakis Argiro , Spence Charles
Published: January 2008

Research has shown that inversion is more detrimental to the perception of faces than to the perception of other types of visual stimuli. Inverting a face results in an impairment of configural information processing that leads to slowed early face processing and reduced accuracy when performance is tested in face recognition tasks. We investigated the effects of inverting speech and non-speech stimuli on audiovisual temporal perception. Upright and inverted audio-visual video clips of a person uttering syllables (experiments 1 and 2), playing musical notes on a piano (experiment 3), or a rhesus monkey producing vocalisations (experiment 4) were presented. Participants made unspeeded temporal-order judgments regarding which modality stream (auditory or visual) appeared to have been presented first. Inverting the visual stream did not have any effect on the sensitivity of temporal discrimination responses in any of the four experiments, thus implying that audiovisual temporal integration is resilient to the effects of orientation in the picture plane. By contrast, the point of subjective simultaneity differed significantly as a function of orientation only for the audiovisual speech stimuli but not for the non-speech stimuli or monkey calls. That is, smaller auditory leads were required for the inverted than for the upright-visual speech stimuli. These results are consistent with the longer processing latencies reported previously when human faces are inverted and demonstrates that the temporal perception of dynamic audiovisual speech can be modulated by changes in the physical properties of the visual speech (ie by changes in orientation).
Learning to Perceive Differences in Solid Shape through Vision and Touch
Authors: Norman J Farley , Clayton Anna Marie , Norman Hideko F , Crabtree Charles E
Published: January 2008

A single experiment was designed to investigate perceptual learning and the discrimination of 3-D object shape. Ninety-six observers were presented with naturally shaped solid objects either visually, haptically, or across the modalities of vision and touch. The observers' task was to judge whether the two sequentially presented objects on any given trial possessed the same or different 3-D shapes. The results of the experiment revealed that significant perceptual learning occurred in all modality conditions, both unimodal and cross-modal. The amount of the observers' perceptual learning, as indexed by increases in hit rate and d', was similar for all of the modality conditions. The observers' hit rates were highest for the unimodal conditions and lowest in the cross-modal conditions. Lengthening the inter-stimulus interval from 3 to 15 s led to increases in hit rates and decreases in response bias. The results also revealed the existence of an asymmetry between two otherwise equivalent cross-modal conditions: in particular, the observers' perceptual sensitivity was higher for the vision—haptic condition and lower for the haptic—vision condition. In general, the results indicate that effective cross-modal shape comparisons can be made between the modalities of vision and active touch, but that complete information transfer does not occur.
Ecological rules governing helminth–microparasite coinfection
Authors: Graham Andrea L.
Published: January 2008

Coinfection of a host by multiple parasite species has important epidemiological and clinical implications. However, the direction and magnitude of effects vary considerably among systems, and, until now, there has been no general framework within which to explain this variation. Community ecology has great potential for application to such problems in biomedicine. Here, metaanalysis of data from 54 experiments on laboratory mice reveals that basic ecological rules govern the outcome of coinfection across a broad spectrum of parasite taxa. Specifically, resource-based (“bottom-up”) and predator-based (“top-down”) control mechanisms combined to determine microparasite population size in helminth-coinfected hosts. Coinfection imposed bottom-up control (resulting in decreased microparasite density) when a helminth that causes anemia was paired with a microparasite species that requires host red blood cells. At the same time, coinfection impaired top-down control of microparasites by the immune system: the greater the helminth-induced suppression of the inflammatory cytokine interferon (IFN)-γ, the greater the increase in microparasite density. These results suggest that microparasite population growth will be most explosive when underlying helminths do not impose resource limitations but do strongly modulate IFN-γ responses. Surprisingly simple rules and an ecological framework within which to analyze biomedical data thus emerge from analysis of this dataset. Through such an interdisciplinary lens, predicting the outcome of coinfection may become tractable.
Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution
Authors: Dacks Joel B. , Poon Pak P. , Field Mark C.
Published: January 2008

The process by which some eukaryotic organelles, for example the endomembrane system, evolved without endosymbiotic input remains poorly understood. This problem largely arises because many major cellular systems predate the last common eukaryotic ancestor (LCEA) and thus do not provide examples of organellogenesis in progress. A model is emerging whereby gene duplication and divergence of multiple “specificity-” or “identity-” encoding proteins for the various endomembranous organelles produced the diversity of nonendosymbiotically derived cellular compartments present in modern eukaryotes. To address this possibility, we analyzed three molecular components of the endocytic membrane-trafficking machinery. Phylogenetic analyses of the endocytic syntaxins, Rab 5, and the β-adaptins each reveal a pattern of ancestral, undifferentiated endocytic homologues in the LCEA. Subsequently, these undifferentiated progenitors independently duplicated in widely divergent lineages, convergently producing components with similar endocytic roles, e.g., β1 and β2-adaptin. In contrast, β3, β4, and all other adaptin complex subunits, as well as paralogues of the syntaxins and Rabs specific for the other membrane-trafficking organelles, all evolved before the LCEA. Thus, the process giving rise to the differentiated organelles of the endocytic system appears to have been interrupted by the major speciation event that produced the extant eukaryotic lineages. These results suggest that although many endocytic components evolved before the LCEA, other major features evolved independently and convergently after diversification into the primary eukaryotic supergroups. This finding provides an example of a basic cellular system that was simpler in the LCEA than in many extant eukaryotes and yields insight into nonendosymbiotic organelle evolution.
Heat-shock protein 90α1 is required for organized myofibril assembly in skeletal muscles of zebrafish embryos
Authors: Du Shao Jun , Li Huiqing , Bian Yuehong , Zhong Yongwang
Published: January 2008

Heat-shock protein 90α (Hsp90α) is a member of the molecular chaperone family involved in protein folding and assembly. The role of Hsp90α in the developmental process, however, remains unclear. Here we report that zebrafish contains two Hsp90α genes, Hsp90α1, and Hsp90α2. Hsp90α1 is specifically expressed in developing somites and skeletal muscles of zebrafish embryos. We have demonstrated that Hsp90α1 is essential for myofibril organization in skeletal muscles of zebrafish embryos. Knockdown of Hsp90α1 resulted in paralyzed zebrafish embryos with poorly organized myofibrils in skeletal muscles. In contrast, knockdown of Hsp90α2 had no effect on muscle contraction and myofibril organization. The filament defects could be rescued in a cell autonomous manner by an ectopic expression of Hsp90α1. Biochemical analyses revealed that knockdown of Hsp90α1 resulted in significant myosin degradation and up-regulation of unc-45b gene expression. These results indicate that Hsp90α1 plays an important role in muscle development, likely through facilitating myosin folding and assembly into organized myofibril filaments.