bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Antibody Responses to Protective Antigen-Based Anthrax Vaccines through Use of Competitive Assays
Authors: Brady Rebecca A. , Verma Anita , Meade Bruce D. , Burns Drusilla L.
Published: July 2010

The licensed anthrax vaccine and many of the new anthrax vaccines being developed are based on protective antigen (PA), a nontoxic component of anthrax toxin. For this reason, an understanding of the immune response to PA vaccination is important. In this study, we examined the antibody response elicited by PA-based vaccines and identified the domains of PA that contribute to that response in humans as well as nonhuman primates (NHPs) and rabbits, animal species that will be used to generate efficacy data to support approval of new anthrax vaccines. To this end, we developed a competitive enzyme-linked immunosorbent assay (ELISA), using purified recombinant forms of intact PA and its individual domains. We found that PA-based vaccines elicited IgG antibodies to each of the four PA domains in all three species. We also developed a competitive toxin neutralization assay, which showed that rabbits, NHPs, and humans all have functional antibody populations that bind to domains 1, 3, and 4. While the domain specificities of the antibody responses elicited by PA-based vaccines were similar in humans, NHPs, and rabbits, competitive assays suggested that humans may have a more significant secondary population of IgG antibodies that bind to partially unfolded or incorrectly folded PA. These findings provide information that will be useful when linking animal protection data to humans via an antibody bridge to establish efficacy of new anthrax vaccines.
Increased Allergic Immune Response toSarcoptes scabieiAntigens in Crusted versus Ordinary Scabies
Authors: Walton Shelley F. , Pizzutto Susan , Slender Amy , Viberg Linda , Holt Deborah , Hales Belinda J. , Kemp David J. , Currie Bart J. , Rolland Jennifer M. , O'Hehir Robyn
Published: July 2010

Scabies, a parasitic skin infestation by the burrowing “itch” miteSarcoptes scabiei, causes significant health problems for children and adults worldwide. Crusted scabies is a particularly severe form of scabies in which mites multiply into the millions, causing extensive skin crusting. The symptoms and signs of scabies suggest host immunity to the scabies mite, but the specific resistant response in humans remains largely uncharacterized. We used 4 scabies mite recombinant proteins with sequence homology to extensively studied house dust mite allergens to investigate a differential immune response between ordinary scabies and the debilitating crusted form of the disease. Subjects with either disease form showed serum IgE against recombinantS. scabieicysteine and serine proteases and apolipoprotein, whereas naive subjects showed minimal IgE reactivity. Significantly (P< 0.05) greater serum IgE and IgG4 binding to mite apolipoprotein occurred in subjects with crusted scabies than in those with ordinary scabies. Both subject groups showed strong proliferative responses (peripheral blood mononuclear cells) to the scabies antigens, but the crusted scabies group showed increased secretion of the Th2 cytokines interleukin 5 (IL-5) and IL-13 and decreased Th1 cytokine gamma interferon (IFN-γ) in response to the active cysteine protease. These data confirm that a nonprotective allergic response occurs in the crusted disease form and demonstrate that clinical severity is associated with differences in the type and magnitude of the antibody and cellular responses to scabies proteins. A quantitative IgE inhibition assay identified IgE immunoreactivity of scabies mite antigens distinct from that of house dust mite antigens, which is potentially important for specific scabies diagnosis and therapy.
Genomic Signatures of the Haarlem Lineage of
Mycobacterium tuberculosis
: Implications of Strain Genetic Variation in Drug and Vaccine Development
Authors: Cubillos-Ruiz Andrés , Sandoval Andrea , Ritacco Viviana , López Beatriz , Robledo Jaime , Correa Nidia , Hernandez-Neuta Iván , Zambrano Maria Mercedes , Del Portillo Patricia
Published: July 2010

Tuberculosis is the world's leading cause of death due to a single infectious agent, and efforts aimed at its control require a better understanding of host, environmental, and bacterial factors that govern disease outcome. Growing evidence indicates that certain
Mycobacterium tuberculosis
strains of distinct phylogeographic lineages elicit unique immunopathological events. However, identifying the genetic basis of these phenotypic peculiarities has proven difficult. Here we report the presence of six large sequence polymorphisms which, together with two single-nucleotide changes previously described by our group, consistently differentiate Haarlem strains from the remaining
M. tuberculosis
lineages. The six newly found Haarlem-specific genetic events are four deletions, which altogether involve more than 13 kb, and two intragenic insertions of the element IS
6110
. The absence of the genes involved in these polymorphisms could have an important physiological impact on Haarlem strains, i.e., by affecting key genes, such as
Rv1354c
and
cyp121
, which have been recently proposed as plausible drug targets. These lineage-specific polymorphisms can serve as genetic markers for the rapid PCR identification of Haarlem strains, providing a useful tool for strain surveillance and molecular epidemiology studies. Strain variability such as that described here underscores the need for the definition of a core set of essential genes in
M. tuberculosis
that are ubiquitously present in all circulating lineages, as a requirement in the development of effective antituberculosis drugs and vaccines.
Diarrheagenic
Escherichia coli
Markers and Phenotypes among Fecal
E. coli
Isolates Collected from Nicaraguan Infants
Authors: Reyes Daniel , Vilchez Samuel , Paniagua Margarita , Colque-Navarro Patricia , Weintraub Andrej , Möllby Roland , Kühn Inger
Published: July 2010

We analyzed the prevalence of diarrheagenic
Escherichia coli
(DEC) markers and common phenotypes in 2,164
E. coli
isolates from 282 DEC-positive samples. Enteropathogenic
E. coli
(EPEC) and enteroaggregative
E. coli
(EAEC) were very diverse and were not correlated with diarrhea. Enterotoxigenic
E. coli
(ETEC)
estA
and enterohemorrhagic
E. coli
(EHEC) belonged to a few phenotypes and were significantly correlated with diarrhea.
Evaluation of Sensitivity of Multiplex PCR for Detection of
Mycobacterium tuberculosis
and
Pneumocystis jirovecii
in Clinical Samples
Authors: Boondireke Sirirat , Mungthin Mathirut , Tan-ariya Peerapan , Boonyongsunchai Petchara , Naaglor Tawee , Wattanathum Anan , Treewatchareekorn Sompong , Leelayoova Saovanee
Published: July 2010

A multiplex PCR assay for the simultaneous detection of
Mycobacterium tuberculosis
and
Pneumocystis jirovecii
was developed using IS
6110
-based detection for
M. tuberculosis
and mitochondrial large-subunit (mtLSU) rRNA gene detection for
P. jirovecii.
Ninety-five pulmonary blinded samples were examined using the developed multiplex PCR assay, and the results were compared with those obtained by the single nested PCRs targeting IS
6110
for
M. tuberculosis
and mtLSU rRNA for
P. jirovecii
. Of the 95 pulmonary samples tested, the multiplex nested PCR developed here could detect 36 cases of
M. tuberculosis
infection, 35 cases of
P. jirovecii
infection, and 17 cases of
M. tuberculosis
and
P. jirovecii
coinfections. The sensitivities of the multiplex nested PCR in detecting
M. tuberculosis
and
P. jirovecii
were 92.1% and 81.4%, respectively, whereas the specificities in detecting
M. tuberculosis
and
P. jirovecii
were 98.2% and 100%, respectively.
Robinsoniella peoriensis
Bacteremia in a Patient with Pancreatic Cancer
Authors: Shen Dingxia , Chen Rong , Ye Liyan , Luo Yanping , Tang Yi-Wei
Published: July 2010

Robinsoniella peoriensis
was recently identified as a Gram-positive, spore-forming, anaerobic rod originally isolated from swine manure storage pits. We describe here a case of
R. peoriensis
bacteremia in a 42-year-old male with pancreatic cancer. The identification was confirmed by unique phenotypic profiles and partial 16S rRNA gene sequences.
Axillary Abscess Due to
Yersinia enterocolitica
Authors: Menzies Barbara E.
Published: July 2010

Yersinia enterocolitica
rarely causes extraintestinal disease. A 54-year-old construction worker with chronic hepatitis C developed an axillary abscess following an injury to his finger. An aspirate from the axillary mass grew
Y. enterocolitica
. Direct inoculation is proposed as the mode of transmission of this classically enteric pathogen.
Evaluation of Specificity of BP3385 for
Bordetella pertussis
Detection
Authors: Register Karen B. , Nicholson Tracy L. , Guthrie J. L.
Published: July 2010

BP3385 has been proposed as a diagnostic PCR target for discriminating between
Bordetella pertussis
and other
Bordetella
species that also infect humans. Our results demonstrate that this gene is also present in some strains of
Bordetella hinzii
and
Bordetella bronchiseptica
.
Genogroup IIb Norovirus Infections and Association with Enteric Symptoms in a Neonatal Nursery in Southern India
Authors: Menon Vipin Kumar , George Santosh , Ramani Sasirekha , Illiayaraja Jeyaram , Sarkar Rajiv , Jana Atanu Kumar , Kuruvilla Kurien Anil , Kang Gagandeep
Published: July 2010

Noroviruses (NoVs) are increasingly recognized as an important cause of acute gastroenteritis in children worldwide. However, there are limited data on the role of NoVs in neonatal infections and disease. The objectives of the present study were to determine the prevalence of NoVs in neonates with gastrointestinal disease using a case-control study design and to characterize the NoV strains infecting neonates. A total of 309 fecal samples from 161 neonates with gastrointestinal symptoms and 148 asymptomatic controls were screened for genogroup II (GII) NoV using reverse transcription-PCR. A subset of PCR-positive amplicons for the polymerase and capsid regions was sequenced. NoV was detected in 26.2% of samples, with the rate of detection being significantly higher among symptomatic neonates (60/161, 37.2%) than asymptomatic neonates (24/148, 14.1%) (
P
< 0.001). On the basis of sequencing of 29 strains, a single NoV strain, GIIb, was identified to be the predominant (27/29, 93.1%) cause of neonatal infections. Coinfection with rotavirus was seen in nearly one-third of symptomatic neonates. The study demonstrates a high prevalence of NoV infections in neonates and indicates that coinfection with rotavirus may result in significantly more gastrointestinal disease in this population.
Characterization of a Putative Ancestor of Coxsackievirus B5
Authors: Gullberg Maria , Tolf Conny , Jonsson Nina , Mulders Mick N. , Savolainen-Kopra Carita , Hovi Tapani , Van Ranst Marc , Lemey Philippe , Hafenstein Susan , Lindberg A. Michael
Published: July 2010

Like other RNA viruses, coxsackievirus B5 (CVB5) exists as circulating heterogeneous populations of genetic variants. In this study, we present the reconstruction and characterization of a probable ancestral virion of CVB5. Phylogenetic analyses based on capsid protein-encoding regions (the VP1 gene of 41 clinical isolates and the entire P1 region of eight clinical isolates) of CVB5 revealed two major cocirculating lineages. Ancestral capsid sequences were inferred from sequences of these contemporary CVB5 isolates by using maximum likelihood methods. By using Bayesian phylodynamic analysis, the inferred VP1 ancestral sequence dated back to 1854 (1807 to 1898). In order to study the properties of the putative ancestral capsid, the entire ancestral P1 sequence was synthesized
de novo
and inserted into the replicative backbone of an infectious CVB5 cDNA clone. Characterization of the recombinant virus in cell culture showed that fully functional infectious virus particles were assembled and that these viruses displayed properties similar to those of modern isolates in terms of receptor preferences, plaque phenotypes, growth characteristics, and cell tropism. This is the first report describing the resurrection and characterization of a picornavirus with a putative ancestral capsid. Our approach, including a phylogenetics-based reconstruction of viral predecessors, could serve as a starting point for experimental studies of viral evolution and might also provide an alternative strategy for the development of vaccines.
Limited Interference at the Early Stage of Infection between Two Recombinant Novirhabdoviruses: Viral Hemorrhagic Septicemia Virus and Infectious Hematopoietic Necrosis Virus
Authors: Biacchesi Stéphane , Lamoureux Annie , Mérour Emilie , Bernard Julie , Brémont Michel
Published: July 2010

The genome sequence of a hypervirulent novirhabdovirus, viral hemorrhagic septicemia virus (VHSV) French strain 23-75, was determined. Compared to the genome of the prototype Fil3 strain, a number of substitutions, deletions, and insertions were observed. Following the establishment of a plasmid-based minigenome replication assay, recombinant VHSV (rVHSV) was successfully recovered. rVHSV exhibits wild-type-like growth properties
in vitro
as well as
in vivo
in rainbow trout. The dispensable role of NV for the novirhabdovirus replication was confirmed by generating rVHSV-ΔNV, in which the NV gene was deleted. This deletion mutant was shown to be as debilitated as that previously described for infectious hematopoietic necrosis virus (IHNV), a distantly related novirhabdovirus (S. Biacchesi, M. I. Thoulouze, M. Bearzotti, Y. X. Yu, and M. Bremont, J. Virol.
74:
11247-11253, 2000). Recombinant VHSV and IHNV expressing tdTomato and GFP
max
reporter genes, respectively, were generated, demonstrating the potential of these rhabdoviruses to serve as viral vectors. Interestingly, rIHNV-GFP
max
could be recovered using the replicative complex proteins of either virus, whereas rVHSV-Tomato could be recovered only by using its own replicative complex, reflecting that the genome signal sequences of VHSV are relatively distant from those of IHNV and do not allow their cross-recognition. Moreover, the use of heterologous protein combinations underlined the importance of strong protein-protein interactions for the formation of a functional ribonucleoprotein complex. The rIHNV-GFP
max
and rVHSV-Tomato viruses were used to simultaneously coinfect cell monolayers. It was observed that up to 74% of the cell monolayer was coinfected by both viruses, demonstrating that a limited interference phenomenon exists during the early stage of primary infection, and it was not mediated by a cellular antiviral protein or by some of the viral proteins.
Advances in Human B19 Erythrovirus Biology
Authors: Servant-Delmas Annabelle , Lefrère Jean-Jacques , Morinet Frédéric , Pillet Sylvie
Published: July 2010

Since its discovery, human parvovirus B19 (B19V), now termed erythrovirus, has been associated with many clinical situations (neurological and myocardium infections, persistent B19V DNAemia) in addition to the prototype clinical manifestations, i.e., erythema infectiosum and erythroblastopenia crisis. In 2002, the use of new molecular tools led to the characterization of three different genotypes of human B19 erythrovirus. Although the genomic organization is conserved, the geographic distribution of the different genotypes varies worldwide, and the nucleotidic divergences can impact the molecular diagnosis of B19 virus infection. The cell cycle of the virus remains partially unresolved; however, recent studies have shed light on the mechanism of cell entry and the interactions of B19V proteins with apoptosis pathways.
Identification of Key Residues in Virulent Canine Distemper Virus Hemagglutinin That Control CD150/SLAM-Binding Activity
Authors: Zipperle Ljerka , Langedijk Johannes P. M. , Örvell Claes , Vandevelde Marc , Zurbriggen Andreas , Plattet Philippe
Published: July 2010

Morbillivirus cell entry is controlled by hemagglutinin (H), an envelope-anchored viral glycoprotein determining interaction with multiple host cell surface receptors. Subsequent to virus-receptor attachment, H is thought to transduce a signal triggering the viral fusion glycoprotein, which in turn drives virus-cell fusion activity. Cell entry through the universal morbillivirus receptor CD150/SLAM was reported to depend on two nearby microdomains located within the hemagglutinin. Here, we provide evidence that three key residues in the virulent canine distemper virus A75/17 H protein (Y525, D526, and R529), clustering at the rim of a large recessed groove created by β-propeller blades 4 and 5, control SLAM-binding activity without drastically modulating protein surface expression or SLAM-independent F triggering.
A Role for Caveolin 1 in Assembly and Budding of the Paramyxovirus Parainfluenza Virus 5
Authors: Ravid Dana , Leser George P. , Lamb Robert A.
Published: July 2010

Caveolin 1 (Cav-1) is an integral membrane protein that forms the coat structure of plasma membrane caveolae and regulates caveola-dependent functions. Caveolae are enriched in cholesterol and sphingolipids and are related to lipid rafts. Many studies implicate rafts as sites of assembly and budding of enveloped virus. We show that Cav-1 colocalizes with the paramyxovirus parainfluenza virus 5 (PIV-5) nucleocapsid (NP), matrix (M), and hemagglutinin-neuraminidase (HN) proteins. Moreover, electron microscopy shows that Cav-1 is clustered at sites of viral budding. HN, M, and F
1
/F
2
are associated with detergent-resistant membranes, and these proteins float on sucrose gradients with Cav-1-rich fractions. A complex containing Cav-1 with M, NP, and HN from virus-infected cells and a complex containing Cav-1 and M from M-transfected cells were found on coimmunoprecipitation. A role of Cav-1 in the PIV-5 life cycle was investigated by utilizing MCF-7 human breast cancer cells that stably express Cav-1 (MCF-7/Cav-1). PIV-5 entry into MCF-7 and MCF-7/Cav-1 was found to be Cav-1 independent. However, the interaction between HN and M proteins was dramatically reduced in the Cav-1 null MCF-7 cells, and PIV-5 grown in MCF-7 cells had a reduced infectivity. Similarly, when PIV-5 was grown in MDCK cells that stably expressed dominant negative Cav-1 (MDCK/P132LCav-1), the virus showed a reduced infectivity. Virions lacking Cav-1 were defective and contained high levels of host cellular proteins and reduced levels of HN and M. These data suggest that Cav-1 affects assembly and/or budding, and this is supported by the finding that Cav-1 is incorporated into mature viral particles.
Nucleotide Variability and Translation Efficiency of the 5′ Untranslated Region of Hepatitis A Virus: Update from Clinical Isolates Associated with Mild and Severe Hepatitis
Authors: Mackiewicz Vincent , Cammas Anne , Desbois Delphine , Marchadier Eric , Pierredon Sandra , Beaulieux Frédérik , Dussaix Elisabeth , Vagner Stephan , Roque-Afonso Anne-Marie
Published: July 2010

Mutations in the internal ribosome entry site (IRES) of hepatitis A virus (HAV) have been associated with enhanced
in vitro
replication and viral attenuation in animal models. To address the possible role of IRES variability in clinical presentation, IRES sequences were obtained from HAV isolates associated with benign (
n
= 8) or severe (
n
= 4) hepatitis. IRES activity was assessed using a bicistronic dual-luciferase expression system in adenocarcinoma (HeLa) and hepatoma (HuH7) cell lines. Activity was higher in HuH7 than in HeLa cells, except for an infrequently isolated genotype IIA strain. Though globally low, significant variation in IRES-dependent translation efficiency was observed between field isolates, reflecting the low but significant genetic variability of this region (94.2% ± 0.5% nucleotide identity). No mutation was exclusive of benign or severe hepatitis, and variations in IRES activity were not associated with a clinical phenotype, indirectly supporting the preponderance of host factors in determining the clinical presentation.
Republished paper: The implications of the NICE guidelines on neurosurgical management for all severe head injuries: systematic review
Authors: Barratt Helen , Wilson Mark , Moore Fionna , Raine Rosalind
Published: July 2010

Head injury is an important cause of death among young adults in the UK, and a significant burden on NHS resources. However, management is inconsistent, governed largely by local resources.

The latest version of the NICE head injury guidelines suggests that more patients with traumatic brain injury should be transferred to receive specialist care. However, this raises issues about the capacity of regional neurosurgical units, particularly to accommodate patients who do not require surgical intervention.

Objectives

To critically evaluate the basis of the NICE recommendations about transfer for neurosurgical care, and examine the configuration of specialist services to assess the implications of increasing the existing number of transfers.

Methods

A systematic literature review was conducted of articles discussing the provision of emergency neurosurgical care for adult head injuries in the UK.

Results

Fifty-eight papers met the criteria for inclusion in the literature review, including seven papers cited in the NICE guidance. Fifty-one papers related to neurosurgical care, including papers on bed occupancy, transfer times and transfer policies.

Conclusions

The evidence NICE cited is of variable quality. Much of the research was conducted outside the UK, which raises questions about its relevance to the NHS. Care of traumatic brain injuries in the UK is already hampered by the inadequate capacity of regional neurosurgical units to meet demand, and transferring more patients would be likely to exacerbate this. Increasing the number of transfers could also worsen inequalities of access for other groups, such as elective patients, particularly in areas where facilities are most stretched.
Unenhanced CT for the evaluation of acute ureteric colic: the essential pictorial guide
Authors: Kennish Steven J , Wah Tze M , Irving Henry C
Published: July 2010

Acute ureteric colic is a common emergency, often dealt with by the emergency physician or general practitioner and referred on to the urologist. Unenhanced CT of the kidneys, ureters and bladder (CTKUB) is the ‘gold standard’ imaging investigation for establishing a diagnosis and guiding management. An appreciation of the CTKUB signs, which support or refute a diagnosis of ureteric colic, is highly valuable to the clinician when making a urological referral, and to the urologist, who must make appropriate management plans. All salient diagnostic and supportive features of ureteric colic are carefully illustrated, as are important radiological mimics, with the objectives of educating and informing the non-radiologist. Ready access to the picture archive and communication system (PACS) allows all specialists involved to interpret the radiological report with the benefit of images. A stone within the ureter may not always be readily apparent. Soft tissue rim sign around a calcific focus is an important indicator of a ureteric stone, whereas a comet tail sign suggests a phlebolith (a calcified venous thrombosis), a radiological mimic of a ureteric stone. Numerous secondary signs of ureteric obstruction may be present including hydronephrosis and perinephric stranding, and can help to confirm the diagnosis. The relative diagnostic weighting of signs is discussed, and a checklist is provided to assist with interpretation. Unexpected alternative radiological diagnoses are also illustrated, which may have significant management consequences necessitating specialist referral.
Imaging in childhood scoliosis: a pictorial review
Authors: Musson Rachel E , Warren Daniel J , Bickle Ian , Connolly Daniel J , Griffiths Paul D
Published: July 2010

Childhood scoliosis is a common clinical entity with a number of different causes. In the majority of cases, the scoliosis is idiopathic, but it may be the manifestation of an occult spinal pathology. The clinical history and examination may elicit certain worrying features such as pain, neurological symptoms or an atypical curve pattern. These findings should prompt advanced imaging, as early and accurate detection of an underlying cause allows optimal planning and timing of surgery and helps reduce associated risks. The most common occult pathologies detected by advanced imaging are Arnold Chiari malformations, syringohydromyelia and closed spinal dysraphism such as diastematomyelia. Advanced imaging techniques, in particular multiplanar MRI, are also increasingly requested in children with known congenital scoliosis associated with spinal dysraphism and developmental causes of scoliosis such as neurofibromatosis and Klippel–Feil syndrome, as it allows superior delineation of the spinal column without the radiation risk. This review aims to examine the different imaging techniques currently used in the evaluation of scoliosis and provide a pictorial summary of the more common causes and associations.
Imaging in acute ischaemic stroke: essential for modern stroke care
Authors: Warren Daniel J , Musson Rachel , Connolly Daniel J A , Griffiths Paul D , Hoggard Nigel
Published: July 2010

Stroke is the second most common cause of death worldwide and the third most common in the UK. ‘Time is brain’ in ischaemic stroke; early reperfusion has been shown to lead to improved clinical outcomes, yet the majority of patients with acute stroke do not attend in time for thrombolysis as it is currently licensed, hence the interest in trials extending the therapeutic window. Defining the ischaemic penumbra is of crucial importance in choosing the appropriate patients for thrombolytic therapy who attend outside the optimal therapeutic window. Integrated stroke imaging, including demonstration of potentially salvageable tissue with either MR perfusion/diffusion studies or CT perfusion, is increasingly likely to play a central role in future management strategies and widening of the potential therapeutic window. This review highlights the basic imaging findings of acute stroke and discusses the role of advanced CT and MR techniques as well as options for vascular imaging.
Ammonia and Nitrate Uptake in the Lower Great Lakes
Authors: Murphy T. P.
Published: July 2010

Uptake of NH4+ is consistent with Michaelis–Menten kinetics in the Lower Great Lakes only if one assumes that the indophenol method of measuring NH4+ overestimates the in situ concentration. Short-term incubations were found necessary to avoid induction of nitrate uptake or changes in the rates of NH4+ uptake that occurred in long-term incubations. Uptake rates of nitrate are slow most of the summer. Since the nitrate is also present in low concentrations, most of the summer regeneration of nitrate must be very slow. The slow turnover of particulate N, low nutrient concentrations, slow rate of uptake relative to their ability to take up nitrogen, and the high affinity for ammonia (low Kt) suggest that in summer the primary productivity of the Lower Great Lakes is restricted by nitrogen deficiency.Key words: ammonia, nitrate, Lower Great Lakes
GRADIENT FLOWS FOR OPTIMIZATION IN QUANTUM INFORMATION AND QUANTUM DYNAMICS: FOUNDATIONS AND APPLICATIONS
Authors: SCHULTE-HERBRÜGGEN THOMAS , GLASER STEFFEN J. , DIRR GUNTHER , HELMKE UWE
Published: July 2010

Many challenges in quantum information and quantum control root in constrained optimization problems on finite-dimensional quantum systems. The constraints often arise from two facts: (i) quantum dynamic state spaces are naturally smooth manifolds (orbits of the respective initial states) rather than being Hilbert spaces; (ii) the dynamics of the respective quantum system may be restricted to a proper subset of the entire state space. Mathematically, either case can be treated by constrained optimization over the reachable set of an underlying control system. Thus, whenever the reachable set takes the form a smooth manifold, Riemannian optimization methods apply. Here, we give a comprehensive account on the foundations of gradient flows on Riemannian manifolds including new applications in quantum information and quantum dynamics. Yet, we do not pursue the problem of designing explicit controls for the underlying control systems.

The framework is sufficiently general for setting up gradient flows on (sub)manifolds, Lie (sub)groups, and (reductive) homogeneous spaces. Relevant convergence conditions are discussed, in particular for gradient flows on compact and analytic manifolds. This is meant to serve as foundation for new achievements and further research.

Illustrative examples and new applications are given: we extend former results on unitary groups to closed subgroups with tensor-product structure, where the finest product partitioning relates to SUloc(2n) := SU(2) ⊗ ⋯ ⊗ SU(2) — known as (qubit-wise) local unitary operations. Such applications include, e.g., optimizing figures of merit on SUloc(2n) relating to distance measures of pure-state entanglement as well as to best rank-1 approximations of higher-order tensors. In quantum information, our gradient flows provide a numerically favorable alternative to standard tensor-SVD techniques.
UNIVERSAL KHOVANOV–ROZANSKY sl(2) COHOMOLOGY
Authors: CAPRAU CARMEN
Published: July 2010

We generalize the Khovanov–Rozansky cohomology theory for n = 2 by using a homogeneous potential that depends on two parameters, to obtain the universal Khovanov-Rozansky sl(2)-link cohomology. This theory is equivalent to the universal sl(2)-link cohomology using foams, after tensoring both theories with appropriate rings.
RATIONAL MOVES ON LINKS: (2, 2)-MOVES AS A CASE STUDY
Authors: DABKOWSKI MIECZYSŁAW K. , ISHIWATA MAKIKO , PRZYTYCKI JÓZEF H.
Published: July 2010

We consider the problem of classification of links up to (2, 2)-moves. Our motivation comes from the theory of skein modules, more specifically from the skein module of S3 based on the deformation of (2, 2)-move. As it was proved in D-P-2, not every link can be reduced to a trivial link by (2, 2)-moves, for instance, the closure of (σ1σ2)6. In this paper, we classify 3-braids up to (2, 2)-moves and, we show how the Harikae–Nakanishi–Uchida conjecture can be modified to hold for closed 3-braids. As an important step in the classification we prove the conjecture for 2-algebraic links and classify (2, 2)-equivalence classes for links up to nine crossings. We also analyze an action of (2, 2)-move on Kei (involutive quandle) associated to a link diagram. We define Burnside Kei, Q(m, n), and ask for which values of m and n, is Q(m, n) finite. This question is motivated by classical Burnside problem.
A NEW PROOF THAT ALTERNATING LINKS ARE NON-TRIVIAL
Authors: MOFFATT IAIN
Published: July 2010

We use a simple geometric argument and small cancellation properties of link groups to prove that alternating links are non-trivial. Unlike most other proofs of this result, this proof uses only classic results in topology and combinatorial group theory.
COLORING INVARIANTS OF SPATIAL GRAPHS
Authors: NIEBRZYDOWSKI MACIEJ
Published: July 2010

We define the fundamental quandle of a spatial graph and several invariants derived from it. In the category of graph tangles, we define an invariant based on the walks in the graph and cocycles from nonabelian quandle cohomology.
A GEOMETRIC INTRODUCTION TO FORKING AND THORN-FORKING
Authors: ADLER HANS
Published: July 2010

A ternary relation [Formula: see text] between subsets of the big model of a complete first-order theory T is called an independence relation if it satisfies a certain set of axioms. The primary example is forking in a simple theory, but o-minimal theories are also known to have an interesting independence relation. Our approach in this paper is to treat independence relations as mathematical objects worth studying. The main application is a better understanding of thorn-forking, which turns out to be closely related to modular pairs in the lattice of algebraically closed sets.
WHEN COTORSION MODULES ARE PURE INJECTIVE
Authors: HERZOG IVO , ROTHMALER PHILIPP
Published: July 2010

We characterize rings over which every cotorsion module is pure injective (Xu rings) in terms of certain descending chain conditions and the Ziegler spectrum, which renders the classes of von Neumann regular rings and of pure semisimple rings as two possible extremes. As preparation, descriptions of pure projective and Mittag–Leffler preenvelopes with respect to so-called definable subcategories and of pure generation for such are derived, which may be of interest on their own. Infinitary axiomatizations lead to coherence results previously known for the special case of flat modules. Along with pseudoflat modules we introduce quasiflat modules, which arise naturally in the model-theoretic and the category-theoretic contexts.
Real-time lens blur effects and focus control
Authors: Lee Sungkil , Eisemann Elmar , Seidel Hans-Peter
Published: July 2010

We present a novel rendering system for defocus blur and lens effects. It supports physically-based rendering and outperforms previous approaches by involving a novel GPU-based tracing method. Our solution achieves more precision than competing real-time solutions and our results are mostly indistinguishable from offline rendering. Our method is also more general and can integrate advanced simulations, such as simple geometric lens models enabling various lens aberration effects. These latter is crucial for realism, but are often employed in artistic contexts, too. We show that available artistic lenses can be simulated by our method. In this spirit, our work introduces an intuitive control over depth-of-field effects. The physical basis is crucial as a starting point to enable new artistic renderings based on a generalized focal surface to emphasize particular elements in the scene while retaining a realistic look. Our real-time solution provides realistic, as well as plausible expressive results.
Reducing shading on GPUs using quad-fragment merging
Authors: Fatahalian Kayvon , Boulos Solomon , Hegarty James , Akeley Kurt , Mark William R. , Moreton Henry , Hanrahan Pat
Published: July 2010

Current GPUs perform a significant amount of redundant shading when surfaces are tessellated into small triangles. We address this inefficiency by augmenting the GPU pipeline to gather and merge rasterized fragments from adjacent triangles in a mesh. This approach has minimal impact on output image quality, is amenable to implementation in fixed-function hardware, and, when rendering pixel-sized triangles, requires only a small amount of buffering to reduce overall pipeline shading work by a factor of eight. We find that a fragment-shading pipeline with this optimization is competitive with the REYES pipeline approach of shading at micropolygon vertices and, in cases of complex occlusion, can perform up to two times less shading work.
Precomputed wave simulation for real-time sound propagation of dynamic sources in complex scenes
Authors: Raghuvanshi Nikunj , Snyder John , Mehra Ravish , Lin Ming , Govindaraju Naga
Published: July 2010

We present a method for real-time sound propagation that captures all wave effects, including diffraction and reverberation, for multiple moving sources and a moving listener in a complex, static 3D scene. It performs an offline numerical simulation over the scene and then applies a novel technique to extract and compactly encode the perceptually salient information in the resulting acoustic responses. Each response is automatically broken into two phases: early reflections (ER) and late reverberation (LR), via a threshold on the temporal density of arriving wavefronts. The LR is simulated and stored in the frequency domain, once per room in the scene. The ER accounts for more detailed spatial variation, by recording a set of peak delays/amplitudes in the time domain and a residual frequency response sampled in octave frequency bands, at each source/receiver point pair in a 5D grid. An efficient run-time uses this precomputed representation to perform binaural sound rendering based on frequency-domain convolution. Our system demonstrates realistic, wave-based acoustic effects in real time, including diffraction low-passing behind obstructions, sound focusing, hollow reverberation in empty rooms, sound diffusion in fully-furnished rooms, and realistic late reverberation.
Terrain-adaptive bipedal locomotion control
Authors: Wu Jia-chi , Popović Zoran
Published: July 2010

We describe a framework for the automatic synthesis of biped locomotion controllers that adapt to uneven terrain at run-time. The framework consists of two components: a per-footstep end-effector path planner and a per-timestep generalized-force solver. At the start of each footstep, the planner performs short-term planning in the space of end-effector trajectories. These trajectories adapt to the interactive task goals and the features of the surrounding uneven terrain at run-time. We solve for the parameters of the planner for different tasks in offline optimizations. Using the per-footstep plan, the generalized-force solver takes ground contacts into consideration and solves a quadratic program at each simulation timestep to obtain joint torques that drive the biped. We demonstrate the capabilities of the controllers in complex navigation tasks where they perform gradual or sharp turns and transition between moving forwards, backwards, and sideways on uneven terrain (including hurdles and stairs) according to the interactive task goals. We also show that the resulting controllers are capable of handling morphology changes to the character.
Optimizing walking controllers for uncertain inputs and environments
Authors: Wang Jack M. , Fleet David J. , Hertzmann Aaron
Published: July 2010

We introduce methods for optimizing physics-based walking controllers for robustness to uncertainty. Many unknown factors, such as external forces, control torques, and user control inputs, cannot be known in advance and must be treated as uncertain. These variables are represented with probability distributions, and a return function scores the desirability of a single motion. Controller optimization entails maximizing the expected value of the return, which is computed by Monte Carlo methods. We demonstrate examples with different sources of uncertainty and task constraints. Optimizing control strategies under uncertainty increases robustness and produces natural variations in style.
Optimal feedback control for character animation using an abstract model
Authors: Ye Yuting , Liu C. Karen
Published: July 2010

Real-time adaptation of a motion capture sequence to virtual environments with physical perturbations requires robust control strategies. This paper describes an optimal feedback controller for motion tracking that allows for on-the-fly re-planning of long-term goals and adjustments in the final completion time. We first solve an offline optimal trajectory problem for an abstract dynamic model that captures the essential relation between contact forces and momenta. A feedback control policy is then derived and used to simulate the abstract model online. Simulation results become dynamic constraints for online reconstruction of full-body motion from a reference. We applied our controller to a wide range of motions including walking, long stepping, and a squat exercise. Results show that our controllers are robust to large perturbations and changes in the environment.
Multi-class blue noise sampling
Authors: Wei Li-Yi
Published: July 2010

Sampling is a core process for a variety of graphics applications. Among existing sampling methods, blue noise sampling remains popular thanks to its spatial uniformity and absence of aliasing artifacts. However, research so far has been mainly focused on blue noise sampling with a single class of samples. This could be insufficient for common natural as well as man-made phenomena requiring multiple classes of samples, such as object placement, imaging sensors, and stippling patterns.

We extend blue noise sampling to multiple classes where each individual class as well as their unions exhibit blue noise characteristics. We propose two flavors of algorithms to generate such multi-class blue noise samples, one extended from traditional Poissonharddisk sampling for explicit control of sample spacing, and another based on oursoftdisk sampling for explicit control of sample count. Our algorithms support uniform and adaptive sampling, and are applicable to both discrete and continuous sample space in arbitrary dimensions. We study characteristics of samples generated by our methods, and demonstrate applications in object placement, sensor layout, and color stippling.
Symmetry factored embedding and distance
Authors: Lipman Yaron , Chen Xiaobai , Daubechies Ingrid , Funkhouser Thomas
Published: July 2010

We introduce the Symmetry Factored Embedding (SFE) and the Symmetry Factored Distance (SFD) as new tools to analyze and represent symmetries in a point set. The SFE provides new coordinates in which symmetry is "factored out," and the SFD is the Euclidean distance in that space. These constructions characterize the space of symmetric correspondences between points -- i.e., orbits. A key observation is that a set of points in the same orbit appears as a clique in a correspondence graph induced by pairwise similarities. As a result, the problem of finding approximate and partial symmetries in a point set reduces to the problem of measuring connectedness in the correspondence graph, a well-studied problem for which spectral methods provide a robust solution. We provide methods for computing the SFE and SFD for extrinsic global symmetries and then extend them to consider partial extrinsic and intrinsic cases. During experiments with difficult examples, we find that the proposed methods can characterize symmetries in inputs with noise, missing data, non-rigid deformations, and complex symmetries, without a priori knowledge of the symmetry group. As such, we believe that it provides a useful tool for automatic shape analysis in applications such as segmentation and stationary point detection.
A connection between partial symmetry and inverse procedural modeling
Authors: Bokeloh Martin , Wand Michael , Seidel Hans-Peter
Published: July 2010

In this paper, we address the problem of
inverse
procedural modeling: Given a piece of exemplar 3D geometry, we would like to find a set of rules that describe objects that are similar to the exemplar. We consider local similarity, i.e., each local neighborhood of the newly created object must match some local neighborhood of the exemplar. We show that we can find explicit shape modification rules that guarantee strict local similarity by looking at the structure of the partial symmetries of the object. By cutting the object into pieces along curves within symmetric areas, we can build shape operations that maintain local similarity by construction. We systematically collect such editing operations and analyze their dependency to build a shape grammar. We discuss how to extract general rewriting systems, context free hierarchical rules, and grid-based rules. All of this information is derived directly from the model, without user interaction. The extracted rules are then used to implement tools for semi-automatic shape modeling by example, which are demonstrated on a number of different example data sets. Overall, our paper provides a concise theoretical and practical framework for inverse procedural modeling of 3D objects.
3D modeling with silhouettes
Authors: Rivers Alec , Durand Frédo , Igarashi Takeo
Published: July 2010

We present a new sketch-based modeling approach in which models are interactively designed by drawing their 2D silhouettes from different views. The core idea of our paper is to limit the input to 2D silhouettes, removing the need to explicitly create or position 3D elements. Arbitrarily complex models can be constructed by assembling them out of parts defined by their silhouettes, which can be combined using CSG operations. We introduce a new simplified algorithm to compute CSG solids that leverages special properties of silhouette cylinders to convert the 3D CSG problem into one that can be handled entirely with 2D operations, making implementation simpler and more robust. We evaluate our approach by modeling a random sampling of man-made objects taken from the words in WordNet, and show that all of the tested man-made objects can be modeled quickly and easily using our approach.
Sampling-based contact-rich motion control
Authors: Liu Libin , Yin KangKang , van de Panne Michiel , Shao Tianjia , Xu Weiwei
Published: July 2010

Human motions are the product of internal and external forces, but these forces are very difficult to measure in a general setting. Given a motion capture trajectory, we propose a method to reconstruct its open-loop control and the implicit contact forces. The method employs a strategy based on randomized sampling of the control within user-specified bounds, coupled with forward dynamics simulation. Sampling-based techniques are well suited to this task because of their lack of dependence on derivatives, which are difficult to estimate in contact-rich scenarios. They are also easy to parallelize, which we exploit in our implementation on a compute cluster. We demonstrate reconstruction of a diverse set of captured motions, including walking, running, and contact rich tasks such as rolls and kip-up jumps. We further show how the method can be applied to physically based motion transformation and retargeting, physically plausible motion variations, and reference-trajectory-free idling motions. Alongside the successes, we point out a number of limitations and directions for future work.
On isomorphisms of intersection types
Authors: Dezani-Ciancaglini Mariangiola , Cosmo Roberto Di , Giovannetti Elio , Tatsuta Makoto
Published: July 2010

The study of type isomorphisms for different λ-calculi started over twenty years ago, and a very wide body of knowledge has been established, both in terms of results and in terms of techniques. A notable missing piece of the puzzle was the characterization of type isomorphisms in the presence of intersection types. While, at first thought, this may seem to be a simple exercise, it turns out that not only finding the right characterization is not simple, but that the very notion of isomorphism in intersection types is an unexpectedly original element in the previously known landscape, breaking most of the known properties of isomorphisms of the typed λ-calculus. In particular, isomorphism is not a congruence and types that are equal in the standard models of intersection types may be nonisomorphic.
A highly expressing Tet-inducible cell line recapitulates in situ developmental changes in prestin's Boltzmann characteristics and reveals early maturational events
Authors: Bian Shumin , Koo Bon W. , Kelleher Stephen , Santos-Sacchi Joseph , Navaratnam Dhasakumar S.
Published: July 2010

Prestin is the motor protein within the lateral membrane of outer hair cells (OHCs), and it is required for mammalian cochlear amplification. Expression of prestin precedes the onset of hearing in mice, and it has been suggested that prestin undergoes a functional maturation within the membrane coincident with the onset of hearing. We have developed a tetracycline-inducible prestin-expressing cell line that we have used to model prestin's functional maturation. We used prestin's voltage-dependent nonlinear charge movement (or nonlinear capacitance) as a test of function and correlated it to biochemical measures of prestin expressed on the cell surface. An initial stage of slow growth in charge density is accompanied by a rapid increase in our estimate of charge carried by an individual motor. A rapid growth in charge density follows and strongly correlates with an increasing ratio between an apparently larger and smaller monomer, suggesting that the latter exerts a dominant-negative effect on function. Finally, there is a gradual depolarizing shift in the voltage of peak capacitance, similar to that observed in developing OHCs. This inducible system offers many opportunities for detailed studies of prestin.