CiteULike: Author Henderson

Information, Relative Entropy of Entanglement, and Irreversibility

L Henderson — 2007-05-24T06:34:07-00:00

Physical Review Letters, Vol. 84, No. 10. (6 March 2000), 2263.

Previously proposed measures of entanglement; such as entanglement of formation and assistance; are shown to be special cases of the relative entropy of entanglement. The difference between these measures for an ensemble of mixed states is shown to depend on the availability of classical information about particular members of the ensemble. Based on this; relations between relative entropy of entanglement and mutual information are derived.

Yet another network simulator

Mathieu Lacage — 2007-09-07T14:51:11-00:00

(2006)

Mechanisms of Internalization of Staphylococcus aureus by Cultured Human Osteoblasts

Marc Jevon — 2008-08-17T14:53:11-00:00

Infect. Immun., Vol. 67, No. 5. (1 May 1999), pp. 2677-2681.

Staphylococcus aureus is an important bone pathogen, and evidence shows that this organism is internalized by chick osteoblasts. Here we report that S. aureus is internalized by human osteoblasts. Internalization was inhibited by monodansylcadaverine and cytochalasin D and to a lesser extent by ouabain, monensin, colchicine, and nocodazole. We propose that internalization occurs via a receptor-mediated pathway, requiring the participation of cytoskeletal elements, principally actin.

Health, cognitive, and psychosocial factors as predictors of mortality in an elderly community sample

AE Korten — 2008-08-17T14:01:41-00:00

Journal of Epidemiology and Community Health, Vol. 53, No. 2. (1 February 1999), pp. 83-88.

The spatial distribution of attention following an exogenous cue.

JM Henderson — 2008-08-17T00:36:38-00:00

Perception & psychophysics, Vol. 53, No. 2. (February 1993), pp. 221-230.

Three target-discrimination experiments were conducted to explore the spatial distribution of covert visual attention following an exogenous cue. On each trial, a brief peripheral onset was followed by a target stimulus in an otherwise empty visual field at one of eight (Experiment 1) or one of four (Experiments 2 and 3) possible locations centered at the fixation point. The spatial relation between the cue and the target was manipulated. The main results were that (1) performance was better at the cued location than at another nearby location in the same visual quadrant; (2) performance was not affected by the major horizontal and vertical visual meridians; and (3) performance was affected by the spatial distance between the cued and target locations. Together, the results suggest that the spatial distribution of exogenously oriented attention can be most easily integrated with a simple gradient model.

Direct visualization of ligand-protein interactions using atomic force microscopy

Calum Neish — 2008-08-15T17:10:42-00:00

Br J Pharmacol, Vol. 135, No. 8. (April 2002), pp. 1943-1950.

A fast 3D Look-Locker method for volumetric T1 mapping

Elizabeth Henderson — 2008-08-14T14:16:56-00:00

Magnetic Resonance Imaging, Vol. 17, No. 8. (October 1999), pp. 1163-1171.

We introduce a fast technique, based on the principles of the 2D Look-Locker T1 measurement scheme, to rapidly acquire the data for accurate maps of T1 in three dimensions. The acquisition time has been shortened considerably by segmenting the acquisition of the ky phase encode lines. Using this technique, the data for a 256 × 128 × 32 volumetric T1 measurement can be acquired in 7.6 min. T1 measurements made in phantoms with T1s between 200 and 1200 ms had an accuracy of 4% and a reproducibility of 3.5%. Measurements of T1 made in normal brain using the fast 3D sequence corresponded well with inversion-recovery fast spin-echo measurements.

Exercise-induced hypersensitivity syndromes in recreational and competitive athletes: a PRACTALL consensus report (what the general practitioner should know about sports and allergy)

Schwartz — 2008-07-12T06:37:32-00:00

Allergy, Vol. 63, No. 8. (August 2008), pp. 953-961.

The genome sequence of Drosophila melanogaster.

MD Adams — 2005-05-09T16:56:36-00:00

Science, Vol. 287, No. 5461. (24 March 2000), pp. 2185-2195.

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease.

RJ Johnson — 2008-08-12T07:59:21-00:00

Medical hypotheses, Vol. 71, No. 1. (2008), pp. 22-31.

Humans have relatively low plasma ascorbate levels and high serum uric acid levels compared to most mammals due to the presence of genetic mutations in l-gulonolactone oxidase and uricase, respectively. We review the major hypotheses for why these mutations may have occurred. In particular, we suggest that both mutations may have provided a survival advantage to early primates by helping maintain blood pressure during periods of dietary change and environmental stress. We further propose that these mutations have the inadvertent disadvantage of increasing our risk for hypertension and cardiovascular disease in today's society characterized by Western diet and increasing physical inactivity. Finally, we suggest that a "planetary biology" approach in which genetic changes are analyzed in relation to their biological action and historical context may provide the ideal approach towards understanding the biology of the past, present and future.

Growth and Growth Biomarker Changes After Adenotonsillectomy: Systematic Review and Meta-Analysis.

Karen Bonuck — 2008-08-12T03:32:27-00:00

Archives of disease in childhood (6 August 2008)

OBJECTIVE: To determine the effect of adenoidectomy and/or tonsillectomy ("adenotonsillectomy") upon growth and growth biomarkers, in the context of sleep disordered breathing (SDB). SDB in children, primarily due to adenotonsillar hypertrophy, increases risk of growth failure. DESIGN: Systematic review and meta-analysis. PubMed, ERIC, and Cochrane Reviews databases from January 1980 inverted exclamation markVNovember 2007 were searched for studies reporting: pre/post-adenotonsillectomy height and weight changes as percentage increased or decreased, raw data, z scores or centiles, or; IGF-1 and/or IGFBP-3 serum-level changes as Z-scores or raw data. Use of SDB criteria in sample selection is identified. For anthropometrics, the meta-analysis included studies presenting Z scores or centiles. SETTING: Observational studies. Patients: Otherwise healthy children, not selected for obesity. MAIN OUTCOME MEASURES: Pre/post-surgery changes in standardized height and weight, and IGF-1 and IGFBP-3. RESULTS: Of 211 citations identified, 20 met systematic review criteria. SDB was an enrollment criterion in 13 of the studies, and one of several enrollment criteria in 3. Meta-analysis findings for pre/post-surgery changes were: standardized height- 10 studies, 363 total children, pooled SMD= 0.34 (95% CI= 0.20-0.47); standardized weight- 11 studies, 390 total children, pooled SMD= 0.57 (95% CI= 0.44-0.70); IGF-1- 7 studies, 177 total children, pooled SMD= 0.53 (95% CI= 0.33-0.73); IGFBP-3- 7 studies, 177 total children, pooled SMD= 0.59 (95% CI= 0.34-0.83). CONCLUSIONS: Standardized height and weight, and IGF-1 and IGFBP-3 increased significantly after adenotonsillectomy. Findings suggest that primary care providers and specialists consider SDB secondary to AT hypertrophy when screening, treating and referring children with growth failure.

On-chip integration of high-frequency electron paramagnetic resonance spectroscopy and Hall-effect magnetometry

HM Quddusi — 2008-08-11T13:13:11-00:00

Review of Scientific Instruments, Vol. 79, No. 7. (2008)

The role of oxidative stress in noise-induced hearing loss.

D Henderson — 2008-08-10T18:51:12-00:00

Ear and hearing, Vol. 27, No. 1. (February 2006), pp. 1-19.

Modern research has provided new insights into the biological mechanisms of noise-induced hearing loss, and with these new insights comes hope for possible prevention or treatment. Underlying the classic set of cochlear pathologies that occur as a result of noise exposure are increased levels of reactive oxygen species (ROS) that play a significant role in noise-induced hair cell death. Both necrotic and apoptotic cell death have been identified in the cochlea. Included in the current review is a brief review of ROS, along with a description of sources of cochlear ROS generation and how ROS can damage cochlear tissue. The pathways of necrotic and apoptotic cell death are also reviewed. Interventions are discussed that target the prevention of noise-induced hair cell death: the use of antioxidants to scavenge and eliminate the damaging ROS, pharmacological interventions to limit the damage resulting from ROS, and new techniques aimed at interrupting the apoptotic biochemical cascade that results in the death of irreplaceable hair cells.

A radical demise. Toxins and trauma share common pathways in hair cell death.

R Kopke — 2008-08-10T18:49:20-00:00

Annals of the New York Academy of Sciences, Vol. 884 (28 November 1999), pp. 171-191.

The pathologic similarities noted after ototoxic and/or traumatic injury to the cochlea as well as the key features of the cochlea that make it susceptible to reactive oxygen species (ROS) damage are reviewed. Recent evidence linking ROS to cochlear damage associated with both ototoxins and/or trauma are presented. Mechanisms of generation of ROS in the cochlea and how these metabolites damage the cochlea and impair function are also reviewed. Finally, examples of novel therapeutic strategies to prevent and reverse hearing loss due to noise and/or ototoxins are presented to illustrate the clinical relevance of these new findings.

MRC Image Processing Programs

RA Crowther — 2008-08-08T17:09:24-00:00

Journal of Structural Biology, Vol. 116, No. 1. (January 1996), pp. 9-16.

Digital image processing is an essential step in the determination of macromolecular structures by electron microscopy. Centrally important procedures are the averaging of many images of the subunit to improve the signal, the correction for various transfer functions, and the generation of a three-dimensional map from a set of two-dimensional projections. The detailed way in which these computational procedures are best carried out depends on the symmetry of the object and the type of specimen preparation. Over many years a large set of programs has been written by various members of the Laboratory of Molecular Biology for processing images of two-dimensional crystals and of particles with helical or icosahedral symmetry. The philosophy has been to write stand-alone programs and the whole system is given coherence by the adoption of standard formats for the storage and interchange of different kinds of data. This paper describes the current state of the programs.

The sequence of the human genome.

JC Venter — 2005-05-11T19:14:50-00:00

Science, Vol. 291, No. 5507. (16 February 2001), pp. 1304-1351.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Evaluation of the ability of a battery of three in vitro genotoxicity tests to discriminate rodent carcinogens and non-carcinogens I. Sensitivity, specificity and relative predictivity.

D Kirkland — 2008-08-05T14:50:40-00:00

Mutation research, Vol. 584, No. 1-2. (4 July 2005), pp. 1-256.

The performance of a battery of three of the most commonly used in vitro genotoxicity tests--Ames+mouse lymphoma assay (MLA)+in vitro micronucleus (MN) or chromosomal aberrations (CA) test--has been evaluated for its ability to discriminate rodent carcinogens and non-carcinogens, from a large database of over 700 chemicals compiled from the CPDB ("Gold"), NTP, IARC and other publications. We re-evaluated many (113 MLA and 30 CA) previously published genotoxicity results in order to categorise the performance of these assays using the response categories we established. The sensitivity of the three-test battery was high. Of the 553 carcinogens for which there were valid genotoxicity data, 93% of the rodent carcinogens evaluated in at least one assay gave positive results in at least one of the three tests. Combinations of two and three test systems had greater sensitivity than individual tests resulting in sensitivities of around 90% or more, depending on test combination. Only 19 carcinogens (out of 206 tested in all three tests, considering CA and MN as alternatives) gave consistently negative results in a full three-test battery. Most were either carcinogenic via a non-genotoxic mechanism (liver enzyme inducers, peroxisome proliferators, hormonal carcinogens) considered not necessarily relevant for humans, or were extremely weak (presumed) genotoxic carcinogens (e.g. N-nitrosodiphenylamine). Two carcinogens (5-chloro-o-toluidine, 1,1,2,2-tetrachloroethane) may have a genotoxic element to their carcinogenicity and may have been expected to produce positive results somewhere in the battery. We identified 183 chemicals that were non-carcinogenic after testing in both male and female rats and mice. There were genotoxicity data on 177 of these. The specificity of the Ames test was reasonable (73.9%), but all mammalian cell tests had very low specificity (i.e. below 45%), and this declined to extremely low levels in combinations of two and three test systems. When all three tests were performed, 75-95% of non-carcinogens gave positive (i.e. false positive) results in at least one test in the battery. The extremely low specificity highlights the importance of understanding the mechanism by which genotoxicity may be induced (whether it is relevant for the whole animal or human) and using weight of evidence approaches to assess the carcinogenic risk from a positive genotoxicity signal. It also highlights deficiencies in the current prediction from and understanding of such in vitro results for the in vivo situation. It may even signal the need for either a reassessment of the conditions and criteria for positive results (cytotoxicity, solubility, etc.) or the development and use of a completely new set of in vitro tests (e.g. mutation in transgenic cell lines, systems with inherent metabolic activity avoiding the use of S9, measurement of genetic changes in more cancer-relevant genes or hotspots of genes, etc.). It was very difficult to assess the performance of the in vitro MN test, particularly in combination with other assays, because the published database for this assay is relatively small at this time. The specificity values for the in vitro MN assay may improve if data from a larger proportion of the known non-carcinogens becomes available, and a larger published database of results with the MN assay is urgently needed if this test is to be appreciated for regulatory use. However, specificity levels of <50% will still be unacceptable. Despite these issues, by adopting a relative predictivity (RP) measure (ratio of real:false results), it was possible to establish that positive results in all three tests indicate the chemical is greater than three times more likely to be a rodent carcinogen than a non-carcinogen. Likewise, negative results in all three tests indicate the chemical is greater than two times more likely to be a rodent non-carcinogen than a carcinogen. This RP measure is considered a useful tool for industry to assess the likelihood of a chemical possessing carcinogenic potential from batteries of positive or negative results.

The physiology of sleep in infants.

Jane L Heraghty — 2008-08-05T03:14:40-00:00

Archives of disease in childhood (24 July 2008)

Summary. Despite the fact that infants spend more time asleep than awake, an understanding of the importance and effects of sleep on the pathophysiology of illness in infancy is a relatively recent development, and is commonly overlooked in paediatric training. In this review we describe some of the characteristics of sleep in infancy, with particular reference to normal developmental physiology and its relevance to the signs, symptoms and pathophysiology of illness in this age group.

Structure of a β1-adrenergic G-protein-coupled receptor

Tony Warne — 2008-06-27T04:54:04-00:00

Nature (25 June 2008)

The synthetic peptide WKYMVm attenuates the function of the chemokine receptors CCR5 and CXCR4 through activation of formyl peptide receptor-like 1.

BQ Li — 2008-07-31T14:43:07-00:00

Blood, Vol. 97, No. 10. (15 May 2001), pp. 2941-2947.

The G protein-coupled 7 transmembrane (STM) chemoattractant receptors can be inactivated by heterologous desensitization. Earlier work showed that formly peptide receptor-like 1 (FPRL1), an STM receptor with low affinity for the bacterial chemotactic peptide formyl-methionyl-leucyl-phenylalamine (fMLF), is activated by peptide domains derived from the human immunodeficiency virus (HIV)-1 envelope glycoprotein gp120 and its activation results in desensitization and down-regulation of the chemokine receptors CCR5 and CXCR4 from monocyte surfaces. This study investigated the possibility of interfering with the function of CCR5 or CXCR4 as HIV-1 coreceptors by activating FPRL1. Cell lines were established expressing FPRL1 in combination with CD4/CXCR4 or CD4/CCR5 and the effect of a synthetic peptide, WKYMVm, a potent activator of formyl peptide receptors with preference for FPRL1 was determined. Both CXCR4 and CCR5 were desensitized by activation of the cells with WKYMVm via a staurosporine-sensitive pathway. This desensitization of CXCR4 and CCR5 also attenuated their capacity as the fusion cofactors for HIV-1 envelope glycoprotein and resulted in a significant inhibition of p24 production by cell lines infected with HIV-1 that use CCR5 or CXCR4 as coreceptors. Furthermore, WKYMVm inhibited the infection of human peripheral monocyte-derived macrophages and CD4(+) T lymphocytes by R5 or X4 strains of HIV-1, respectively. These results indicate that heterologous desensitization of CCR5 and CXCR4 by an FPRL1 agonist attenuates their major biologic functions and suggest an approach to the development of additional anti-HIV-1 agents. (Blood. 2001;97:2941-2947)

Quality of arthritis information on the Internet.

NT Ansani — 2008-07-29T14:38:18-00:00

American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists, Vol. 62, No. 11. (1 June 2005), pp. 1184-1189.

PURPOSE: The quality and reliability of Internet-based arthritis information were studied. METHODS: The search terms "arthritis," "osteoarthritis," and 'rheumatoid arthritis" were entered into the AOL, MSN, Yahoo, Google, and Lycos search engines. The Web sites for the first 40 matches generated by each search engine were grouped by URL suffix and evaluated on the basis of four categories of criteria: disease and medication information content, Web-site navigability, required literacy level, and currentness of information. Ratings were assigned by using an assessment tool derived from published literature (maximum score of 15 points). RESULTS: Of the 600 arthritis Web sites identified, only 69 were unique and included in the analysis. Fifty-seven percent were .com sites, 20% .org sites, 7% .gov sites, 6% .edu sites, and 10% other sites. Total scores for individual sites reviewed ranged from 3 to 14. Eighty percent of .gov sites, 75% of .edu sites, 29% of other sites, 36% of .com sites, and 21% of .org sites were within the top tertile of scores. No Web site met the criterion for being understandable to people with no more than a sixth-grade reading ability. .Gov sites scored significantly higher overall than .com sites, .org sites, and other sites. .Edu sites also scored relatively well. CONCLUSION: The quality of arthritis information on the Internet varied widely. Sites with URLs having suffixes of .gov and .edu were ranked higher than other types of sites.

A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability.

N Kovacević — 2005-06-01T13:52:56-00:00

Cereb Cortex, Vol. 15, No. 5. (May 2005), pp. 639-645.

Although there is growing interest in finding mouse models of human disease, no technique for quickly and quantitatively determining anatomical mutants currently exists. Magnetic resonance imaging (MRI) is ideally suited to probe fine structures in mice. This technology is three-dimensional, non-destructive and rapid compared to histopathology; hence MRI scientists have been able to create detailed three-dimensional images of 60 mum resolution or better. The data is digital which lends itself to sophisticated image processing algorithms. Here we show a variational MRI atlas constructed from nine excised brains of 8 week old 129S1/SvImJ male mice. This new type of atlas is comprised of an unbiased average brain--created from alignment of the individual brains--and the mathematical descriptors of anatomical variation across the individuals. We found that the majority of internal points in the individuals never varied more than 117 microm from equivalent points in the atlas. A three-dimensional annotation of the average image was performed and used to estimate the mean and standard deviation of volumes in a variety of structures across the individual brains; these volumes never differed by more than 5%. Our results indicate that variational atlases of inbred strains represent a well-defined basis against which mutant outliers can be readily compared.

Increased Retention of Early Computer Science and Software Engineering Students Using Pair Programming

Carver — 2008-07-24T18:47:53-00:00

cseet, Vol. 00 (2007), pp. 115-122.

An important problem faced by many Computer Science and Software Engineering programs is declining enrollment. In an effort to reverse that trend at Mississippi State University, we have instituted pair programming for the laboratory exercises in the introductory programming course. This paper describes a study performed to analyze whether using pair programming would increase retention. An important goal of this study was not only to measure increased retention, but to provide insight into why retention increased or decreased. The results of the study showed that retention significantly increased for those students already majoring in Computer Science, Software Engineering, or Computer Engineering. In addition, survey results indicated that the students viewed many aspects of pair programming to be very beneficial to their learning experience.

Blue Native electrophoresis to study mitochondrial and other protein complexes.

LG Nijtmans — 2008-07-24T09:18:31-00:00

Methods (San Diego, Calif.), Vol. 26, No. 4. (April 2002), pp. 327-334.

The biogenesis and maintenance of mitochondria relies on a sizable number of proteins. Many of these proteins are organized into complexes, which are located in the mitochondrial inner membrane. Blue Native polyacrylamide gel electrophoresis (BN-PAGE) is a method for the isolation of intact protein complexes. Although it was initially used to study mitochondrial respiratory chain enzymes, it can also be applied to other protein complexes. The use of BN-PAGE has increased exponentially over the past few years and new applications have been developed. Here we review how to set up the basic system and outline modifications that can be applied to address specific research questions. Increasing the upper mass limit of complexes that can be separated by BN-PAGE can be achieved by using agarose instead of acrylamide. BN-PAGE can also be used to study assembly of mitochondrial protein complexes. Other applications include in-gel measurements of enzyme activity by histochemical staining and preparative native electrophoresis to isolate a protein complex. Finally, new ways of identifying protein spots in Blue Native gels using mass spectrometry are briefly discussed.

The changing usage of a mature campus-wide wireless network

Tristan Henderson — 2007-12-03T18:57:41-00:00

(September 2004), pp. 187-201.

Wireless Local Area Networks (WLANs) are now commonplace on many academic and corporate campuses. As “Wi-Fi” technology becomes ubiquitous, it is increasingly important to understand trends in the usage of these networks. \\par This paper analyzes an extensive network trace from a mature 802.11 WLAN, including more than 550 access points and 7000 users over seventeen weeks. We employ several measurement techniques, including syslogs, telephone records, SNMP polling and tcpdump packet sniffing. This is the largest WLAN study to date, and the first to look at a large, mature WLAN and consider geographic mobility. We compare this trace to a trace taken after the network's initial deployment two years ago. \\par We found that the applications used on the WLAN changed dramatically. Initial WLAN usage was dominated by Web traffic; our new trace shows significant increases in peer-to-peer, streaming multimedia, and voice over IP (VoIP) traffic. On-campus traffic now exceeds off-campus traffic, a reversal of the situation at the WLAN's initial deployment. Our study indicates that VoIP has been used little on the wireless network thus far, and most VoIP calls are made on the wired network. Most calls last less than a minute. \\par We saw greater heterogeneity in the types of clients used, with more embedded wireless devices such as PDAs and mobile VoIP clients. We define a new metric for mobility, the “session diameter.” We use this metric to show that embedded devices have different mobility characteristics than laptops, and travel further and roam to more access points. Overall, users were surprisingly non-mobile, with half remaining close to home about 98% of the time.

The Genome Sequence of Drosophila melanogaster

Mark Adams — 2005-06-14T01:43:05-00:00

Science, Vol. 287, No. 5461. (24 March 2000), pp. 2185-2195.

Optimization of an Escherichia coli system for cell-free synthesis of selectively N-labelled proteins for rapid analysis by NMR spectroscopy.

K Ozawa — 2006-06-01T12:52:51-00:00

Eur J Biochem, Vol. 271, No. 20. (October 2004), pp. 4084-4093.

Cell-free protein synthesis offers rapid access to proteins that are selectively labelled with [15N]amino acids and suitable for analysis by NMR spectroscopy without chromatographic purification. A system based on an Escherichia coli cell extract was optimized with regard to protein yield and minimal usage of 15N-labelled amino acid, and examined for the presence of metabolic by-products which could interfere with the NMR analysis. Yields of up to 1.8 mg of human cyclophilin A per mL of reaction medium were obtained by expression of a synthetic gene. Equivalent yields were obtained using transcription directed by either T7 or tandem phage lambdapR and pL promoters, when the reactions were supplemented with purified phage T7 or E. coli RNA polymerase. Nineteen samples, each selectively labelled with a different 15N-enriched amino acid, were produced and analysed directly by NMR spectroscopy after ultracentrifugation. Cross-peaks from metabolic by-products were evident in the 15N-HSQC spectra of 13 of the samples. All metabolites were found to be small molecules that could be separated readily from the labelled proteins by dialysis. No significant transamination activity was observed except for [15N]Asp, where an enzyme in the cell extract efficiently converted Asp-->Asn. This activity was suppressed by replacing the normally high levels of potassium glutamate in the reaction mixture with ammonium or potassium acetate. In addition, the activity of peptide deformylase appeared to be generally reduced in the cell-free expression system.

The impact of homework on student achievement

Eren — 2008-07-15T06:55:30-00:00

The Econometrics Journal, Vol. 11, No. 2. (July 2008), pp. 326-348.

Patient-specific analysis of the volume of tissue activated during deep brain stimulation.

CR Butson — 2008-04-15T16:19:07-00:00

NeuroImage, Vol. 34, No. 2. (15 January 2007), pp. 661-670.

Despite the clinical success of deep brain stimulation (DBS) for the treatment of movement disorders, many questions remain about its effects on the nervous system. This study presents a methodology to predict the volume of tissue activated (VTA) by DBS on a patient-specific basis. Our goals were to identify the intersection between the VTA and surrounding anatomical structures and to compare activation of these structures with clinical outcomes. The model system consisted of three fundamental components: (1) a 3D anatomical model of the subcortical nuclei and DBS electrode position in the brain, each derived from magnetic resonance imaging (MRI); (2) a finite element model of the DBS electrode and electric field transmitted to the brain, with tissue conductivity properties derived from diffusion tensor MRI; (3) VTA prediction derived from the response of myelinated axons to the applied electric field, which is a function of the stimulation parameters (contact, impedance, voltage, pulse width, frequency). We used this model system to analyze the effects of subthalamic nucleus (STN) DBS in a patient with Parkinson's disease. Quantitative measurements of bradykinesia, rigidity, and corticospinal tract (CST) motor thresholds were evaluated over a range of stimulation parameter settings. Our model predictions showed good agreement with CST thresholds. Additionally, stimulation through electrode contacts that improved bradykinesia and rigidity generated VTAs that overlapped the zona incerta/fields of Forel (ZI/H2). Application of DBS technology to various neurological disorders has preceded scientific characterization of the volume of tissue directly affected by the stimulation. Synergistic integration of clinical analysis, neuroimaging, neuroanatomy, and neurostimulation modeling provides an opportunity to address wide ranging questions on the factors linked with the therapeutic benefits and side effects of DBS.

CRAWDAD workshop 2007

Jihwang Yeo — 2008-07-14T07:23:15-00:00

SIGCOMM Comput. Commun. Rev., Vol. 38, No. 3. (July 2008), pp. 79-82.

Development of a high resolution three-dimensional surgical atlas of the murine head for strains 129S1/SvImJ and C57Bl/6J using magnetic resonance imaging and micro-computed tomography.

E Chan — 2007-08-23T19:12:49-00:00

Neuroscience, Vol. 144, No. 2. (19 January 2007), pp. 604-615.

The mouse has emerged as a major experimental model system for examining the functional properties of the mammalian CNS; both during development and following CNS injury. Histologic procedures currently used to determine the relative position of structures within the CNS are presently limited in their ability to take full advantage of this system for surgical and morphometric procedures. We present here the first three-dimensional interactive digital atlas of the murine brain and skull for two genetically important strains of mice; 129S1/SvImJ and C57Bl/6J. The final resolution of these digital atlases is 54 micro m(3). These representations of the murine brain and skull, in conjunction with our development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate "off-axis" surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambda-bregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system. The aim of these studies is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice.

Type V Protein Secretion Pathway: the Autotransporter Story

Ian Henderson — 2006-12-31T16:29:56-00:00

Microbiol. Mol. Biol. Rev., Vol. 68, No. 4. (1 December 2004), pp. 692-744.

Gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. To overcome this barrier, bacteria have developed several systems for protein secretion. The type V secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type Vc or AT-2 family of proteins. Since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the advent of the genomic age, to become the largest group of secreted proteins in gram-negative bacteria. Several of these proteins play essential roles in the pathogenesis of bacterial infections and have been characterized in detail, demonstrating a diverse array of function including the ability to condense host cell actin and to modulate apoptosis. However, most of the autotransporter proteins remain to be characterized. In light of new discoveries and controversies in this research field, this review considers the autotransporter secretion process in the context of the more general field of bacterial protein translocation and exoprotein function. 10.1128/MMBR.68.4.692-744.2004

The ORFeome of Staphylococcus aureus v 1.1

Christina Brandner — 2008-07-07T13:08:53-00:00

BMC Genomics, Vol. 9, No. 1. (2008)

BACKGROUND:The bacterium Staphylococcus aureus causes significant morbidity and mortality in humans, primarily due to the emergence of strains that are resistant to antibiotics--notably methicillin-resistant S. aureus (MRSA) isolates. Development of effective strategies for the control and treatment of MRSA infections may best be achieved through 'omics' approaches, which first requires cloning the entire set of S. aureus' protein-encoding open reading frames (ORFs), or ORFeome. RESULTS:The complete genome sequence of S. aureus strain Mu50 has 2697 predicted protein-coding ORFs. Based on the sequence of this strain we designed PCR primers to construct from an S.aureus (non-MRSA) clinical isolate an ORFeome library based on this strain that contains 2562 unique Gateway(R) entry clones (95% coverage), each corresponding to a defined ORF. The high quality of the ORFeome library was verified by DNA sequencing and PCR amplification, and its functionality was demonstrated by expressing recombinant proteins and observing protein interactions in a yeast 2-hybrid homodimerization screen. CONCLUSION:This first ORFeome library for S. aureus provides an essential new tool for investigating the systems biology of this important pathogen.

Portal hypertension and variceal bleeding: an AASLD single topic symposium.

ND Grace — 2008-07-11T05:57:01-00:00

Hepatology (Baltimore, Md.), Vol. 28, No. 3. (September 1998), pp. 868-880.

Testing experimental data for univariate normality.

AR Henderson — 2008-07-11T03:48:49-00:00

Clinica chimica acta; international journal of clinical chemistry, Vol. 366, No. 1-2. (April 2006), pp. 112-129.

BACKGROUND: Many experimentally-derived data sets are generated in the practice of clinical chemistry. Graphical presentation is essential to assess the data distribution. The distribution must also be assessed quantitatively. These approaches will determine if the data is Normal or not. Finally the results of these tests of Normality must be shown to be free of sample size effects. METHODS: Four experimentally-derived data sets were used. They represented normal, positive kurtotic, positive- and negatively-skewed distributions. These data sets were examined by graphical techniques, by moment tests, by tests of Normality, and monitored for sample size effects. RESULTS: The preferred graphical techniques are the histogram and the box-and-whisker plots that may be supplemented, with advantage, by quantile-quantile or probability-probability plots. Classical tests of skewness and kurtosis can produce conflicting and often confusing results and, as a consequence, the alternative use of the newer L-moments is advocated. Normality tests included the Kolmogorov-Smirnov (Lilliefors modification), Cramér-von Mises and Anderson-Darling tests (empirical distribution function statistics) and the Gan-Koehler, Shapiro-Wilk, Shapiro-Francia, and Filliben tests (regression/correlation techniques). Of these only the Anderson-Darling, Shapiro-Wilk, and Shapiro-Francia tests correctly classified all four test samples. The effect of sample size on the resulting p-value was investigated using Royston's V'/v' graphical test. CONCLUSIONS: A systematic approach to Normality testing should follow the route of graphical presentation, the use of L-moments, the use of Anderson-Darling, Shapiro-Wilk, or Shapiro-Francia testing, and Royston's sample size monitoring.

HER2 and response to paclitaxel in node-positive breast cancer.

DF Hayes — 2008-07-11T03:46:46-00:00

The New England journal of medicine, Vol. 357, No. 15. (11 October 2007), pp. 1496-1506.

BACKGROUND: The status of human epidermal growth factor receptor type 2 (HER2) in breast-cancer cells predicts clinical outcomes in women who receive adjuvant anthracycline-based chemotherapy. We hypothesized that HER2 positivity predicts a benefit from adjuvant doxorubicin doses above standard levels, from the addition of paclitaxel after adjuvant chemotherapy with doxorubicin plus cyclophosphamide, or from both. METHODS: We randomly selected 1500 women from 3121 women with node-positive breast cancer who had been randomly assigned to receive doxorubicin (60, 75, or 90 mg per square meter of body-surface area) plus cyclophosphamide (600 mg per square meter) for four cycles, followed by four cycles of paclitaxel (175 mg per square meter) or observation. Tissue blocks from 1322 of these 1500 women were available. Immunohistochemical analyses of these tissue specimens for HER2 with the CB11 monoclonal antibody against HER2 or with a polyclonal-antibody assay kit and fluorescence in situ hybridization for HER2 amplification were performed. RESULTS: No interaction was observed between HER2 positivity and doxorubicin doses above 60 mg per square meter. HER2 positivity was, however, associated with a significant benefit from paclitaxel. The interaction between HER2 positivity and the addition of paclitaxel to the treatment was associated with a hazard ratio for recurrence of 0.59 (P=0.01). Patients with a HER2-positive breast cancer benefited from paclitaxel, regardless of estrogen-receptor status, but paclitaxel did not benefit patients with HER2-negative, estrogen-receptor-positive cancers. CONCLUSIONS: The expression or amplification, or both, of HER2 by a breast cancer is associated with a benefit from the addition of paclitaxel after adjuvant treatment with doxorubicin (<60 mg per square meter) plus cyclophosphamide in node-positive breast cancer, regardless of estrogen-receptor status. Patients with HER2-negative, estrogen-receptor-positive, node-positive breast cancer may gain little benefit from the administration of paclitaxel after adjuvant chemotherapy with doxorubicin plus cyclophosphamide.

Analysis of longitudinal data with drop-out: objectives, assumptions and a proposal

Peter Diggle — 2007-10-01T18:33:20-00:00

Journal of the Royal Statistical Society: Series C (Applied Statistics), Vol. 56, No. 5. (2007), pp. 499-550.

Summary. The problem of analysing longitudinal data that are complicated by possibly informative drop-out has received considerable attention in the statistical literature. Most researchers have concentrated on either methodology or application, but we begin this paper by arguing that more attention could be given to study objectives and to the relevant targets for inference. Next we summarize a variety of approaches that have been suggested for dealing with drop-out. A long-standing concern in this subject area is that all methods require untestable assumptions. We discuss circumstances in which we are willing to make such assumptions and we propose a new and computationally efficient modelling and analysis procedure for these situations. We assume a dynamic linear model for the expected increments of a constructed variable, under which subject-specific random effects follow a martingale process in the absence of drop-out. Informal diagnostic procedures to assess the tenability of the assumption are proposed. The paper is completed by simulations and a comparison of our method and several alternatives in the analysis of data from a trial into the treatment of schizophrenia, in which approximately 50% of recruited subjects dropped out before the final scheduled measurement time.

Common variants on chromosome 5p12 confer susceptibility to estrogen receptor–positive breast cancer

Simon Stacey — 2008-05-29T14:31:29-00:00

Nature Genetics, Vol. 40, No. 6. (27 April 2008), pp. 703-706.

Feature-based reverse engineering of mechanical parts

WB Thompson — 2008-07-02T17:28:54-00:00

Robotics and Automation, IEEE Transactions on, Vol. 15, No. 1. (1999), pp. 57-66.

Reverse engineering of mechanical parts requires extraction of information about an instance of a particular part sufficient to replicate the part using appropriate manufacturing techniques. This is important in a wide variety of situations, since functional CAD models are often unavailable or unusable for parts which must be duplicated or modified. Computer vision techniques applied to three-dimensional (3-D) data acquired using noncontact, 3-D position digitizers have the potential for significantly aiding the process. Serious challenges must be overcome, however, if sufficient accuracy is to be obtained and if models produced from sensed data are to be truly useful for manufacturing operations. The paper describes a prototype of a reverse engineering system which uses manufacturing features as geometric primitives. This approach has two advantages over current practice. The resulting models can be directly imported into feature-based CAD systems without loss of the semantics and topological information inherent in feature-based representations. In addition, the feature-based approach facilitates methods capable of producing highly accurate models, even when the original 3-D sensor data has substantial errors

The PHOBOS perspective on discoveries at RHIC

BB Back — 2008-07-02T09:37:28-00:00

Nuclear Physics A, Vol. 757, No. 1-2. (8 August 2005), pp. 28-101.

This paper describes the conclusions that can be drawn from the data taken thus far with the PHOBOS detector at RHIC. In the most central Au + Au collisions at the highest beam energy, evidence is found for the formation of a very high energy density system whose description in terms of simple hadronic degrees of freedom is inappropriate. Furthermore, the constituents of this novel system are found to undergo a significant level of interaction. The properties of particle production at RHIC energies are shown to follow a number of simple scaling behaviors, some of which continue trends found at lower energies or in simpler systems. As a function of centrality, the total number of charged particles scales with the number of participating nucleons. When comparing Au + Au at different centralities, the dependence of the yield on the number of participants at higher pT (~4 GeV/c) is very similar to that at low transverse momentum. The measured values of charged particle pseudorapidity density and elliptic flow were found to be independent of energy over a broad range of pseudorapidities when effectively viewed in the rest frame of one of the colliding nuclei, a property we describe as "extended longitudinal scaling". Finally, the centrality and energy dependences of several observables were found to factorize to a surprising degree.

Testimonial Beliefs and Epistemic Competence

Henderson — 2008-05-05T10:15:59-00:00

Noûs, Vol. 42, No. 2. (June 2008), pp. 190-221.

CRAWDAD: a community resource for archiving wireless data at Dartmouth

Jihwang Yeo — 2008-05-15T05:57:42-00:00

SIGCOMM Comput. Commun. Rev., Vol. 36, No. 2. (April 2006), pp. 21-22.

CRAWDAD: A Community Resource for Archiving Wireless Data at Dartmouth

David Kotz — 2008-06-27T19:01:55-00:00

IEEE Pervasive Computing, Vol. 4, No. 4. (October 2005), pp. 12-14.