bluuebunny/crossref_metadata_2025 huggingface dataset:
MONTE CARLO SIMULATION OF THE KINETICS IN THE GROWTH OF SEMICONDUCTOR QUANTUM DOTS
Authors: ZHAO CHANG , ZHAO M. , WANG Y. , LV A. J. , WU G. M. , XING G. J.
Published: March 2011

By means of kinetic Monte Carlo simulation, which is based on the random selection of the surface hops of single adatom, we investigate the atoms' kinetics during the growth of the semiconductor quantum dots in a molecular beam epitaxy system, the deposition, diffusion and nucleation are considered as the main relevant processes during the growth of the quantum dots, taking into account the contribution of the dangling bond of the adatoms in the simulation. The dependence of the quantum dot size on the temperature and flux as well as the atomic kinetic effects are discussed in detail. The simulation results are in good qualitative agreement with those of the experiment.
LINEAR AND NONLINEAR INTERSUBBAND OPTICAL ABSORPTION OF FINITE AND INFINITE SEMI-PARABOLIC QUANTUM WELLS
Authors: KARIMI M. J. , KESHAVARZ A. , POOSTFORUSH A.
Published: March 2011

In this work, the optical absorption coefficients and the refractive index changes for the infinite and finite semi-parabolic quantum well are calculated. Numerical calculations are performed for typical GaAs / Al x Ga 1-x As semi-parabolic quantum well. The energy eigenvalues and eigenfunctions of these systems are calculated numerically. Optical properties are obtained using the compact density matrix approach. Results show that the energy eigenvalues and the matrix elements of the infinite and finite cases are different. The calculations reveal that the resonant peaks of the optical properties of the finite case occur at lower values of the incident photon energy with respect to the infinite case. Results indicate that the maximum value of the refractive index changes for the finite case are greater than that of the infinite case. Our calculations also show that in contrast to the infinite case, the resonant peak value of the total absorption coefficient in the case of the finite well is a non-monotonic function of the semi-parabolic confinement frequency.
FATIGUE CRACK STATISTICS IN FASTENER HOLES
Authors: HARLOW D. GARY
Published: March 2011

Structural components in aircraft are often required to be operative beyond their original design service objectives (DSO). Vital issues for aging infrastructures are estimation and prediction, with confidence, of residual life, reliability, and availability, given the service history. Uncertainty increasingly is considered to be a major factor. Demanding high reliability exacerbates the role of uncertainty. One aspect of life cycle management for aging aircraft was investigated by replicating laboratory specimens subjected to fatigue loading that is typical for a class of military aircraft wing skins. Samples were fabricated from 7075-T6 plate aluminum alloy similar to that used for wing panels. A total of 15 specimens were tested. Tests were terminated when the fatigue life expended (FLE) reached a prescribed value of 100%, 150%, or 200% of the component DSO. Then, microscopy was used to quantify the size of fatigue cracks within high stress regions of simulated fastener holes in laboratory specimens. Cumulative distribution functions (cdfs) for geometrical properties of cracks and constituent particles in the alloy were characterized statistically as input for residual life estimations and for life cycle management analyses. Insights into crack initiation and growth are also provided.
A PROBABILISTIC FATIGUE LIFE ESTIMATION APPROACH FOR COMPLEX STRUCTURE AND COMPONENT
Authors: XIE LIYANG , WU NINGXIANG , QIAN WENXUE
Published: March 2011

Fatigue life corresponding to specific failure probability is much more significant than mean life, since fatigue fracture is a highly uncertain phenomenon. For a complex structural component with several damage sites, the contributions of the every damage site are stochastic in nature. Moreover, the damages or fatigue lives of the individual vulnerable sites are neither completely correlated nor perfectly independent of each other. The present paper develops a probabilistic fatigue life evaluation approach to predict the probabilistic fatigue life of complex mechanical or structural components containing multiple damage sites. By correctly dealing with the failure dependence of the every damage sites and characterizing the fatigue life random variable of a multi-site-damage (MSD) structure or component using the extreme statistic of the fatigue lives of the individual damage sites, probabilistic fatigue life of MSD structural component is reasonably predicted.
DETERMINING MINIMUM SURVEY SAMPLE SIZE FOR MULTI-CELL CASE
Authors: CHEN ZHENMIN , ZHAO FANG
Published: March 2011

Survey analysis method is widely used in many areas such as social study, marketing research, economics, public health, clinical trials and transportation data analysis. Minimum sample size determination is always needed before a survey is conducted to avoid huge cost. Some statistical methods can be found from the literature for finding the minimum required sample size. This paper proposes a method for finding the minimum total sample size needed for the survey when the population is divided into cells. The proposed method can be used for both the infinite population case and the finite population case. A computer program is needed to realize the sample size calculation. The computer program the authors used is SAS/IML, which is a special integrated matrix language (IML) procedure of the Statistical Analysis System (SAS) software.
A COMPLETE DESCRIPTION OF MAXIMAL SOLUTIONS OF FUNCTIONAL EQUATIONS ARISING FROM MULTIPLICATION OF QUANTUM INTEGERS
Authors: NGUYEN LAN
Published: March 2011

In this paper, we resolve a problem raised by Nathanson concerning the maximal solutions to functional equations naturally arising from multiplication of quantum integers ([4]). Together with our results obtained in [11], which treats the case where the field of coefficients is ℚ, this provides a complete description of the maximal solutions to these functional equations and their support bases P in characteristic zero setting.
SEISMIC DEMAND OF BUCKLING-RESTRAINED BRACES INSTALLED IN STEEL ARCH BRIDGES UNDER REPEATED EARTHQUAKES
Authors: CHEN XI , GE HANBIN , USAMI TSUTOMU
Published: March 2011

A steel arch bridge originally designed against moderate earthquakes is retrofitted by installation of buckling-restrained braces (BRBs) to sustain severe earthquakes. Two retrofitting methods are considered to obtain good seismic performance of this arch bridge. The original model and retrofitted models subjected to the major earthquakes are investigated by dynamic analyses using 12 patterns of severe (level 2) earthquakes as input ground motions. It is found that the retrofitted models using BRBs can greatly improve seismic performance (displacement, section force, strain, reaction force, etc.) of the steel arch bridge. In addition, to investigate the influence of repeated earthquakes on the seismic responses of the main structure and the demands of BRBs, 12 patterns of earthquake ground motions are repeated by three times. Based on the analytical results, the seismic demands of BRBs against repeated earthquakes are obtained, and the required capacity of BRBs is recommended using a safety factor concluded by comparing the demands under the earthquake applied one and three times. Finally, the influence of the different yield stress on the demand of BRBs is examined by changing the steel grade of BRBs.
IDENTIFICATION OF DAMAGE IN REINFORCED CONCRETE COLUMNS UNDER PROGRESSIVE SEISMIC EXCITATION STAGES
Authors: WU ZHISHEN , ADEWUYI ADEKUNLE PHILIPS , XUE SONGTAO
Published: March 2011

Prompt and accurate detection of realistic damage in constructed facilities is critical for effective condition assessment and structural health monitoring. This paper reports the experimental investigations of eccentric reinforced concrete columns mounted onto a shaking table and subject to progressively increasing seismic excitations. The investigation was aimed at studying the changes in the dynamic parameters in order to assess the structural conditions of the concrete columns after each post-seismic stage. The dynamic response of the structure was measured using accelerometers, traditional foil-strain gauges, and long-gauge fiber Bragg grating (FBG) sensors. The post-seismic conditions of the columns were evaluated via vibration-based damage identification methods. Results from this study demonstrate the applicability of specially packaged surface-mounted long-gauge FBG sensors for detecting the initiation and the progression of cracks due to reverse dynamic loads. The concept of modal macrostrain analysis was also introduced to identify and localize mild damage due to the applied seismic excitations of increasing intensities. The performance of the sensors for structural identification is also discussed.
Grid computing's future
Authors: Kroeker Kirk L.
Published: March 2011

Outreach programs and usability improvements are drawing many researchers to grid computing from disciplines that have not traditionally used such resources.
Memristors
Authors: Anthes Gary
Published: March 2011

The device may revolutionize data storage, replacing flash memory and perhaps even disks. Whether they can be reliably and cheaply manufactured, though, is an open question.
Managing time
Authors: Denning Peter J.
Published: March 2011

Professionals overwhelmed with information glut can find hope from new insights about time management.
Computer and information science and engineering
Authors: Snir Marc
Published: March 2011

Mathematics is no longer the only foundation for computing and information research and education in academia.
Data structures in the multicore age
Authors: Shavit Nir
Published: March 2011

The advent of multicore processors as the standard computing platform will force major changes in software design.
Governing Web 2.0
Authors: De Hertogh Steven , Viaene Stijn , Dedene Guido
Published: March 2011

Grounding principles to get the most out of enterprise 2.0 investments.
Partitioned Triangular Tridiagonalization
Authors: Rozložník Miroslav , Shklarski Gil , Toledo Sivan
Published: March 2011

We present a partitioned algorithm for reducing a symmetric matrix to a tridiagonal form, with partial pivoting. That is, the algorithm computes a factorization
PAPT
=
LTLT
, where,
P
is a permutation matrix,
L
is lower triangular with a unit diagonal and entries’ magnitudes bounded by 1, and
T
is symmetric and tridiagonal. The algorithm is based on the basic (nonpartitioned) methods of Parlett and Reid and of Aasen. We show that our factorization algorithm is componentwise backward stable (provided that the growth factor is not too large), with a similar behavior to that of Aasen’s basic algorithm. Our implementation also computes the
QR
factorization of
T
and solves linear systems of equations using the computed factorization. The partitioning allows our algorithm to exploit modern computer architectures (in particular, cache memories and high-performance
blas
libraries). Experimental results demonstrate that our algorithms achieve approximately the same level of performance as the partitioned Bunch-Kaufman factor and solve routines in
lapack
.
Algorithm 912
Authors: Kodama Masao
Published: March 2011

The present algorithm provides a module for calculating the cylindrical functions
Jv
(
z
),
Yv
(
z
),
Hv
(1)(
z
), and
Hv
(2)(
z
), where the order
v
is complex and the complex argument
z
satisfies −
π
< arg
z
≤
π
. The algorithm is written in Fortran 90 and calculates the functions using real and complex numbers of any intrinsic data type whose kind type parameter the user’s Fortran system accepts. The methods of calculating the functions are based on two kinds of series expansions and numerical integration. Wronskian tests examine the functional values computed by this algorithm with double precision at 4,100,625 pseudorandom test points in the region |Re
v
| ≤ 60, |Im
v
| ≤ 60, |Re
z
| ≤ 300, |Im
z
| ≤ 300. From the results of the tests, we find that the errors of two kinds of Wronskians are less than 6.42 × 10−14.
HADI
Authors: Kang U. , Tsourakakis Charalampos E. , Appel Ana Paula , Faloutsos Christos , Leskovec Jure
Published: March 2011

Given large, multimillion-node graphs (e.g., Facebook, Web-crawls, etc.), how do they evolve over time? How are they connected? What are the central nodes and the outliers? In this article we define the Radius plot of a graph and show how it can answer these questions. However, computing the Radius plot is prohibitively expensive for graphs reaching the planetary scale.

There are two major contributions in this article: (a) We propose HADI (HAdoop DIameter and radii estimator), a carefully designed and fine-tuned algorithm to compute the radii and the diameter of massive graphs, that runs on the top of the
Hadoop
/
MapReduce
system, with excellent scale-up on the number of available machines (b) We run HADI on several real world datasets including YahooWeb (6B edges, 1/8 of a Terabyte), one of the largest public graphs ever analyzed.

Thanks to HADI, we report fascinating patterns on large networks, like the surprisingly small effective diameter, the multimodal/bimodal shape of the Radius plot, and its palindrome motion over time.
Temporal Link Prediction Using Matrix and Tensor Factorizations
Authors: Dunlavy Daniel M. , Kolda Tamara G. , Acar Evrim
Published: March 2011

The data in many disciplines such as social networks, Web analysis, etc. is link-based, and the link structure can be exploited for many different data mining tasks. In this article, we consider the problem of temporal link prediction: Given link data for times 1 through
T
, can we predict the links at time
T
+ 1? If our data has underlying periodic structure, can we predict out even further in time, i.e., links at time
T
+ 2,
T
+ 3, etc.? In this article, we consider bipartite graphs that evolve over time and consider matrix- and tensor-based methods for predicting future links. We present a weight-based method for collapsing multiyear data into a single matrix. We show how the well-known Katz method for link prediction can be extended to bipartite graphs and, moreover, approximated in a scalable way using a truncated singular value decomposition. Using a CANDECOMP/PARAFAC tensor decomposition of the data, we illustrate the usefulness of exploiting the natural three-dimensional structure of temporal link data. Through several numerical experiments, we demonstrate that both matrix- and tensor-based techniques are effective for temporal link prediction despite the inherent difficulty of the problem. Additionally, we show that tensor-based techniques are particularly effective for temporal data with varying periodic patterns.
Fast Algorithms for Approximating the Singular Value Decomposition
Authors: Menon Aditya Krishna , Elkan Charles
Published: March 2011

A low-rank approximation to a matrix
A
is a matrix with significantly smaller rank than
A
, and which is close to
A
according to some norm. Many practical applications involving the use of large matrices focus on low-rank approximations. By reducing the rank or dimensionality of the data, we reduce the complexity of analyzing the data. The singular value decomposition is the most popular low-rank matrix approximation. However, due to its expensive computational requirements, it has often been considered intractable for practical applications involving massive data. Recent developments have tried to address this problem, with several methods proposed to approximate the decomposition with better asymptotic runtime. We present an empirical study of these techniques on a variety of dense and sparse datasets. We find that a sampling approach of Drineas, Kannan and Mahoney is often, but not always, the best performing method. This method gives solutions with high accuracy much faster than classical SVD algorithms, on large sparse datasets in particular. Other modern methods, such as a recent algorithm by Rokhlin and Tygert, also offer savings compared to classical SVD algorithms. The older sampling methods of Achlioptas and McSherry are shown to sometimes take longer than classical SVD.
SnowFlock
Authors: Lagar-Cavilla H. Andrés , Whitney Joseph A. , Bryant Roy , Patchin Philip , Brudno Michael , de Lara Eyal , Rumble Stephen M. , Satyanarayanan M. , Scannell Adin
Published: March 2011

A basic building block of cloud computing is virtualization. Virtual machines (VMs) encapsulate a user’s computing environment and efficiently isolate it from that of other users. VMs, however, are large entities, and no clear APIs exist yet to provide users with programatic, fine-grained control on short time scales.

We present SnowFlock, a paradigm and system for cloud computing that introduces VM cloning as a first-class cloud abstraction. VM cloning exploits the well-understood and effective semantics of UNIX fork. We demonstrate multiple usage models of VM cloning: users can incorporate the primitive in their code, can wrap around existing toolchains via scripting, can encapsulate the API within a parallel programming framework, or can use it to load-balance and self-scale clustered servers.

VM cloning needs to be efficient to be usable. It must efficiently transmit VM state in order to avoid cloud I/O bottlenecks. We demonstrate how the semantics of cloning aid us in realizing its efficiency: state is propagated in parallel to multiple VM clones, and is transmitted during runtime, allowing for optimizations that substantially reduce the I/O load. We show detailed microbenchmark results highlighting the efficiency of our optimizations, and macrobenchmark numbers demonstrating the effectiveness of the different usage models of SnowFlock.
Bridging the gaps between HCI and social media
Authors: McCarthy Joe
Published: March 2011

"Social Mediator" is a new
interactions
forum exploring the ways that HCI research and principles interact --- or might interact --- with practices in the social media world.

Joe McCarthy, Editor
Up and coming SIGWEB supported conferences
Authors: Deshpande Yogesh
Published: March 2011

SIGWEB supports several specialized conferences, short courses, and workshops, as well as the Annual Hypertext Conference. SIGWEB sponsored conferences focus on timely topics in applied and computational hypertext and Web disciplines and provide a place for members and the entire applied Hypermedia and Web community to exchange ideas and to meet with and expand their network of colleagues. In this article, we provide a brief overview of SIGWEB sponsored conferences, in addition to events that are in cooperation with SIGWEB. http://doi.acm.org/10.1145/1942800.1942805.
Attaining system performance points
Authors: Gupta Vishakha , Knauerhase Rob , Schwan Karsten
Published: March 2011

Trends indicate a rapid increase in the number of cores on chip, exhibiting various types of performance and functional asymmetries present in hardware to gain scalability with balanced power vs. performance requirements. This poses new challenges in platform resource management, which are further exacerbated by the need for runtime power budgeting and by the increased dynamics in workload behavior observed in consolidated datacenter and cloudcomputing systems. This paper considers the implications of these challenges for the virtualization layer of abstraction, which is the base layer for resource management in such heterogeneous multicore platforms. Specifically, while existing and upcoming management methods routinely leverage system-level information available to the hypervisor about current and global platform state, we argue that for future systems there will be an increased necessity for additional information about applications and their needs. This 'end-to-end' argument leads us to propose 'performance points' as a general interface between the virtualization system and higher layers like the guest operating systems that run application workloads. Building on concrete examples from past work on APIs with which applications can inform systems of phase or workload changes and conversely, with which systems can indicate to applications desired changes in power consumption, performance points are shown to be an effective way to better exploit asymmetries and gain the power/performance improvements promised by heterogeneous multicore systems.
Bridging functional heterogeneity in multicore architectures
Authors: Reddy Dheeraj , Koufaty David , Brett Paul , Hahn Scott
Published: March 2011

Heterogeneous processors that mix big high performance cores with small low power cores promise excellent single-threaded performance coupled with high multi-threaded throughput and higher performance-per-watt. A significant portion of the commercial multicore heterogeneous processors are likely to have a common instruction set architecture( ISA). However, due to limited design resources and goals, each core is likely to contain ISA extensions not yet implemented in the other core. Therefore, such heterogeneous processors will have inherent functional asymmetry at the ISA level and face significant software challenges. This paper analyzes the software challenges to the operating system and the application layer software on a heterogeneous system with functional asymmetry, where the ISA of the small and big cores overlaps. We look at the widely deployed Intel® Architecture and propose solutions to the software challenges that arise when a heterogeneous processor is designed around it. We broadly categorize functional asymmetries into those that can be exposed to application software and those that should be handled by system software. While one can argue that new software written should be heterogeneity-aware, it is important that we find ways in which legacy software can extract the best performance from heterogeneous multicore systems.
Differentiated storage services
Authors: Mesnier Michael P. , Akers Jason B.
Published: March 2011

This article presents a Differentiated Storage Services architecture for file and storage systems. By classifying data at the block-level, a filesystem can request that different classes of data (e.g., file, directory, executable, text) be handled with different policies (e.g., low-latency versus highbandwidth), and it is left to the storage system to enforce these policies. Our approach assumes that an I/O classifier can be included in-band with each I/O request (e.g., using a field in the SCSI block command set) and that the policy for each class can be specified out-of-band through the management interface of the storage system.

We describe our prototypes based on Linux Ext3, Windows NTFS, and hybrid storage systems composed of rotating and solid-state disks. With very little modification, filesystems can identify latency sensitive I/O classes (e.g., small files, directories, metadata, and the journal) and request that the storage system provision the solid-state storage for just these classes; and this is simply one of many possibilities. As part of our ongoing work, across a variety of file and storage systems, we are exploring other policies and mechanisms that can be used to improve application performance, reliability, and security.
Direct data flows
Authors: Raghunath Arun , Keys John , Vij Mona
Published: March 2011

Reducing power consumption of Mobile Internet Devices (MID) and smartphones is critical as battery life is a key feature for mobility. Most vendors use System-On-Chip designs integrating more and more fixed-function hardware modules in a bid to reduce power consumption. On the other hand the explosion of new applications has increased the demand for PC-like processing capabilities on these devices. They are best supported by general purpose CPUs and Operating Systems which consume more power. Traditional system architectures focus on a data transfer model with the CPU as one of the endpoints. Consequently there are numerous usage scenarios where the general purpose CPU just acts as an intermediary between hardware modules, transferring data from a hardware module to memory and vice-versa. We propose Direct Data Flows, an SoC focused system architecture where the OS can configure fixed-function hardware modules to communicate data directly with each other. This eliminates unnecessary data hops and reduces CPU interrupts allowing the general purpose CPU to be opportunistically brought into lower power states, reducing overall power consumption. We have created a prototype Direct Data Flow setup for network file downloads which demonstrates up to 65% energy savings for typical file sizes.
RFS
Authors: Dong Yuan , Zhu Haiyang , Peng Jinzhan , Wang Fang , Mesnier Michael P. , Wang Dawei , Chan Sun C.
Published: March 2011

Due to the increasing number of applications (and their data) being placed on mobile devices, access to dependable storage is becoming a key issue in mobile system design -- and cloud storage is becoming an attractive solution. However, this introduces a number of new issues related to unpredictable wireless network connectivity and data privacy over the network.

In this article we present RFS, a wireless-friendly network file system for mobile devices and the cloud. RFS provides deviceaware cache management and client-driven data security and privacy protection. We implement the RFS client in the Linux kernel and the RFS server with Amazon S3 cloud storage, and we employ two new optimizations: server prepush (a server-side data pre-fetching mechanism) and client reintegration (synchronizing a mobile device's cache with the cloud).

The empirical results over wired, WiFi and 3G networks show that RFS achieves good performance compared to Coda and FScache, and it reduces network activity visibly. Further, the privacy overhead is acceptable when RFS is run over wireless networks. We present a case study of booting Android over RFS, thereby demonstrating the ability for RFS to host a full mobile system. Overall, RFS can deliver a good user experience under undependable network conditions, allowing mobile users to seamlessly, and safely, use the cloud for data storage.
Inclusive technologies for enhancing the accessibility of digital television
Authors: Bhachu Amritpal Singh
Published: March 2011

Digital Television (DTV) is full of interactive content that was not previously available through analogue television. However, the interactive content can be complex to use, which in turn creates obstacles for users, and in particular older adults, to access this content. This project work looks into ways in which DTV content can be made accessible for older adults through novel DTV menu interface design and alternative input types.
Generating efficient feedback and enabling interaction in virtual worlds for users with visual impairments
Authors: Oktay Bugra
Published: March 2011

Despite the efforts for making virtual worlds accessible to users with visual impairments (VI), we still lack an effective way of describing the virtual environment and having the users interact with it. This work aims to complete these missing parts by generating meaningful textual/audio feedbacks as necessary and by providing text-based interaction capabilities.
The automation of spinal non-manual signals in American Sign Language
Authors: Semler Lindsay
Published: March 2011

American Sign Language (ASL) is the first language of the Deaf in the United States. The most effective method for communication between the Deaf and Hearing is certified ASL interpreters, however interpreters are not always available. In this case, the use of a translator producing 3D animations of ASL could improve communication, however the characterization of ASL for automated 3D animation is still an open question. The goal of this research is to determine how and when non-manual signals are used in ASL sentences, and develop a methodology to portray them as 3D animations.
Evolution of Photosynthesis
Authors: Hohmann-Marriott Martin F. , Blankenship Robert E.
Published: March 2011

Energy conversion of sunlight by photosynthetic organisms has changed Earth and life on it. Photosynthesis arose early in Earth's history, and the earliest forms of photosynthetic life were almost certainly anoxygenic (non-oxygen evolving). The invention of oxygenic photosynthesis and the subsequent rise of atmospheric oxygen approximately 2.4 billion years ago revolutionized the energetic and enzymatic fundamentals of life. The repercussions of this revolution are manifested in novel biosynthetic pathways of photosynthetic cofactors and the modification of electron carriers, pigments, and existing and alternative modes of photosynthetic carbon fixation. The evolutionary history of photosynthetic organisms is further complicated by lateral gene transfer that involved photosynthetic components as well as by endosymbiotic events. An expanding wealth of genetic information, together with biochemical, biophysical, and physiological data, reveals a mosaic of photosynthetic features. In combination, these data provide an increasingly robust framework to formulate and evaluate hypotheses concerning the origin and evolution of photosynthesis.
Regulation of HSF1 Function in the Heat Stress Response: Implications in Aging and Disease
Authors: Anckar Julius , Sistonen Lea
Published: March 2011

To dampen proteotoxic stresses and maintain protein homeostasis, organisms possess a stress-responsive molecular machinery that detects and neutralizes protein damage. A prominent feature of stressed cells is the increased synthesis of heat shock proteins (Hsps) that aid in the refolding of misfolded peptides and restrain protein aggregation. Transcriptional activation of the heat shock response is orchestrated by heat shock factor 1 (HSF1), which rapidly translocates to hsp genes and induces their expression. Although the role of HSF1 in protecting cells and organisms against severe stress insults is well established, many aspects of how HSF1 senses qualitatively and quantitatively different forms of stresses have remained poorly understood. Moreover, recent discoveries that HSF1 controls life span have prompted new ways of thinking about an old transcription factor. Here, we review the established role of HSF1 in counteracting cell stress and prospect the role of HSF1 as a regulator of disease states and aging.
DNA Replicases from a Bacterial Perspective
Authors: McHenry Charles S.
Published: March 2011

Bacterial replicases are complex, tripartite replicative machines. They contain a polymerase, polymerase III (Pol III), a β2 processivity factor, and a DnaX complex ATPase that loads β2 onto DNA and chaperones Pol III onto the newly loaded β2. Bacterial replicases are highly processive, yet cycle rapidly during Okazaki fragment synthesis in a regulated way. Many bacteria encode both a full-length τ and a shorter γ form of DnaX by a variety of mechanisms. γ appears to be uniquely placed in a single position relative to two τ protomers in a pentameric ring. The polymerase catalytic subunit of Pol III, α, contains a PHP domain that not only binds to a prototypical ε Mg2+-dependent exonuclease, but also contains a second Zn2+-dependent proofreading exonuclease, at least in some bacteria. This review focuses on a critical evaluation of recent literature and concepts pertaining to the above issues and suggests specific areas that require further investigation.
Class I Ribonucleotide Reductases: Metallocofactor Assembly and Repair In Vitro and In Vivo
Authors: Cotruvo Joseph A. , Stubbe JoAnne
Published: March 2011

Incorporation of metallocofactors essential for the activity of many enyzmes is a major mechanism of posttranslational modification. The cellular machinery required for these processes in the case of mono- and dinuclear nonheme iron and manganese cofactors has remained largely elusive. In addition, many metallocofactors can be converted to inactive forms, and pathways for their repair have recently come to light. The class I ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides and require dinuclear metal clusters for activity: an FeIIIFeIII-tyrosyl radical (Y•) cofactor (class Ia), a MnIIIMnIII-Y• cofactor (class Ib), and a MnIVFeIII cofactor (class Ic). The class Ia, Ib, and Ic RNRs are structurally homologous and contain almost identical metal coordination sites. Recent progress in our understanding of the mechanisms by which the cofactor of each of these RNRs is generated in vitro and in vivo and by which the damaged cofactors are repaired is providing insight into how nature prevents mismetallation and orchestrates active cluster formation in high yields.
Journey of a Molecular Biologist
Authors: Nomura Masayasu
Published: March 2011

My journey into a research career began in fermentation biochemistry in an applied science department during the difficult post-World War II time in Japan. Subsequently, my desire to do research in basic science developed. I was fortunate to be a postdoctoral fellow in the United States during the early days of molecular biology. From 1957 to 1960, I worked with three pioneers of molecular biology, Sol Spiegelman, James Watson, and Seymour Benzer. These experiences helped me develop into a basic research scientist. My initial research projects at Osaka University, and subsequently at the University of Wisconsin, Madison, were on the mode of action of colicins as well as on mRNA and ribosomes. Following success in the reconstitution of ribosomal subunits, my efforts focused more on ribosomes, initially on the aspects of structure, function, and in vitro assembly, such as the construction of the 30S subunit assembly map. After this, my laboratory studied the regulation of the synthesis of ribosomes and ribosomal components in Escherichia coli. Our achievements included the discovery of translational feedback regulation of ribosomal protein synthesis and the identification of several repressor ribosomal proteins used in this regulation. In 1984, I moved to the University of California, Irvine, and initiated research on rRNA transcription by RNA polymerase I in the yeast Saccharomyces cerevisiae. The use of yeast genetics combined with biochemistry allowed us to identify genes uniquely involved in rRNA synthesis and to elucidate the mechanism of initiation of transcription. This essay is a reflection on my life as a research scientist.
My Life with Nature
Authors: Adler Julius
Published: March 2011

After a childhood in Germany and being a youth in Grand Forks, North Dakota, I went to Harvard University, then to graduate school in biochemistry at the University of Wisconsin. Then to Washington University and Stanford University for postdoctoral training in biochemistry and genetics. Then at the University of Wisconsin, as a professor in the Department of Biochemistry and the Department of Genetics, I initiated research on bacterial chemotaxis. Here, I review this research by me and by many, many others up to the present moment. During the past few years, I have been studying chemotaxis and related behavior in animals, namely in Drosophila fruit flies, and some of these results are presented here. My current thinking is described.
Developmental and Pathological Angiogenesis
Authors: Chung Alicia S. , Ferrara Napoleone
Published: March 2011

The formation of the vascular network is an intricate and complex process that is an obligate requirement during vertebrate development. The cardiovascular system is the first organ to develop and reach a functional state, which underscores the crucial role of the vasculature in the developing embryo. The development of the vasculature into highly branched conduits needs to occur in numerous sites and in precise patterns to supply oxygen and nutrients to the rapidly expanding tissue of the embryo. This process is mediated by the coordinated response of vascular endothelial and mural cells to the heterogeneous angiogenic cues provided by tissues and organs, whereas aberrant regulation and coordination of angiogenic signals during development result in lethality, impaired organ development, or disease states. This article reviews the essential signaling pathways required for establishment of the vertebrate vasculature with a major focus on a key regulatory factor, vascular endothelial growth factor (VEGF). We also discuss current knowledge of physiological angiogenic processes as well as their disruptions in pathological processes, particularly tumorigenesis.
Transmembrane Collagen Receptors
Authors: Leitinger Birgit
Published: March 2011

Collagen, the most abundant protein in animals, is a key component of extracellular matrices. Not only do collagens provide essential structural support for connective tissues, but they are also intimately involved in controlling a spectrum of cellular functions such as growth, differentiation, and morphogenesis. All collagens possess triple-helical regions through which they interact with a host of other proteins including cell surface receptors. A structurally diverse group of transmembrane receptors mediates the recognition of the collagen triple helix: integrins, discoidin domain receptors, glycoprotein VI, and leukocyte-associated immunoglobulin-like receptor-1. These collagen receptors regulate a wide range of behaviors including cell adhesion and migration, hemostasis, and immune function. Here these collagen receptors are discussed in terms of their molecular basis of collagen recognition, their signaling and developmental functions, and their roles in disease.
The Coupling of X-Chromosome Inactivation to Pluripotency
Authors: Deuve Jane Lynda , Avner Philip
Published: March 2011

X-chromosome inactivation, or the silencing of one X chromosome that occurs initially in the female somatic four-cell-stage embryo, is reversed during embryonic development first at the time of inner cell mass formation and again during formation of germ cell precursors. Such X-chromosome reactivation in the mouse implies the silencing of the Xist gene and the transcription of its antisense partner, Tsix, from both X chromosomes. In murine embryonic stem cells, both genes are under the transcriptional control of a series of critical pluripotency factors, namely, OCT3/4, NANOG, SOX2, KLF4, C-MYC and REX1. Although the inactive/active status of the two X chromosomes present in female human embryonic stem cells remains controversial, the reactivation of X-chromosome inactivation seems to be a signature for the naive pluripotent state.
The Ins and Outs of the Epithelial to Mesenchymal Transition in Health and Disease
Authors: Nieto M. Angela
Published: March 2011

The epithelial to mesenchymal transition (EMT) converts epithelial cells into migratory and invasive cells and is a fundamental event in morphogenesis. Although its relevance in the progression of cancer and organ fibrosis had been debated until recently, the EMT is now established as an important step in the metastatic cascade of epithelial tumors. The similarities between pathological and developmental EMTs validate the embryo as the best model to understand the molecular and cellular mechanisms involved in this process, identifying those that are hijacked during the progression of cancer and organ degeneration. Our ever-increasing understanding of how transcription factors regulate the EMT has revealed complex regulatory loops coupled to posttranscriptional and epigenetic regulatory programs. The EMT is now integrated into the systemic activities of whole organisms, establishing links with cell survival, stemness, inflammation, and immunity. In addition, the EMT now constitutes a promising target for the treatment of cancer and organ-degenerative diseases.
Mechanisms of Intracellular Scaling
Authors: Levy Daniel L. , Heald Rebecca
Published: March 2011

Cell size varies widely among different organisms as well as within the same organism in different tissue types and during development, which places variable metabolic and functional demands on organelles and internal structures. A fundamental question is how essential subcellular components scale to accommodate cell size differences. Nuclear transport has emerged as a conserved means of scaling nuclear size. A meiotic spindle scaling factor has been identified as the microtubule-severing protein katanin, which is differentially regulated by phosphorylation in two different-sized frog species. Anaphase mechanisms and levels of chromatin compaction both act to coordinate cell size with spindle and chromosome dimensions to ensure accurate genome distribution during cell division. Scaling relationships and mechanisms for many membrane-bound compartments remain largely unknown and are complicated by their heterogeneity and dynamic nature. This review summarizes cell and organelle size relationships and the experimental approaches that have elucidated mechanisms of intracellular scaling.
Looking Back
Authors: Raff Martin
Published: March 2011

In this Perspective, I review my scientific career, which began after I trained in medicine in Montreal and in neurology in Boston. I started in immunology in London with Avrion Mitchison, using antibodies against cell-surface antigens to study the development and functions of mouse T and B cells. The finding that antibody binding causes immunoglobulin on B cells to redistribute rapidly on the cell surface and be endocytosed transformed me from an immunologist into a cell biologist. I moved with Mitchison to University College London, where my colleagues and I used the antibody approach to study cells of the rodent nervous system, focusing on the intrinsic and extrinsic molecular mechanisms that control the development and behavior of myelinating glial cells—Schwann cells and oligodendrocytes. I retired from active research in 2002 and now spend much of my time on scientific advisory boards and thinking about autism.
Degrading Devices: Invadosomes in Proteolytic Cell Invasion
Authors: Linder Stefan , Wiesner Christiane , Himmel Mirko
Published: March 2011

Podosomes and invadopodia, collectively known as invadosomes, are cell-matrix contacts in a variety of cell types, such as monocytic cells or cancer cells, that have to cross tissue barriers. Both structures share an actin-rich core, which distinguishes them from other matrix contacts, and are regulated by a multitude of signaling pathways including RhoGTPases, kinases, actin-associated proteins, and microtubule-dependent transport. Invadosomes recruit and secrete proteinases and are thus able to lyse extracellular matrix components. They are therefore considered to be potential key structures in proteolytic cell invasion in both physiological and pathological settings. This review provides an overview of the field, with special focus on current developments such as intracellular transport processes, ultrastructural analysis, the possible involvement of invadosomes in disease, and the tentative identification of invadosomes in 3D environments and in vivo.
Membrane-Anchored Serine Proteases in Vertebrate Cell and Developmental Biology
Authors: Szabo Roman , Bugge Thomas H.
Published: March 2011

Analysis of vertebrate genome sequences at the turn of the millennium revealed that a vastly larger repertoire of enzymes execute proteolytic cleavage reactions within the pericellular and extracellular environments than was anticipated from biochemical and molecular analysis. Most unexpected was the unveiling of an entire new family of structurally unique multidomain serine proteases that are anchored directly to the plasma membrane. Unlike secreted serine proteases, which function primarily in tissue repair, immunity, and nutrient uptake, these membrane-anchored serine proteases regulate fundamental cellular and developmental processes, including tissue morphogenesis, epithelial barrier function, ion and water transport, cellular iron export, and fertilization. Here the cellular and developmental biology of this fascinating new group of proteases is reviewed. Particularly highlighted is how the study of membrane-anchored serine proteases has expanded our knowledge of the range of physiological processes that require regulated proteolysis at the cell surface.
Epithelial Progenitor Cells in Lung Development, Maintenance, Repair, and Disease
Authors: Rock Jason R. , Hogan Brigid L.M.
Published: March 2011

The vertebrate lung is elegantly patterned to carry out gas exchange and host defense. Similar to other organ systems, endogenous stem and progenitor cells fuel the organogenesis of the lung and maintain homeostasis in the face of normal wear and tear. In the context of acute injury, these progenitor populations are capable of effecting efficient repair. However, chronic injury, inflammation, and immune rejection frequently result in pathological airway remodeling and serious impairment of lung function. Here, we review the development, maintenance, and repair of the vertebrate respiratory system with an emphasis on the roles of epithelial stem and progenitor cells. We discuss what is currently known about their identities, lineage relationships, and the mechanisms that regulate their differentiation along various lineages. A deeper understanding of these progenitor populations will undoubtedly accelerate the discovery of improved cellular, genetic, molecular, and bioengineered therapies for lung disease.
Principles of Unconventional Myosin Function and Targeting
Authors: Hartman M. Amanda , Finan Dina , Sivaramakrishnan Sivaraj , Spudich James A.
Published: March 2011

Unconventional myosins are a superfamily of actin-based motors implicated in diverse cellular processes. In recent years, much progress has been made in describing their biophysical properties, and headway has been made into analyzing their cellular functions. Here, we focus on the principles that guide in vivo motor function and targeting to specific cellular locations. Rather than describe each motor comprehensively, we outline the major themes that emerge from research across the superfamily and use specific examples to illustrate each. In presenting the data in this format, we seek to identify open questions in each field as well as to point out commonalities between them. To advance our understanding of myosins' roles in vivo, clearly we must identify their cellular cargoes and the protein complexes that regulate motor attachment to fully appreciate their functions on the cellular and developmental levels.
Advances in Insect Phylogeny at the Dawn of the Postgenomic Era
Authors: Trautwein Michelle D. , Wiegmann Brian M. , Beutel Rolf , Kjer Karl M. , Yeates David K.
Published: March 2011

Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).