bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaural fluctuations and the detection of interaural incoherence. IV. The effect of compression on stimulus statistics
Authors: Goupell Matthew J.
Published: January 2011

The purpose of this experiment was to determine whether the normalized interaural cross-correlation (CC) model or a model based on interaural phase and level differences can better describe incoherence detection data. The ability to detect interaural incoherence in three sets of reproducible dichotic noises was tested in six listeners. The first set contained noises with a constrained value of the CC and the CC including signal compression. The second set contained noises with a constrained value of the CC including signal compression. The third set contained noises with constrained values in the fluctuations in the interaural differences. Modeling showed that neither the CC model nor the model using the interaural differences could account for the data in any set. Examination of the statistical properties of the stimuli showed that including compression before the calculation of the interaural CC causes a substantial correlation of this metric to the fluctuations in the interaural phase difference. This finding implies that it may be more difficult to discriminate between the common types of binaural models than previously thought.
Genomic Signatures Predict Migration and Spawning Failure in Wild Canadian Salmon
Authors: Miller Kristina M. , Li Shaorong , Kaukinen Karia H. , Ginther Norma , Hammill Edd , Curtis Janelle M. R. , Patterson David A. , Sierocinski Thomas , Donnison Louise , Pavlidis Paul , Hinch Scott G. , Hruska Kimberly A. , Cooke Steven J. , English Karl K. , Farrell Anthony P.
Published: January 2011

High mortality of sockeye salmon in the Fraser River is associated with signals of metabolic and immune stress.
Supracolloidal Reaction Kinetics of Janus Spheres
Authors: Chen Qian , Whitmer Jonathan K. , Jiang Shan , Bae Sung Chul , Luijten Erik , Granick Steve
Published: January 2011

Colloidal particles that are charged on one side and hydrophobic on the other can form chiral helices in salt solutions.
Writing About Testing Worries Boosts Exam Performance in the Classroom
Authors: Ramirez Gerardo , Beilock Sian L.
Published: January 2011

Write Your Worries Away

Tests and exams are stressful for many people. Students who “choke” at an exam may perform less well than their knowledge base warrants. Such results can accumulate to generate reduced educational achievements and expectations. Studying young adults performing math tests,
Ramirez and Beilock
(p.
211
) found that a brief intervention—writing about their anxiety about the upcoming exam—helped students to do better in the exam. Perhaps by acknowledging their fears, students were able to tame distracting emotions.
Computing the Climate and More
A Vast Machine
Computer Models, Climate Data, and the Politics of Global Warming

by Paul N. Edwards

MIT Press, Cambridge, MA, 2010. 546 pp. $32.95, £24.95. ISBN 9780262013925.

Science in the Age of Computer Simulation
by Eric B. Winsberg

University of Chicago Press, Chicago, 2010. 164 pp. $66. ISBN 9780226902029. Paper, $24. ISBN 9780226902043.
Authors: Somerville Richard C. J.
Published: January 2011

Edwards explores the use of computer simulations and models in climate research, and Winsberg offers a philosophical perspective on the roles of computer simulation in contemporary science.
A New Twist for Electron Beams
Authors: Herring Rodney Arthur
Published: January 2011

Passing an electron beam through carefully prepared holograms creates electron vortex beams that improve resolution and allow samples to be manipulated.
Northern Meltwater Pulses, CO
2
, and Changes in Atlantic Convection
Authors: Sarnthein Michael
Published: January 2011

Detailed evidence of how the North Atlantic Meridional Overturning Circulation behaved after the last ice age.
John Bennett Fenn (1917–2010)
Authors: Muddiman David C.
Published: January 2011

The hallmark of a southern gentleman's serpentine path to the Nobel Prize was his admiration for truth and the stimulation of a curious, prepared, and creative mind.
Pint-Sized Predator Rattles The Dinosaur Family Tree
Authors: Balter Michael
Published: January 2011

On page 206 of this week's issue of
Science
, a team working in Argentina reports the discovery of a very early dinosaur—possibly a distant ancestor of
Tyrannosaurus rex
—that lived about 230 million years ago, during what paleontologists call the dawn of the dinosaurs.
Did the First Cities Grow From Marshes?
Authors: Lawler Andrew
Published: January 2011

The world's earliest large settlements may owe their existence as much to the swamps of southern Iraq as to irrigation and agriculture.
What Heated Up the Eocene?
Authors: Kerr Richard A.
Published: January 2011

Fifty-five million years ago, carbon dioxide gushed into the atmosphere over as little as a millennium, acidifying the ocean and scorching the world of the Eocene epoch with a 5˚C greenhouse warming. In one presentation, earth systems modelers suggested an ocean source for all that carbon dioxide.
Worry But Don't Panic Over Glacial Losses
Authors: Kerr Richard A.
Published: January 2011

Glaciers are suddenly galloping to the sea in Greenland and the "weak underbelly" of Antarctic ice is beginning to give way, but a couple of glaciologists at the meeting say that at least in the short term, the situation, while bad, is not always quite as bad as it looks.
Development of Two Types of Rapid Diagnostic Test Kits To Detect the Hemagglutinin or Nucleoprotein of the Swine-Origin Pandemic Influenza A Virus H1N1
Authors: Mizuike Rika , Sasaki Tadahiro , Baba Koichi , Iwamoto Hisahiko , Shibai Yusuke , Kosaka Mieko , Kubota-Koketsu Ritsuko , Yang Cheng-Song , Du Anariwa , Sakudo Akikazu , Tsujikawa Muneo , Yunoki Mikihiro , Ikuta Kazuyoshi
Published: January 2011

Since its emergence in April 2009, pandemic influenza A virus H1N1 (H1N1 pdm), a new type of influenza A virus with a triple-reassortant genome, has spread throughout the world. Initial attempts to diagnose the infection in patients using immunochromatography (IC) relied on test kits developed for seasonal influenza A and B viruses, many of which proved significantly less sensitive to H1N1 pdm. Here, we prepared monoclonal antibodies that react with H1N1 pdm but not seasonal influenza A (H1N1 and H3N2) or B viruses. Using two of these antibodies, one recognizing viral hemagglutinin (HA) and the other recognizing nucleoprotein (NP), we developed kits for the specific detection of H1N1 pdm and tested them using clinical specimens of nasal wash fluid or nasopharyngeal fluid from patients with influenza-like illnesses. The specificities of both IC test kits were very high (93% for the HA kit, 100% for the NP kit). The test sensitivities for detection of H1N1 pdm were 85.5% with the anti-NP antibody, 49.4% with the anti-HA antibody, and 79.5% with a commercially available influenza A virus detection assay. Use of the anti-NP antibody could allow the rapid and accurate diagnosis of H1N1 pdm infections.
A Novel Monoclonal Antibody against FbaA Can Inhibit the Binding of the Complement Regulatory Protein Factor H to Group A Streptococcus
Authors: Ma Cuiqing , Guo Yiyang , Gu Haiyan , Zhang Ling , Liu Hainan , Feng Huidong , Wei Lin
Published: January 2011

Some microbial pathogens utilize human complement regulatory proteins, such as factor H (FH) and factor H-like protein 1 (FHL-1), for immune evasion. FbaA is an FHL-1 and FH binding protein expressed on the surface of group A streptococcus (GAS), a common agent of pharyngeal, skin, and soft tissue infections. In this study, we prepared monoclonal antibodies (MAbs) against FbaA, assayed them for specificity, and located their binding domains in FbaA. We found an MAb called FbaA MAb2, which demonstrated the highest affinity to GAS among all of the MAbs. Based on the binding with component peptides, the detected epitope, which was specific for FbaA MAb2, was the amino acid residues 95 to 118 of FbaA; on the other hand, it did not bind with the truncated protein of the internally deleted residues of the segment from 95 to 118 of FbaA. Furthermore, the predominant amino acids specific for FbaA MAb2 screened by phage display epitope library were I, T, P, D, and L, corresponding to the amino acid residues 101, 103, 105, 106, and 110 of FbaA, respectively. The binding location of FbaA with FH and FHL-1 was a 16-amino-acid region corresponding to amino acid residues 97 to 112 of FbaA, which overlapped the FbaA MAb2 binding domain, as confirmed by competitive inhibition enzyme-linked immunosorbent assay and immunofluorescence microscopy. Based on the results of the invasion assay, FbaA MAb2 can inhibit the binding of FH to GAS.
Evaluation of Four Rapid Immunochromatographic Tests for the Detection of Cardiac Troponin I
Authors: Ramparany Lovasoa , Ramirez José , Nizou Jacques-Yves , Le Saux David , Richard Vincent , Talarmin Antoine
Published: January 2011

Cardiac troponin I (cTnI) is a sensitive and specific marker of acute coronary syndromes and myocardial damage. During the past few years, it has become the preferred biochemical marker of myocardial infarction. However, due to the sensitivity required for its detection, only automated systems can be used in developed countries. However, these are rather expensive and unaffordable for most laboratories in developing countries. Many manufacturers have therefore proposed rapid immunochromatographic tests to detect cTnI. The aim of this study was to assess the limit of detection (LOD) and performance of four rapid immunochromatographic tests available in Madagascar. The four tests evaluated were Hexagon Troponin, Nadal troponin I cassette, Troponitest+, and Amicheck-Trop. Amicheck-Trop had a sensitivity and negative predictive value of about 80%, whereas for the three others, they were about 20%. The specificity of Amicheck-Trop of 87.3% was lower than the specificities of the other tests (98% to 100%). These differences were explained by the limits of detection of the tests: 0.3 to 0.4 ng/ml for Amicheck-Trop but only 1.8 to 2 ng/ml for the three other tests. It was concluded that Amicheck-Trop could be useful in the management of acute myocardial infarction or myocarditis in sparsely equipped laboratories in developing countries.
Redundancy and Specificity of
Escherichia coli
Iron Acquisition Systems during Urinary Tract Infection
Authors: Garcia Erin C. , Brumbaugh Ariel R. , Mobley Harry L. T.
Published: January 2011

Uropathogenic
Escherichia coli
(UPEC), the predominant cause of uncomplicated urinary tract infection (UTI), utilizes an array of outer membrane iron receptors to facilitate siderophore and heme import from within the iron-limited urinary tract. While these systems are required for UPEC
in vivo
fitness and are assumed to be functionally redundant, the relative contributions of specific receptors to pathogenesis are unknown. To delineate the relative roles of distinct UPEC iron acquisition systems in UTI, isogenic mutants in UPEC strain CFT073 or 536 lacking individual receptors were competed against one another
in vivo
in a series of mixed infections. When combinations of up to four mutants were coinoculated using a CBA/J mouse model of ascending UTI, catecholate receptor mutants (Δ
fepA
, Δ
iha
, and Δ
iroN
mutants) were equally fit, suggesting redundant function. However, noncatecholate siderophore receptor mutants, including the Δ
iutA
aerobactin receptor mutant and the Δ
fyuA
yersiniabactin receptor mutant, were frequently outcompeted by coinoculated mutants, indicating that these systems contribute more significantly to UPEC iron acquisition
in vivo
. A tissue-specific preference for heme acquisition was also observed, as a heme uptake-deficient Δ
hma
Δ
chuA
double mutant was outcompeted by siderophore receptor mutants specifically during kidney colonization. The relative contribution of each receptor to UTI only partially correlated with
in vivo
levels of receptor gene expression, indicating that other factors likely contributed to the observed fitness differences. Overall, our results suggest that UPEC iron receptors provide both functional redundancy and niche specificity for this pathogen as it colonizes distinct sites within the urinary tract.
Genetic Characterization Indicates that a Specific Subpopulation of Pseudomonas aeruginosa Is Associated with Keratitis Infections
Authors: Stewart Rosalind M. K. , Wiehlmann Lutz , Ashelford Kevin E. , Preston Stephanie J. , Frimmersdorf Eliane , Campbell Barry J. , Neal Timothy J. , Hall Neil , Tuft Stephen , Kaye Stephen B. , Winstanley Craig
Published: January 2011

Pseudomonas aeruginosa
is a common opportunistic bacterial pathogen that causes a variety of infections in humans. Populations of
P. aeruginosa
are dominated by common clones that can be isolated from diverse clinical and environmental sources. To determine whether specific clones are associated with corneal infection, we used a portable genotyping microarray system to analyze a set of 63
P. aeruginosa
isolates from patients with corneal ulcers (keratitis). We then used population analysis to compare the keratitis isolates to a wider collection of
P. aeruginosa
from various nonocular sources. We identified various markers in a subpopulation of
P. aeruginosa
associated with keratitis that were in strong disequilibrium with the wider
P. aeruginosa
population, including
oriC
,
exoU
,
katN
, unmodified flagellin, and the carriage of common genomic islands. The genome sequencing of a keratitis isolate (39016; representing the dominant serotype O11), which was associated with a prolonged clinical healing time, revealed several genomic islands and prophages within the accessory genome. The PCR amplification screening of all 63 keratitis isolates, however, provided little evidence for the shared carriage of specific prophages or genomic islands between serotypes.
P. aeruginosa
twitching motility, due to type IV pili, is implicated in corneal virulence. We demonstrated that 46% of the O11 keratitis isolates, including 39016, carry a distinctive
pilA
, encoding the pilin of type IV pili. Thus, the keratitis isolates were associated with specific characteristics, indicating that a subpopulation of
P. aeruginosa
is adapted to cause corneal infection.
Comparison of the Broth Microdilution (BMD) Method of the European Committee on Antimicrobial Susceptibility Testing with the 24-Hour CLSI BMD Method for Testing Susceptibility of Candida Species to Fluconazole, Posaconazole, and Voriconazole by Use of Epidemiological Cutoff Values
Authors: Pfaller M. A. , Espinel-Ingroff A. , Boyken L. , Hollis R. J. , Kroeger J. , Messer S. A. , Tendolkar S. , Diekema D. J.
Published: January 2011

The antifungal broth microdilution (BMD) method of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) was compared with CLSI BMD method M27-A3 for fluconazole, posaconazole, and voriconazole susceptibility testing of 1,056 isolates of
Candida
. The isolates were obtained in 2009 from more than 60 centers worldwide and included 560 isolates of
C. albicans
, 175 of
C. glabrata
, 162 of
C. parapsilosis
, 124 of
C. tropicalis
, and 35 of
C. krusei
. The overall essential agreement (EA) between EUCAST and CLSI results ranged from 96.9% (voriconazole) to 98.6% (fluconazole). The categorical agreement (CA) between methods and species of
Candida
was assessed using previously determined epidemiological cutoff values (ECVs). The ECVs (expressed as μg/ml) for fluconazole, posaconazole, and voriconazole, respectively, were as follows: 0.12, 0.06, and 0.03 for
C. albicans
; 32, 2, and 0.5 for
C. glabrata
; 2, 0.25, and 0.12 for
C. parapsilosis
; 2, 0.12, and 0.06 for
C. tropicalis
; 64, 0.5, and 0.5 for
C. krusei
. Excellent CA was observed for all comparisons between the EUCAST and CLSI results for fluconazole, posaconazole, and voriconazole, respectively, for each species: 98.9%, 93.6%, and 98.6% for
C. albicans
; 96.0%, 98.9%, and 93.7% for
C. glabrata
; 90.8%, 98.1%, and 98.1% for
C. parapsilosis
; 99.2%, 99.2%, and 96.8% for
C. tropicalis
; 97.1%, 97.1%, and 97.1% for
C. krusei
. We demonstrate high levels of EA and CA between the CLSI and EUCAST BMD methods for testing of triazoles against
Candida
when the MICs were determined after 24 h and ECVs were used to differentiate wild-type (WT) from non-WT strains. These results provide additional data in favor of the harmonization of these two methods.
Ebolavirus Proteins Suppress the Effects of Small Interfering RNA by Direct Interaction with the Mammalian RNA Interference Pathway
Authors: Fabozzi Giulia , Nabel Christopher S. , Dolan Michael A. , Sullivan Nancy J.
Published: January 2011

Cellular RNA interference (RNAi) provides a natural response against viral infection, but some viruses have evolved mechanisms to antagonize this form of antiviral immunity. To determine whether Ebolavirus (EBOV) counters RNAi by encoding suppressors of RNA silencing (SRSs), we screened all EBOV proteins using an RNAi assay initiated by exogenously delivered small interfering RNAs (siRNAs) against either an EBOV or a reporter gene. In addition to viral protein 35 (VP35), we found that VP30 and VP40 independently act as SRSs. Here, we present the molecular mechanisms of VP30 and VP35. VP30 interacts with Dicer independently of siRNA and with one Dicer partner, TRBP, only in the presence of siRNA. VP35 directly interacts with Dicer partners TRBP and PACT in an siRNA-independent fashion and in the absence of effects on interferon (IFN). Taken together, our findings elucidate a new mechanism of RNAi suppression that extends beyond the role of SRSs in double-stranded RNA (dsRNA) binding and IFN antagonism. The presence of three suppressors highlights the relevance of host RNAi-dependent antiviral immunity in EBOV infection and illustrates the importance of RNAi in shaping the evolution of RNA viruses.
Sustained High Levels of Interleukin-6 Contribute to the Pathogenesis of Enterovirus 71 in a Neonate Mouse Model
Authors: Khong Wei Xin , Foo Damian G. W. , Trasti Scott L. , Tan Eng Lee , Alonso Sylvie
Published: January 2011

Enterovirus 71 (EV71) is the major causative agent of hand, foot, and mouth disease (HFMD) in young children and has been consistently associated with the most severe complications of the disease, including central nervous system inflammation and pulmonary edema. Increasing frequency and amplitude of EV71 outbreaks have raised awareness and concerns worldwide. Previous reports proposed that overwhelming virus replication combined with the induction of massive proinflammatory cytokines is responsible for the pathogenicity of EV71. Specifically, elevated interleukin-6 (IL-6) levels were observed consistently in patients and strongly correlated with disease severity. In this study, we show in the neonate mouse model that sustained high levels of IL-6 produced upon EV71 infection lead to severe tissue damage and eventually death of the animals. Administration of anti-IL-6 neutralizing antibodies after the onset of the clinical symptoms successfully improved the survival rates and clinical scores of the infected hosts. Compared to untreated infected controls, anti-IL-6-treated mice displayed reduced tissue damage, absence of splenic atrophy, and increased immune cell activation. In addition, markedly elevated systemic levels of IL-10 were measured in the protected animals. Furthermore, there was no significant difference in virus titers between anti-IL-6-treated mice and untreated mice, indicating that the anti-IL-6 antibody-mediated protection is independent of the virus load. Our findings thus demonstrate that IL-6 plays a major role in EV71-induced immunopathogenesis. As there is still neither vaccine nor treatment available against EV71, anti-IL-6 antibody treatment represents a potential therapeutic approach to providing protection from the most severe complications of the disease.
The Role of Aldehyde Dehydrogenase and Hsp70 in Suppression of White Spot Syndrome Virus Replication at High Temperature
Authors: Lin Ying-Ru , Hung Hsiao-Chun , Leu Jiann-Horng , Wang Hao-Ching , Kou Guang-Hsiung , Lo Chu-Fang
Published: January 2011

High temperature (32 to 33°C) has been shown to reduce mortality in white spot syndrome virus (WSSV)-infected shrimps, but the mechanism still remains unclear. Here we show that in WSSV-infected shrimps cultured at 32°C, transcriptional levels of representative immediate-early, early, and late genes were initially higher than those at 25°C. However, neither the IE1 nor VP28 protein was detected at 32°C, suggesting that high temperature might inhibit WSSV protein synthesis. Two-dimensional gel electrophoresis analysis revealed two proteins, NAD-dependent aldehyde dehydrogenase (ALDH) and the proteasome alpha 4 subunit (proteasome α4), that were markedly upregulated in WSSV-infected shrimps at 32°C. Reverse transcription-PCR (RT-PCR) analysis of members of the heat shock protein family also showed that
hsp70
was upregulated at 32°C. When
aldh
,
proteasome α4
, and
hsp70
were knocked down by double-stranded RNA interference and shrimps were challenged with WSSV, the
aldh
and
hsp70
knockdown shrimps became severely infected at 32°C, while the
proteasome α4
knockdown shrimps remained uninfected. Our results therefore suggest that ALDH and Hsp70 both play an important role in the inhibition of WSSV replication at high temperature.
Glycosylphosphatidylinositol Anchor-Dependent Stimulation Pathway Required for Generation of Baculovirus-Derived Recombinant Scrapie Prion Protein
Authors: Imamura Morikazu , Kato Nobuko , Yoshioka Miyako , Okada Hiroyuki , Iwamaru Yoshifumi , Shimizu Yoshihisa , Mohri Shirou , Yokoyama Takashi , Murayama Yuichi
Published: January 2011

The pathogenic isoform (PrP
Sc
) of the host-encoded cellular prion protein (PrP
C
) is considered to be an infectious agent of transmissible spongiform encephalopathy (TSE). The detailed mechanism by which the PrP
Sc
seed catalyzes the structural conversion of endogenous PrP
C
into nascent PrP
Sc
in vivo
still remains unclear. Recent studies reveal that bacterially derived recombinant PrP (recPrP) can be used as a substrate for the
in vitro
generation of protease-resistant recPrP (recPrP
res
) by protein-misfolding cyclic amplification (PMCA). These findings imply that PrP modifications with a glycosylphosphatidylinositol (GPI) anchor and asparagine (N)-linked glycosylation are not necessary for the amplification and generation of recPrP
Sc
by PMCA. However, the biological properties of PrP
Sc
obtained by
in vivo
transmission of recPrP
res
are unique or different from those of PrP
Sc
used as the seed, indicating that the mechanisms mediated by these posttranslational modifications possibly participate in reproductive propagation of PrP
Sc
. In the present study, using baculovirus-derived recombinant PrP (Bac-PrP), we demonstrated that Bac-PrP is useful as a PrP
C
substrate for amplification of the mouse scrapie prion strain Chandler, and PrP
Sc
that accumulated in mice inoculated with Bac-PrP
res
had biochemical and pathological properties very similar to those of the PrP
Sc
seed. Since Bac-PrP modified with a GPI anchor and brain homogenate of
Prnp
knockout mice were both required to generate Bac-PrP
res
, the interaction of GPI-anchored PrP with factors in brain homogenates is essential for reproductive propagation of PrP
Sc
. Therefore, the Bac-PMCA technique appears to be extremely beneficial for the comprehensive understanding of the GPI anchor-mediated stimulation pathway.
Sensitivity of the Phadia EliA connective tissue disease screen for less common disease-specific autoantibodies
Authors: Parker Jennifer C , Bunn Christopher C
Published: January 2011

Aim

To evaluate the sensitivity of a commercial autoantibody screening method (Phadia EliA connective tissue disease (CTD) screen) for the detection of less common antibody specificities associated with connective tissue disease.

Methods

399 sera positive for anti-PM/Scl (n=102), anti-RNA polymerase III (n=199), anti-fibrillarin (n=50), anti-Mi-2 (n=12), anti-proliferating cell nuclear antigen (PCNA) (n=13) and anti-ribosomal P (n=23) were analysed using the solid phase assay. Each well was coated with the respective antigens for these autoantibodies and also with the antigens Ro, La, Jo-1, Scl-70, CENP-B, U1-RNP, Sm and native DNA.

Results

All the anti-ribosomal P, anti-PCNA and anti-Mi-2 sera and 94% of the anti-PM/Scl sera were positive. For anti-fibrillarin, 36 (68%) were positive and 12 (22%) were equivocal. For anti-RNA polymerase III, 131 (67%) were positive, 23 (11%) were equivocal and 45 (22%) were negative.

Conclusions

The sensitivity of the Phadia EliA CTD screen is currently insufficient for the assay to be used as a screening test for anti-fibrillarin and anti-RNA polymerase III, but appears to be satisfactory for the other autoantibodies tested.
SEMI-SUPERVISED ANALYSIS OF HUMAN BRAIN TUMOURS FROM PARTIALLY LABELED MRS INFORMATION, USING MANIFOLD LEARNING MODELS
Authors: CRUZ-BARBOSA RAÚL , VELLIDO ALFREDO
Published: January 2011

Medical diagnosis can often be understood as a classification problem. In oncology, this typically involves differentiating between tumour types and grades, or some type of discrete outcome prediction. From the viewpoint of computer-based medical decision support, this classification requires the availability of accurate diagnoses of past cases as training target examples. The availability of such labeled databases is scarce in most areas of oncology, and especially so in neuro-oncology. In such context, semi-supervised learning oriented towards classification can be a sensible data modeling choice. In this study, semi-supervised variants of Generative Topographic Mapping, a model of the manifold learning family, are applied to two neuro-oncology problems: the diagnostic discrimination between different brain tumour pathologies, and the prediction of outcomes for a specific type of aggressive brain tumours. Their performance compared favorably with those of the alternative Laplacian Eigenmaps and Semi-Supervised SVM for Manifold Learning models in most of the experiments.
AN EVALUATION OF MULTIPLE FEED-FORWARD NETWORKS ON GPUs
Authors: LOPES NOEL , RIBEIRO BERNARDETE
Published: January 2011

The Graphics Processing Unit (GPU) originally designed for rendering graphics and which is difficult to program for other tasks, has since evolved into a device suitable for general-purpose computations. As a result graphics hardware has become progressively more attractive yielding unprecedented performance at a relatively low cost. Thus, it is the ideal candidate to accelerate a wide variety of data parallel tasks in many fields such as in Machine Learning (ML). As problems become more and more demanding, parallel implementations of learning algorithms are crucial for a useful application. In particular, the implementation of Neural Networks (NNs) in GPUs can significantly reduce the long training times during the learning process. In this paper we present a GPU parallel implementation of the Back-Propagation (BP) and Multiple Back-Propagation (MBP) algorithms, and describe the GPU kernels needed for this task. The results obtained on well-known benchmarks show faster training times and improved performances as compared to the implementation in traditional hardware, due to maximized floating-point throughput and memory bandwidth. Moreover, a preliminary GPU based Autonomous Training System (ATS) is developed which aims at automatically finding high-quality NNs-based solutions for a given problem.
BAND SURGERY ON KNOTS AND LINKS
Authors: KANENOBU TAIZO
Published: January 2011

We give some relationships of the Jones and Q polynomials between two links which are related by a band surgery. Then we consider two applications: The first one is to an evaluation of the ribbon-fusion number, the least fusion number of a ribbon knot. The second one is to DNA knot theory, helping us to understand the action of the Xer site-specific recombination at psi site.
SURGERY ON LINKS WITH UNKNOTTED COMPONENTS AND THREE-MANIFOLDS
Authors: GUO YU , YU LI
Published: January 2011

It is shown that any closed three-manifold M obtained by integral surgery on a knot in the three-sphere can always be constructed from integral surgeries on a 3-component link [Formula: see text] with each component being an unknot in the three-sphere. It is also interesting to notice that infinitely many different integral surgeries on the same link [Formula: see text] could give the same three-manifold M.
THE ALGEBRAIC CONCORDANCE ORDER OF A KNOT
Authors: LIVINGSTON CHARLES
Published: January 2011

The algebraic concordance group contains elements of order two, four, and of infinite order. Elements of infinite order are detected by the signature function. This paper develops computable invariants to simplify the computation of the order of torsion classes. The results are applied to determine the algebraic orders of all prime knots of 12 or fewer crossings.
GRAVITATIONAL WAVES FROM COALESCING BINARY SOURCES
Authors: MAIA M. D.
Published: January 2011

Coalescing binary systems (e.g. pulsars, neutron stars and black holes) are currently considered to be the most likely sources of gravitational radiation, yet to be detected on or near Earth, where the local gravitational field is negligible and the Poincaré symmetry rules. On the other hand, the general theory of gravitational waves emitted by axially symmetric rotating sources predicts the existence of a nonvanishing news function. The existence of such function implies that, for a distant observer, the asymptotic group of isometries, the BMS group, has a translational symmetry that depends on the orbit periodicity of the source, thus breaking the isotropy of the Poincaré translations. These results suggest that the asymptotic BMS-covariant wave equation should be applied to obtain a proper theoretical basis for the gravitational waves observations from those binary sources.
SPIN-SURFING THE SPACE–TIME FOAM
Authors: UNNIKRISHNAN C. S. , GILLIES G. T.
Published: January 2011

We present the quantum spin as a novel test tool for probing directly the Planck scale space–time foam of quantum gravity. Quantum fluctuations of spatial support for the electric vector associated with the spin-one photon affect its polarization sufficiently to allow us to gain deep insights and unprecedented constraints on the most important and fundamental aspect of quantum gravity — the fluctuating structure of space–time with a Planck scale three-dimensional web. We show that the survival of strong polarization of X-rays and gamma rays from the Crab Nebula rejects the conventional space–time foam at Planck length scale and constrains the microscopic scale of quantum gravitational fluctuations to below 2 × 10-8l P .
PARALLEL ITERATIVE REGULARIZATION ALGORITHMS FOR LARGE OVERDETERMINED LINEAR SYSTEMS
Authors: ANH PHAM KY , DUNG VU TIEN
Published: January 2011

In this paper, we study the performance of some parallel iterative regularization methods for solving large overdetermined systems of linear equations.
OSCILLATIONS OF A WATER JET WITH A RECTANGULAR SECTION
Authors: ISSHIKI H. , YOON B. S.
Published: January 2011

When we regulate an outflow of water from a kitchen tap or a teapot nozzle, we observe an alternating change in the vertical cross-section. This is basically an oscillation of the cross-section composed of the same fluid particles. The surface tension imparts a recovering force to the oscillation, and the fluid motions provide inertial force. A nonlinear equation of motion for the oscillation is developed for cases neglecting and including gravity. The numerical solution clearly illustrates the nonlinear effects. For example, the oscillation period becomes longer, as the amplitude increases. Experiments are conducted, and the estimated frequency agrees with that determined experimentally.
NONLINEAR STRUCTURAL ANALYSIS USING DYNAMIC RELAXATION METHOD WITH IMPROVED CONVERGENCE RATE
Authors: REZAIEE-PAJAND M. , SARAFRAZI S. R.
Published: January 2011

This paper develops the optimal time-step ratio and the critical damping for nonlinear structural analysis, when using dynamic relaxation method (DRM). The convergence rate of the DRM depends on the value of the time step and the critical damping factor. In the present study, the effect of the time-step ratio is separated from the time-step value. Additionally, the effect of the eigenvalue on the error function is investigated. Using the eigenvalue definition, the critical damping is updated in each dynamic relaxation (DR) step to decrease the required computations. Moreover, the optimal time-step ratio is calculated. It is also shown that the value of the constant time step has no effect on the rate of convergence. The proposed procedure provides a simple and accelerated DRM, which can be used in the linear and nonlinear analyses of structures. The efficiency of the new method was verified by its application to a wide range of typical structures. The results show that the suggested scheme accelerates the convergence rate of the DR process.
LAGRANGE'S FOUR SQUARES THEOREM WITH VARIABLES OF SPECIAL TYPE
Authors: CAI YINGCHUN
Published: January 2011

Let N denote a sufficiently large integer satisfying N ≡ 4 (mod 24), and Pr denote an almost-prime with at most r prime factors, counted according to multiplicity. In this paper, we proved that the equation [Formula: see text] is solvable in one prime and three P42, or in four P13. These results constitute improvements upon that of Heath-Brown and Tolev.
IWASAWA λ-INVARIANTS AND Γ-TRANSFORMS OF p-ADIC MEASURES ON ${\mathbb Z}_{p}^n$
Authors: BARMAN RUPAM , SAIKIA ANUPAM
Published: January 2011

In this paper, we determine a relation between the λ-invariants of a p-adic measure on [Formula: see text] and its Γ-transform. Along the way we also determine p-adic properties of certain Mahler coefficients.
ON A CONJECTURE ON RAMANUJAN PRIMES
Authors: LAISHRAM SHANTA
Published: January 2011

For n ≥ 1, the nth Ramanujan prime is defined to be the smallest positive integer Rn with the property that if x ≥ Rn, then [Formula: see text] where π(ν) is the number of primes not exceeding ν for any ν > 0 and ν ∈ ℝ. In this paper, we prove a conjecture of Sondow on upper bound for Ramanujan primes. An explicit bound of Ramanujan primes is also given. The proof uses explicit bounds of prime π and θ functions due to Dusart.
THE SECOND MOMENT OF THE RIEMANN ZETA FUNCTION WITH UNBOUNDED SHIFTS
Authors: BETTIN SANDRO
Published: January 2011

We prove an asymptotic formula for the second moment (up to height T) of the Riemann zeta function with two shifts. The case we deal with is where the real parts of the shifts are very close to zero and the imaginary parts can grow up to T2-ε, for any ε > 0.
TRANSIENT TEMPERATURE DISTRIBUTION IN HUMAN DERMAL PART WITH PROTECTIVE LAYER AT LOW ATMOSPHERIC TEMPERATURE
Authors: GURUNG D. B. , SAXENA V. P.
Published: January 2011

A mathematical model of temperature distribution in human dermal part under cooling is discussed in this paper. The skin is assumed to be covered by artificial protective layer which absorbs sweat. The metabolic heat generation rate in subcutaneous part is assumed to be decreasing exponentially. Also the quantitative behavior of blood flow rate due to cooling is considered in this part. Finite element approach based on calculus of variations has been employed to solve the model equations with appropriate considerations regarding parameters.
GEOMETRICAL AND TOPOLOGICAL DUALITY IN CROWD DYNAMICS
Authors: IVANCEVIC V. G. , REID D. J.
Published: January 2011

The purpose of this paper is to establish strong theoretical basis for solving practical problems in modeling the behavior of crowds. Based on the previously developed (entropic) geometrical model of crowd behavior dynamics, in this paper we formulate two duality theorems related to the crowd manifold. Firstly, we formulate the geometrical crowd-duality theorem and prove it using Lie-functorial and Riemannian proofs. Secondly, we formulate the topological crowd-duality theorem and prove it using cohomological and homological proofs. After that we discuss the related question of the connection between Lagrangian and Hamiltonian crowd-duality, and finally establish the globally dual structure of crowd dynamics. All used terms from algebraic topology are defined in Appendix A.
Geology, petrology and alteration geochemistry of the Palaeoproterozoic intrusive hosted Älgträsk Au deposit, Northern Sweden
Authors: Bejgarn Therese , Årebäck Hans , Weihed Pär , Nylander Juhani
Published: January 2011

The Älgträsk intrusive hosted Au deposit, Skellefte district, northern Sweden, is situated in the oldest, most heterogeneous part of the
c
. 1.89–1.86 Ga Jörn granitoid complex, which intruded a complex volcano–sedimentary succession in an island arc or continental margin arc environment. The Tallberg porphyry Cu deposit, situated only 3 km west of Älgträsk, is associated with quartz feldspar porphyritic dykes. These dykes are suggested to be genetically related to similar porphyry dykes in Älgträsk and the tonalitic host rock in Tallberg. The granodiorite hosting the Älgträsk Au-deposit does not appear to be genetically related to the tonalite or the porphyry dykes.
Protective cross talk between activated protein C and TNF signaling in vascular endothelial cells: implication of EPCR, noncanonical NF-κB, and ERK1/2 MAP kinases
Authors: Guitton Christophe , Cottereau Alice , Gérard Nathalie , Quillard Thibaut , Chauveau Annabelle , Devallière Julie , Tonnerre Pierre , Charreau Béatrice
Published: January 2011

Activated protein C (APC) is a natural anticoagulant protease that displays cytoprotective and antiinflammatory activities and has been demonstrated to reduce mortality of patients with severe sepsis. However, APC signaling is not fully understood. This study further investigated the antiinflammatory effects of APC in vascular endothelial cells (EC) and examined the cross talk between APC and TNF signaling. Analysis of the regulatory mechanisms mediated by APC on vascular human EC shows that APC impairs TNF signaling by triggering a preemptive activation of intracellular pathways. We found that APC signaling causes a moderate but significant induction of cell adhesion molecules (CAMs) including VCAM-1 at mRNA and protein levels. Activation of the noncanonical NF-κB and ERK1/2 are both pivotal to APC signaling leading to VCAM-1 expression. APC upregulates TNF receptor-associated factor 2 (TRAF2) and phosphorylates NF-κB p65 at Ser276 and Ser536 independently of IκB degradation. The ultimate protective antiinflammatory effect of APC in response to TNF is associated with a sustained activation of ERK1/2 and Akt while phosphorylation of NF-κB p65 is precluded. Inhibitors of ERK (PD98059 and U0126) abolish the antiinflammatory signal mediated by APC. Blocking antibodies and silencing assays also suggest that, in EC, protease-activated receptor 1 and endothelial protein C receptor (EPCR) both conduct ERK activation and VCAM-1 induction in response to APC. To conclude, APC protects EC by attenuating CAM expression during inflammation. APC engages a regulatory cross talk involving EPCR, ERK, and NF-κB that impairs TNF signaling.
Dynamic interplay of excitatory and inhibitory coupling modes of neuronal L-type calcium channels
Authors: Geier Petra , Lagler Michael , Boehm Stefan , Kubista Helmut
Published: January 2011

L-type voltage-gated calcium channels (LTCCs) have long been considered as crucial regulators of neuronal excitability. This role is thought to rely largely on coupling of LTCC-mediated Ca2+ influx to Ca2+-dependent conductances, namely Ca2+-dependent K+ (KCa) channels and nonspecific cation (CAN) channels, which mediate afterhyperpolarizations (AHPs) and afterdepolarizations (ADPs), respectively. However, in which manner LTCCs, KCa channels, and CAN channels co-operate remained scarcely known. In this study, we examined how activation of LTCCs affects neuronal depolarizations and analyzed the contribution of Ca2+-dependent potassium- and cation-conductances. With the use of hippocampal neurons in primary culture, pulsed current-injections were applied in the presence of tetrodotoxin (TTX) for stepwise depolarization and the availability of LTCCs was modulated by BAY K 8644 and isradipine. By varying pulse length and current strength, we found that weak depolarizing stimuli tend to be enhanced by LTCC activation, whereas in the course of stronger depolarizations LTCCs counteract excitation. Both effect modes appear to involve the same channels that mediate ADP and AHP, respectively. Indeed, ADPs were activated at lower stimulation levels than AHPs. In the absence of TTX, activation of LTCCs prolonged or shortened burst firing, depending on the initial burst duration, and invariably augmented brief unprovoked (such as excitatory postsynaptic potentials) and provoked electrical events. Hence, regulation of membrane excitability by LTCCs involves synchronous activity of both excitatory and inhibitory Ca2+-activated ion channels. The overall enhancing or dampening effect of LTCC stimulation on excitability does not only depend on the relative abundance of the respective coupling partner but also on the stimulus intensity.
Concentration of MgSO4in the intestinal lumen ofOpsanus betalimits osmoregulation in response to acute hypersalinity stress
Authors: Genz Janet , McDonald M. Danielle , Grosell Martin
Published: January 2011

Marine teleosts constantly lose water to their surrounding environment, a problem exacerbated in fish exposed to salinity higher than normal seawater. Some fish undergo hypersaline exposures in their natural environments, such as short- and long-term increases in salinity occurring in small tidal pools and other isolated basins, lakes, or entire estuaries. Regardless of the degree of hypersalinity in the ambient water, intestinal absorption of monovalent ions drives water uptake to compensate for water loss, concentrating impermeable MgSO4in the lumen. This study considers the potential of luminal [MgSO4] to limit intestinal water absorption, and therefore osmoregulation, in hypersalinity. The overall tolerance and physiological response of toadfish ( Opsanus beta) to hypersalinity exposure were examined. In vivo, fish in hypersaline waters containing artificially low [MgSO4] displayed significantly lower osmolality in both plasma and intestinal fluids, and increased survival at 85 parts per thousand, indicating improved osmoregulatory ability than in fish exposed to hypersalinity with ionic ratios similar to naturally occurring ratios. Intestinal sac preparations revealed that in addition to the osmotic pressure difference across the epithelium, the luminal ionic composition influenced the absorption of Na+, Cl−, and water. Hypersalinity exposure increased urine flow rates in fish fitted with ureteral catheters regardless of ionic composition of the ambient seawater, but it had no effect on urine osmolality or pH. Overall, concentrated MgSO4within the intestinal lumen, rather than renal or branchial factors, is the primary limitation for osmoregulation by toadfish in hypersaline environments.
GSK3β inactivation in podocytes results in decreased phosphorylation of p70S6Kaccompanied by cytoskeletal rearrangements and inhibited motility
Authors: George Britta , Vollenbröker Beate , Saleem Moin A. , Huber Tobias B. , Pavenstädt Hermann , Weide Thomas
Published: January 2011

The inhibition of mTOR kinase after renal transplantation has been associated with podocyte injury and proteinuria; however, the signaling pathways regulating these effects are not well understood. We found that prolonged rapamycin treatment in podocytes leads to an increase in glycogen synthase kinase 3β (GSK3β) phosphorylation, resulting in inactivation of total GSK3β kinase activity. To investigate the cellular consequences of the inactivation of GSK3β, we used two inhibitors reducing kinase activity and studied the cross talk between GSK3 function and the Akt/mammalian target of rapamycin (mTOR) pathway. Both GSK3 inhibitors reduced the phosphorylation of the mTOR downstream target, p70S6K, indicating that GSK3 inhibition in podocytes is able to cause similar effects as treatment with rapamycin. Moreover, GSK3 inhibition was accompanied by the reduced expression of slit diaphragm-associated proteins and resulted in an altered cytoskeletal structure and reduced motility of podocytes, suggesting that GSK3 kinase can modulate Akt/mTOR-dependent signaling in podocytes.
Chronic sodium-retaining action of insulin in diabetic dogs
Authors: Manhiani M. Marlina , Cormican Michael T. , Brands Michael W.
Published: January 2011

Insulin-mediated sodium retention is implicated as a mechanism for hypertension in metabolic syndrome and type II diabetes. However, there is no direct experimental evidence for a sustained antinatriuretic effect of insulin outside of rodents, and all previous studies in dogs have been negative. This study used a novel approach to test for a chronic sodium-retaining action of insulin in dogs, by testing the hypothesis that natriuresis in type I diabetes is dependent on the decrease in insulin, rather than being due solely to osmotic actions of hyperglycemia. Dogs were chronically instrumented and housed in metabolic cages. Fasting blood glucose in alloxan-treated dogs was maintained at ∼65 mg/dl by continuous intravenous insulin infusion. Then, a 6-day diabetic period was induced by either 1) decreasing the insulin infusion to induce type I diabetes (D; blood glucose = 449 ± 40 mg/dl) or 2) clamping the insulin infusion and infusing glucose continuously (DG; blood glucose = 470 ± 56 mg/dl). Control urinary sodium excretion (UnaV) averaged 70 ± 5 (D) and 69 ± 5 (DG) meq/day and increased on day 1 in both groups. UnaV remained elevated in the D group (115 ± 15 meq/day days 2– 6), but it returned to control in the DG group (69 ± 11 meq/day days 2– 6) and was accompanied by decreased lithium clearance. Thus, insulin had a sustained antinatriuretic action that was triggered by increased glucose, and it was powerful enough to completely block the natriuresis caused by hyperglycemia. These data may reveal an unrecognized physiologic function of insulin as a protector against hyperglycemia-induced salt wasting in diabetes.
1H-NMR-based metabonomic analysis of metabolic profiling in diabetic nephropathy rats induced by streptozotocin
Authors: Zhao Liangcai , Gao Hongchang , Lian Fulin , Liu Xia , Zhao Yongxiang , Lin Donghai
Published: January 2011

Elucidation of the metabolic profiling in diabetic nephropathy (DN) rats is of great assistance for understanding the pathogenesis of DN. In this study,1H-nuclear magnetic resonance (NMR)-based metabonomics combined with HPLC measurements was used to quantitatively analyze the metabolic changes in urine and kidney extracts from diabetic 2-wk and 8-wk rats induced by streptozotocin (STZ). Pattern recognition analysis of either urine or kidney extracts indicated that the two diabetic groups were separated obviously from the control group, suggesting that the metabolic profiles of the diabetic groups were markedly different from the control. The diabetic 8-wk rats showed lower levels of creatine, dimethylamine, and higher levels of ascorbate, succinate, lactate, citrate, allantoin, 2-ketoglutarate, and 3-hydrobutyrate (3-HB) in the urine samples. Moreover, the diabetic 8-wk rats displayed lower levels of succinate, creatine, myo-inositol, alanine, lactate, and ATP, and higher levels of 3-HB and glucose in the kidney extracts. The observed metabolic changes imply the enhanced pathways of either lipid or ketone body synthesis and decreased pathways of either tricarboxylic acid cycle or glycolysis in DN rats compared with the control. Our results suggest that the energy metabolic changes are associated with the pathogenic process of DN.