bluuebunny/crossref_metadata_2025 huggingface dataset:
Multicenter Evaluation of a Commercial Cytomegalovirus Quantitative Standard: Effects of Commutability on Interlaboratory Concordance
Authors: Hayden R. T. , Shahbazian M. D. , Valsamakis A. , Boonyaratanakornkit J. , Cook L. , Pang X. L. , Preiksaitis J. K. , Schönbrunner E. R. , Caliendo A. M.
Published: September 2013

Commutability of quantitative reference materials has proven important for reliable and accurate results in clinical chemistry. As international reference standards and commercially produced calibration material have become available to address the variability of viral load assays, the degree to which such materials are commutable and the effect of commutability on assay concordance have been questioned. To investigate this, 60 archived clinical plasma samples, which previously tested positive for cytomegalovirus (CMV), were retested by five different laboratories, each using a different quantitative CMV PCR assay. Results from each laboratory were calibrated both with lab-specific quantitative CMV standards (“lab standards”) and with common, commercially available standards (“CMV panel”). Pairwise analyses among laboratories were performed using mean results from each clinical sample, calibrated first with lab standards and then with the CMV panel. Commutability of the CMV panel was determined based on difference plots for each laboratory pair showing plotted values of standards that were within the 95% prediction intervals for the clinical specimens. Commutability was demonstrated for 6 of 10 laboratory pairs using the CMV panel. In half of these pairs, use of the CMV panel improved quantitative agreement compared to use of lab standards. Two of four laboratory pairs for which the CMV panel was noncommutable showed reduced quantitative agreement when that panel was used as a common calibrator. Commutability of calibration material varies across different quantitative PCR methods. Use of a common, commutable quantitative standard can improve agreement across different assays; use of a noncommutable calibrator can reduce agreement among laboratories.
Actinomyces urogenitalis Bacteremia and Tubo-Ovarian Abscess after an
In Vitro
Fertilization (IVF) Procedure
Authors: Van Hoecke Frederik , Beuckelaers Ellen , Lissens Peter , Boudewijns Michael
Published: September 2013

We describe the first case of bacteremia due to
Actinomyces urogenitalis
. Bacteremia was secondary to a tubo-ovarian abscess following transvaginal oocyte retrieval. Identification was established by matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and confirmed by 16S rRNA gene sequencing.
A. urogenitalis
should be considered as a potential causative agent of infection after gynecological procedures.
Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin Receptor Binding Site
Authors: Hong Minsun , Lee Peter S. , Hoffman Ryan M. B. , Zhu Xueyong , Krause Jens C. , Laursen Nick S. , Yoon Sung-il , Song Langzhou , Tussey Lynda , Crowe James E. , Ward Andrew B. , Wilson Ian A.
Published: September 2013

Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in antigenicity but fortunately was not nearly as deadly. 5J8 is a human antibody that potently neutralizes a broad spectrum of H1N1 viruses, including the 1918 and 2009 pandemic viruses. Here, we present the crystal structure of 5J8 Fab in complex with a bacterially expressed and refolded globular head domain from the hemagglutinin (HA) of the A/California/07/2009 (H1N1) pandemic virus. 5J8 recognizes a conserved epitope in and around the receptor binding site (RBS), and its HCDR3 closely mimics interactions of the sialic acid receptor. Electron microscopy (EM) reconstructions of 5J8 Fab in complex with an HA trimer from a 1986 H1 strain and with an engineered stabilized HA trimer from the 2009 H1 pandemic virus showed a similar mode of binding. As for other characterized RBS-targeted antibodies, 5J8 uses avidity to extend its breadth and affinity against divergent H1 strains. 5J8 selectively interacts with HA insertion residue 133a, which is conserved in pandemic H1 strains and has precluded binding of other RBS-targeted antibodies. Thus, the RBS of divergent HAs is targeted by 5J8 and adds to the growing arsenal of common recognition motifs for design of therapeutics and vaccines. Moreover, consistent with previous studies, the bacterially expressed H1 HA properly refolds, retaining its antigenic structure, and presents a low-cost and rapid alternative for engineering and manufacturing candidate flu vaccines.
An Amino Acid of Human Parainfluenza Virus Type 3 Nucleoprotein Is Critical for Template Function and Cytoplasmic Inclusion Body Formation
Authors: Zhang Shengwei , Chen Longyun , Zhang Guangyuan , Yan Qin , Yang Xiaodan , Ding Binbin , Tang Qiaopeng , Sun Shengjun , Hu Zhulong , Chen Mingzhou
Published: September 2013

The nucleoprotein (N) and phosphoprotein (P) interaction of nonsegmented negative-strand RNA viruses is essential for viral replication; this includes N
0
-P (N
0
, free of RNA) interaction and the interaction of N-RNA with P. The precise site(s) within N that mediates the N-P interaction and the detailed regulating mechanism, however, are less clear. Using a human parainfluenza virus type 3 (HPIV3) minigenome assay, we found that an N mutant (N
L478A
) did not support reporter gene expression. Using
in vivo
and
in vitro
coimmunoprecipitation, we found that N
L478A
maintains the ability to form N
L478A
0
-P, to self-assemble, and to form N
L478A
-RNA but that N
L478A
-RNA does not interact with P. Using an immunofluorescence assay, we found that N-P interaction provides the minimal requirement for the formation of cytoplasmic inclusion bodies, which contain viral RNA, N, P, and polymerase in HPIV3-infected cells. N
L478A
was unable to form inclusion bodies when coexpressed with P, but the presence of N rescued the ability of N
L478A
to form inclusion bodies and the transcriptional function of N
L478A
, thereby suggesting that hetero-oligomers formed by N and N
L478A
are functional and competent to form inclusion bodies. Furthermore, we found that N
L478A
is also defective in virus growth. To our knowledge, we are the first to use a paramyxovirus to identify a precise amino acid within N that is critical for N-RNA and P interaction but not for N
0
-P interaction for the formation of inclusion bodies, which appear to be bona fide sites of RNA synthesis.
The Structure and Host Entry of an Invertebrate Parvovirus
Authors: Meng Geng , Zhang Xinzheng , Plevka Pavel , Yu Qian , Tijssen Peter , Rossmann Michael G.
Published: September 2013

The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (
Acheta domesticus
densovirus [
Ad
DNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the
Ad
DNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid.
In vitro
, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.
A Direct and Versatile Assay Measuring Membrane Penetration of Adenovirus in Single Cells
Authors: Suomalainen Maarit , Luisoni Stefania , Boucke Karin , Bianchi Sarah , Engel Daniel A. , Greber Urs F.
Published: September 2013

Endocytosis is the most prevalent entry port for viruses into cells, but viruses must escape from the lumen of endosomes to ensure that viral genomes reach a site for replication and progeny formation. Endosomal escape also helps viruses bypass endolysosomal degradation and presentation to certain Toll-like intrinsic immunity receptors. The mechanisms for cytosolic delivery of nonenveloped viruses or nucleocapsids from enveloped viruses are poorly understood, in part because no quantitative assays are readily available which directly measure the penetration of viruses into the cytosol. Following uptake by clathrin-mediated endocytosis or macropinocytosis, the nonenveloped adenoviruses penetrate from endosomes to the cytosol, and they traffic with cellular motors on microtubules to the nucleus for replication. In this report, we present a novel single-cell imaging assay which quantitatively measures individual cytosolic viruses and distinguishes them from endosomal viruses or viruses at the plasma membrane. Using this assay, we showed that the penetration of human adenoviruses of the species C and B occurs rapidly after virus uptake. Efficient penetration does not require acidic pH in endosomes. This assay is versatile and can be adapted to other adenoviruses and members of other nonenveloped and enveloped virus families.
Middle East Respiratory Syndrome Coronavirus Accessory Protein 4a Is a Type I Interferon Antagonist
Authors: Niemeyer Daniela , Zillinger Thomas , Muth Doreen , Zielecki Florian , Horvath Gabor , Suliman Tasnim , Barchet Winfried , Weber Friedemann , Drosten Christian , Müller Marcel A.
Published: September 2013

Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe acute respiratory infection with as yet unclear epidemiology. We previously showed that MERS-CoV counteracts parts of the innate immune response in human bronchiolar cells. Here we analyzed accessory proteins 3, 4a, 4b, and 5 for their abilities to inhibit the type I interferon response. Accessory protein 4a was found to block interferon induction at the level of melanoma differentiation-associated protein 5 (MDA5) activation presumably by direct interaction with double-stranded RNA.
Structural Analysis of the Hemagglutinin from the Recent 2013 H7N9 Influenza Virus
Authors: Yang Hua , Carney Paul J. , Chang Jessie C. , Villanueva Julie M. , Stevens James
Published: September 2013

In March 2013, the Chinese Center for Disease Control and Prevention reported human infections with an H7N9 influenza virus, and by 20 July 2013, the numbers of laboratory-confirmed cases had climbed to 134, including 43 fatalities and 127 hospitalizations. The newly emerging H7N9 viruses constitute an obvious public health concern because of the apparent severity of this outbreak. Here we focus on the hemagglutinins (HAs) of these viruses and assess their receptor binding phenotype in relation to previous HAs studied. Glycan microarray and kinetic analyses of recombinant A(H7N9) HAs were performed to compare the receptor binding profile of wild-type receptor binding site variants at position 217, a residue analogous to one of two positions known to switch avian to human receptor preference in H2N2 and H3N2 viruses. Two recombinant A(H7N9) HAs were structurally characterized, and a mutational study of the receptor binding site was performed to analyze important residues that can affect receptor preference and affinity. Results highlight a weak human receptor preference of the H7N9 HAs, suggesting that these viruses require further adaptation in order to adapt fully to humans.
Kaposi's Sarcoma-Associated Herpesvirus K7 Modulates Rubicon-Mediated Inhibition of Autophagosome Maturation
Authors: Liang Qiming , Chang Brian , Brulois Kevin F. , Castro Kamilah , Min Chan-Ki , Rodgers Mary A. , Shi Mude , Ge Jianning , Feng Pinghui , Oh Byung-Ha , Jung Jae U.
Published: September 2013

Autophagy is an important innate safeguard mechanism for protecting an organism against invasion by pathogens. We have previously discovered that Kaposi's sarcoma-associated herpesvirus (KSHV) evades this host defense through tight suppression of autophagy by targeting multiple steps of autophagy signal transduction. Here, we report that KSHV K7 protein interacts with Rubicon autophagy protein and inhibits the autophagosome maturation step by blocking Vps34 enzymatic activity, further highlighting how KSHV deregulates autophagy-mediated host immunity for its life cycle.
Homologous Recombination in E3 Genes of Human Adenovirus Species D
Authors: Singh Gurdeep , Robinson Christopher M. , Dehghan Shoaleh , Jones Morris S. , Dyer David W. , Seto Donald , Chodosh James
Published: September 2013

Genes within the E3 transcription unit of human adenoviruses modulate host immune responses to infection. A comprehensive genomics and bioinformatics analysis of the E3 transcription unit for 38 viruses within human adenovirus species D (HAdV-D) revealed distinct and surprising patterns of homologous recombination. Homologous recombination was identified in open reading frames for E3 CR1α, CR1β, and CR1γ, similar to that previously observed with genes encoding the three major structural capsid proteins, the penton base, hexon, and fiber.
Structure, Adsorption to Host, and Infection Mechanism of Virulent Lactococcal Phage p2
Authors: Bebeacua Cecilia , Tremblay Denise , Farenc Carine , Chapot-Chartier Marie-Pierre , Sadovskaya Irina , van Heel Marin , Veesler David , Moineau Sylvain , Cambillau Christian
Published: September 2013

Lactococcal siphophages from the 936 and P335 groups infect the Gram-positive bacterium
Lactococcus lactis
using receptor binding proteins (RBPs) attached to their baseplate, a large multiprotein complex at the distal part of the tail. We have previously reported the crystal and electron microscopy (EM) structures of the baseplates of phages p2 (936 group) and TP901-1 (P335 group) as well as the full EM structure of the TP901-1 virion. Here, we report the complete EM structure of siphophage p2, including its capsid, connector complex, tail, and baseplate. Furthermore, we show that the p2 tail is characterized by the presence of protruding decorations, which are related to adhesins and are likely contributed by the major tail protein C-terminal domains. This feature is reminiscent of the tail of
Escherichia coli
phage λ and
Bacillus subtilis
phage SPP1 and might point to a common mechanism for establishing initial interactions with their bacterial hosts. Comparative analyses showed that the architecture of the phage p2 baseplate differs largely from that of lactococcal phage TP901-1. We quantified the interaction of its RBP with the saccharidic receptor and determined that specificity is due to lower
k
off
values of the RBP/saccharidic dissociation. Taken together, these results suggest that the infection of
L. lactis
strains by phage p2 is a multistep process that involves reversible attachment, followed by baseplate activation, specific attachment of the RBPs to the saccharidic receptor, and DNA ejection.
A Single Amino Acid Mutation in the Envelope Cytoplasmic Tail Restores the Ability of an Attenuated Simian Immunodeficiency Virus Mutant To Deplete Mucosal CD4
+
T Cells
Authors: Breed Matthew W. , Jordan Andrea P. O. , Aye Pyone P. , Sugimoto Chie , Alvarez Xavier , Kuroda Marcelo J. , Pahar Bapi , Keele Brandon F. , Hoxie James A. , Lackner Andrew A.
Published: September 2013

Disruption of the conserved motif GYxxØ in the simian immunodeficiency virus (SIV) SIVmac239 envelope (Env) cytoplasmic tail resulted in a virus (ΔGY) that exhibited a high plasma peak but uniquely failed to acutely deplete mucosal CD4
+
T cells. Here, we show that ΔGY containing a flanking S727P mutation that was acquired in ΔGY-infected macaques reacquired the ability to rapidly deplete CD4
+
T cells in lamina propria. This suggests that the GYxxØ motif and S727P each contribute to SIV's targeting to mucosal tissues.
Influenza A Virus Proteins NS1 and Hemagglutinin Along with M2 Are Involved in Stimulation of Autophagy in Infected Cells
Authors: Zhirnov O. P. , Klenk H. D.
Published: September 2013

The NS1 protein of influenza A virus is known to downregulate apoptosis early in infection in order to support virus replication (O. P. Zhirnov, T. E. Konakova, T. Wolff, and H. D. Klenk, J. Virol. 76:1617–1625, 2002). In the present study, we analyzed the development of autophagy, another mechanism to protect cells from degradation that depends on NS1 expression. To this end, we compared autophagy in cells infected with wild-type (WT) influenza virus and virus lacking the NS1 gene (delNS1 virus). The results show that in WT-infected cells but not in delNS1 virus-infected cells, synthesis of the autophagy marker LC3-II, the lipidated form of microtubule light chain-associated protein LC3, is stimulated and that LC3-II accumulates in a perinuclear zone enriched with double-layered membrane vesicles characteristic of autophagosomes. Transfection experiments revealed that NS1 expressed alone was unable to upregulate autophagy, whereas hemagglutinin (HA) and M2 were. Proteolytic cleavage of HA increased autophagy. Taken together, these observations indicate that NS1 stimulates autophagy indirectly by upregulating the synthesis of HA and M2. Thus, it appears that NS1, besides downregulating apoptosis, is involved in upregulation of autophagy and that it supports the survival of infected cells by both mechanisms.
The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns
Authors: Naccache Samia N. , Greninger Alexander L. , Lee Deanna , Coffey Lark L. , Phan Tung , Rein-Weston Annie , Aronsohn Andrew , Hackett John , Delwart Eric L. , Chiu Charles Y.
Published: September 2013

Next-generation sequencing was used for discovery and
de novo
assembly of a novel, highly divergent DNA virus at the interface between the
Parvoviridae
and
Circoviridae
. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.
Epstein-Barr Virus Induces Global Changes in Cellular mRNA Isoform Usage That Are Important for the Maintenance of Latency
Authors: Homa Nicholas J. , Salinas Raul , Forte Eleonora , Robinson Timothy J. , Garcia-Blanco Mariano A. , Luftig Micah A.
Published: September 2013

Oncogenic viruses promote cell proliferation through the dramatic reorganization of host transcriptomes. In addition to regulating mRNA abundance, changes in mRNA isoform usage can have a profound impact on the protein output of the transcriptome. Using Epstein-Barr virus (EBV) transformation of primary B cells, we have studied the ability of an oncogenic virus to alter the mRNA isoform profile of its host. Using the algorithm called SplicerEX with two complementary Affymetrix microarray platforms, we uncovered 433 mRNA isoform changes regulated by EBV during B-cell transformation. These changes were largely orthogonal with the 2,163 mRNA abundance changes observed during transformation, such that less than one-third of mRNAs changing at the level of isoform also changed in overall abundance. While we observed no preference for a mechanistic class of mRNA isoform change, we detected a significant shortening of 3′ untranslated regions and exclusion of cassette exons in EBV-transformed cells relative to uninfected B cells. Gene ontology analysis of the mRNA isoform changes revealed significant enrichment in nucleic acid binding proteins. We validated several of these isoform changes and were intrigued by those in two mRNAs encoding the proteins XBP1 and TCF4, which have both been shown to bind and activate the promoter of the major EBV lytic
trans
-activator BZLF1. Our studies indicate that EBV latent infection promotes the usage of mRNA isoforms of XBP1 and TCF4 that restrict BZLF1 activation. Therefore, characterization of global changes in mRNA isoform usage during EBV infection identifies a new mechanism for the maintenance of latent infection.
Hyponatraemia induced hyperCKaemia
Authors: Khandhadiya Ketki , Prabhu Krishnananda , Shivashankara K N , Rao Pragna
Published: September 2013

A 32-year-old woman presented to Kasturba Hospital, Manipal with the features of gastroenteritis and one episode of generalised tonic clonic seizure with loss of consciousness for 5 min. No abnormalities were found during neurological examination. Her baseline investigations showed low sodium, low serum osmolality, normal renal and liver function tests, urine myoglobin and antinuclear antibodies profile were negative. Incidentally her creatine kinase (CK) levels were found to be very high. She was treated with intravenous fluids and high salt diet for hyponatraemia. With correction of hyponatraemia, CK levels also improved, suggesting the probable diagnosis of hyponatraemia induced myopathy leading to hyperCKaemia. The importance of early recognition of this potentially-dangerous and rare condition is emphasised.
Emergency Care Handover (ECHO study) across care boundaries: the need for joint decision making and consideration of psychosocial history
Authors: Sujan Mark A , Chessum Peter , Rudd Michelle , Fitton Laurence , Inada-Kim Matthew , Spurgeon Peter , Cooke Matthew W
Published: September 2013

Background

Inadequate handover in emergency care is a threat to patient safety. Handover across care boundaries poses particular problems due to different professional, organisational and cultural backgrounds. While there have been many suggestions for standardisation of handover content, relatively little is known about the verbal behaviours that shape handover conversations. This paper explores both what is communicated (content) and how this is communicated (verbal behaviours) during different types of handover conversations across care boundaries in emergency care.

Methods

Three types of interorganisational (ambulance service to emergency department (ED) in ‘resuscitation’ and ‘majors’ areas) and interdepartmental handover conversations (referrals to acute medicine) were audio recorded in three National Health Service EDs. Handover conversations were segmented into utterances. Frequency counts for content and language forms were derived for each type of handover using Discourse Analysis. Verbal behaviours were identified using Conversation Analysis.

Results

203 handover conversations were analysed. Handover conversations involving ambulance services were predominantly descriptive (60%–65% of utterances), unidirectional and focused on patient presentation (75%–80%). Referrals entailed more collaborative talk focused on the decision to admit and immediate care needs. Across all types of handover, only 1.5%–5% of handover conversation content related to the patient's social and psychological needs.

Conclusions

Handover may entail both descriptive talk aimed at information transfer and collaborative talk aimed at joint decision-making. Standardisation of handover needs to accommodate collaborative aspects and should incorporate communication of information relevant to the patient's social and psychological needs to establish appropriate care arrangements at the earliest opportunity.
Liquefaction potential evaluations: energy-based method versus stress-based method
Authors: Kokusho Takaji
Published: September 2013

A dataset of undrained cyclic triaxial tests for liquefaction with parametrically changing relative density and fines content is reviewed and interpreted in the scope of energy. It is found that the strain amplitude or pore-pressure buildup during cyclic loading is uniquely correlated not only to the energy dissipated in soil specimens, but also to strain energy given from outside. Hence, an energy-based method (EBM) is developed in which liquefaction potential can be evaluated by comparing strain energy for liquefaction in a sand layer with upcoming seismic energy without regard to the differences in seismic motions. Comparative studies in soil models demonstrate that the effect of various input motions is intrinsically included in EBM, whereas it has to be considered by choosing proper coefficients in a conventional stress-based method (SBM). Another significant difference is that liquefaction potential tends to be higher for a shallower depth in EBM, while it is vice versa in SBM in a uniform sand deposit.
Using pollutant release and transfer register data in human health research: a scoping review
Authors: Wine Osnat , Hackett Cian , Campbell Sandy , Cabrera-Rivera Orlando , Buka Irena , Zaiane Osmar , DeVito Stephen C. , Osornio-Vargas Alvaro
Published: September 2013

Pollutant release and transfer registers (PRTRs) collect and provide information on chemicals released to the environment or otherwise managed as waste. They support the public’s right-to-know and provide useful information in gauging performance of facilities, sectors, and governments. The extent to which these data have been used in research, particularly in relation to human health, has not been documented. In this scoping review our objective was to learn from scholarly literature the extent and nature of the use of PRTR data in human health research. We performed literature searches (1994–2011) using various search engines and (or) key words. Articles selected for review were chosen following predefined criteria, to extract and analyze data. One hundred and eighty four papers were identified. Forty investigated possible relations with health outcomes: 33 of them identified positive associations. The rest explored other uses of PRTR data. Papers identified challenges, some imputable to the PRTR. We conclude that PRTR data are useful for research, including health-related studies, and have significant potential for prioritizing research needs that can influence policy, management, and ultimately human health. In spite of their inherent limitations, PRTRs represent a perfectible, unique useful source, whose application to human health research appears to be underutilized. Developing strategies to overcome these limitations could improve data quality and increase its utility in future environmental health research and policy applications.
SOLUTION OF THE DIRAC EQUATION WITH POSITION-DEPENDENT MASS IN A COULOMB AND SCALAR FIELDS IN A CONICAL SPACETIME
Authors: MARQUES GEUSA DE A. , BEZERRA V. B. , DONG SHI-HAI
Published: September 2013

We consider the problem of a relativistic particle with position-dependent mass in the presence of a Coulomb and a scalar potentials in the background spacetime generated by a cosmic string. The scalar potential arises from the self-interaction potential which is induced by the conical geometry of the spacetime under consideration. We find the solution of the corresponding Dirac equation and determine the energy spectrum of the particle. The behavior of the energy levels on the parameters associated with the presence of the cosmic string and with the fact that the mass of the particle depends on its position is also analyzed.
EFFECT OF EXTERNAL PERIODIC PULSES ON SPIRAL DYNAMICS AND CONTROL OF SPIRAL WAVES
Authors: YUAN GUO-YONG , WANG XIAO-MING , WANG GUANG-RUI , YANG SHI-PING
Published: September 2013

In this paper, we study the effect of external periodic pulses on spiral dynamics. Resonant entrainment bands were observed on the period T-axis, and T is close to rational multiples of the path curvature period of the spiral tip on the bands. It is also shown that spiral waves are drifted and eliminated by applying the driving method with suitable control parameters, and we reveal the mechanism which forces the spiral wave to periodically shift and rotate. In the domain near the spiral tip, the bidirectional wave excitations are periodically generated by external pulses, and each excitation induces a straight drift of the spiral wave tip. Numerical results show that the parameter range of the external pulse period T, used to successfully eliminate spiral waves, is broaden by appropriately increasing the values of the pulse width and the amplitude. The low-amplitude control scheme is operable in many real systems, and its study is beneficial to understand the forced spiral dynamics.
COMPUTING PUSH PLANS FOR DISK-SHAPED ROBOTS
Authors: DE BERG MARK , GERRITS DIRK H. P.
Published: September 2013

Suppose we want to move a passive object along a given path, among obstacles in the plane, by pushing it with an active robot. We present two algorithms to compute a push plan for the case that the object and robot are disks and the obstacles are non-intersecting line segments. (When only the object's destination and not its full path is given these algorithms can still be used as subroutines in a larger algorithm to compute such a path.) The first algorithm assumes that the robot must maintain contact with the object at all times, and produces a shortest path. There are also situations, however, where the robot has no choice but to let go of the object occasionally. Our second algorithm handles such cases, but no longer guarantees that the produced path is the shortest possible.
Multiple scattering of electromagnetic waves by finitely many point-like obstacles
Authors: Challa Durga Prasad , Hu Guanghui , Sini Mourad
Published: September 2013

This paper is concerned with the direct and inverse time-harmonic electromagnetic scattering problems for a finite number of isotropic point-like obstacles in three dimensions. In the first part, we show that the representation of scattered fields obtained using the Foldy physical assumption "on the proportionality of the strength of the scattered wave on a given scatterer to the external field on it" is the same as the one derived from the model corresponding to the scattering by Dirac-like refraction indices. Using the regularization approach known in quantum mechanics, we rigorously deduce the solution operator (Green's tensor) of the last model in appropriate weighted spaces. Intermediate levels of the scattering between the Born and Foldy models are also described. In the second part, we apply the MUSIC algorithm to the inverse problem of detecting both the position of point-like scatterers and the scattering coefficients attached to them from the far-field measurements of finitely many incident plane waves, with an emphasis on discussing the effect of multiple scattering.
THE ROLE OF TASTE AFFINITY IN AGENT-BASED MODELS FOR SOCIAL RECOMMENDATION
Authors: CIMINI GIULIO , ZENG AN , MEDO MATÚŠ , CHEN DUANBING
Published: September 2013

In the Internet era, online social media emerged as the main tool for sharing opinions and information among individuals. In this work, we study an adaptive model of a social network where directed links connect users with similar tastes, and over which information propagates through social recommendation. Agent-based simulations of two different artificial settings for modeling user tastes are compared with patterns seen in real data, suggesting that users differing in their scope of interests is a more realistic assumption than users differing only in their particular interests. We further introduce an extensive set of similarity metrics based on users' past assessments, and evaluate their use in the given social recommendation model with both artificial simulations and real data. Superior recommendation performance is observed for similarity metrics that give preference to users with small scope — who thus act as selective filters in social recommendation.
SCENARIO ANALYSIS OF TECHNOLOGY PRODUCTS WITH AN AGENT-BASED SIMULATION AND DATA MINING FRAMEWORK
Authors: SHINDE AMIT , HAGHNEVIS MOEED , JANSSEN MARCO A. , RUNGER GEORGE C. , JANAKIRAM MANI
Published: September 2013

A framework is presented to simulate and analyze the effect of multiple business scenarios on the adoption behavior of a group of technology products. Diffusion is viewed as an emergent phenomenon that results from the interaction of consumers. An agent-based model is used in which potential adopters of technology product are allowed to be influenced by their local interactions within the social network. Along with social influence, the effect of product features is important and we ascribe feature sensing attributes to the consumer agents along with sensitivities to social influence. The model encompasses utility theory and discrete choice models in the decision-making process for the consumers. We use expressive machine learning algorithms that can handle complex, nonlinear, and interactive effects to identify important inputs that contribute to the model and to graphically summarize their effects. We present a realistic case study that demonstrates the ability of this framework to model changes in market shares for a group of products in response to business scenarios such as new product introduction and product discontinuation under different pricing strategies. The models and other tools developed here are envisioned to be a part of a recommender system that provides insights into the effects of various business scenarios on shaping market shares of different product groups.
COMPARISON OF MACROMOLECULAR COMPONENT DISTRIBUTIONS IN OSTEOARTHRITIC AND HEALTHY CARTILAGES BY FOURIER TRANSFORM INFRARED IMAGING
Authors: YIN JIANHUA , XIA YANG , XIAO ZHIYAN
Published: September 2013

Fourier transform infrared imaging (FTIRI) was used to examine the depth-dependent content variations of macromolecular components, collagen and proteoglycan (PG), in osteoarthritic and healthy cartilages. Dried 6 μm thick sections of canine knee cartilages were imaged at 6.25 μm pixel-size in FTIRI. By analyzing the infrared (IR) images and spectra, the depth dependence of characteristic band (sugar) intensity of PG show obvious difference between the cartilage sections of (OA) and health. The result confirms that PG content decreases in the osteoarthritic cartilage. However, no clear change occurs to collagen, suggesting that the OA influences little on the collagen content at early stage of OA. This observation will be helpful to further understand PG loss associated with pathological conditions in OA, and demonstrates that FTIRI has the potential to become an important analytical tool to identify early clinical signs of tissue degradation, such as PG loss even collagen disruption.
Finite element model to study the effect of exogenous buffer on calcium dynamics in dendritic spines
Authors: Jha Amrita , Adlakha Neeru
Published: September 2013

Dendritic spine plays an important role in calcium regulation in a neuron cell. It serves as a storage site for synaptic strength and receives input from a single synapse of axon. In order to understand the calcium dynamics in a neuron cell, it is crucial to understand the calcium dynamics in dendritic spines. In this paper, an attempt has been made to study the calcium dynamics due to the exogenous buffers, in dendritic spines with the help of a sectional model. The compartments of dendritic spines are discretized using triangular elements. Appropriate boundary conditions have been framed. Finite element method has been employed to obtain the solution in the region for a two-dimensional unsteady state case. MATLAB 7.11 is used for simulation of the problem and numerical computations. The numerical results have been used to study the effect of exogenous buffers on calcium distribution in dendritic spines.
The Wonderful World of Archaeal Viruses
Authors: Prangishvili David
Published: September 2013

This review presents a personal account of research on archaeal viruses and describes many new viral species and families, demonstrating that viruses of Archaea constitute a distinctive part of the virosphere and display morphotypes that are not associated with the other two domains of life, Bacteria and Eukarya. I focus primarily on viruses that infect hyperthermophilic members of the phylum Crenarchaeota. These viruses' distinctiveness extends from their morphotypes to their genome sequences and the structures of the proteins they encode. Moreover, the mechanisms underlying the interactions of these viruses with their hosts also have unique features. Studies of archaeal viruses provide new perspectives concerning the nature, diversity, and evolution of virus-host interactions. Considering these studies, I associate the distinctions between bacterial and archaeal viruses with the fundamental differences in the envelope compositions of their host cells.
FusariumPathogenomics
Authors: Ma Li-Jun , Geiser David M. , Proctor Robert H. , Rooney Alejandro P. , O'Donnell Kerry , Trail Frances , Gardiner Donald M. , Manners John M. , Kazan Kemal
Published: September 2013

Fusarium is a genus of filamentous fungi that contains many agronomically important plant pathogens, mycotoxin producers, and opportunistic human pathogens. Comparative analyses have revealed that the Fusarium genome is compartmentalized into regions responsible for primary metabolism and reproduction (core genome), and pathogen virulence, host specialization, and possibly other functions (adaptive genome). Genes involved in virulence and host specialization are located on pathogenicity chromosomes within strains pathogenic to tomato (Fusarium oxysporum f. sp. lycopersici) and pea (Fusarium ‘solani’ f. sp. pisi). The experimental transfer of pathogenicity chromosomes from F. oxysporum f. sp. lycopersici into a nonpathogen transformed the latter into a tomato pathogen. Thus, horizontal transfer may explain the polyphyletic origins of host specificity within the genus. Additional genome-scale comparative and functional studies are needed to elucidate the evolution and diversity of pathogenicity mechanisms, which may help inform novel disease management strategies against fusarial pathogens.
TRP channel Ca2+ sparklets: fundamental signals underlying endothelium-dependent hyperpolarization
Authors: Sullivan Michelle N. , Earley Scott
Published: September 2013

Important functions of the vascular endothelium, including permeability, production of antithrombotic factors, and control of vascular tone, are regulated by changes in intracellular Ca2+. The molecular identities and regulation of Ca2+ influx channels in the endothelium are incompletely understood, in part because of experimental difficulties associated with application of patch-clamp electrophysiology to native endothelial cells. However, advances in confocal and total internal reflection fluorescence microscopy and the development of fast, high-affinity Ca2+-binding fluorophores have recently allowed for direct visualization and characterization of single-channel transient receptor potential (TRP) channel Ca2+ influx events in endothelial cells. These events, called “TRP channel Ca2+ sparklets,” have been optically recorded from primary endothelial cells and the intact endothelium, and the biophysical properties and fundamental significance of these Ca2+ signals in vasomotor regulation have been characterized. This review will first briefly discuss the role of endothelial cell TRP channel Ca2+ influx in endothelium-dependent vasodilation, describe improved methods for recording unitary TRP channel activity using optical methods, and highlight discoveries regarding the regulation and physiological significance of TRPV4 Ca2+ sparklets in the vascular endothelium enabled by this new technology. Perspectives on the potential use of these techniques to evaluate changes in TRP channel Ca2+ influx activity associated with endothelial dysfunction are offered.
Roux-en-Y gastric bypass surgery reduces bone mineral density and induces metabolic acidosis in rats
Authors: Abegg Kathrin , Gehring Nicole , Wagner Carsten A. , Liesegang Annette , Schiesser Marc , Bueter Marco , Lutz Thomas A.
Published: September 2013

Roux-en-Y gastric bypass (RYGB) surgery leads to bone loss in humans, which may be caused by vitamin D and calcium malabsorption and subsequent secondary hyperparathyroidism. However, because these conditions occur frequently in obese people, it is unclear whether they are the primary causes of bone loss after RYGB. To determine the contribution of calcium and vitamin D malabsorption to bone loss in a rat RYGB model, adult male Wistar rats were randomized for RYGB surgery, sham-operation–ad libitum fed, or sham-operation–body weight-matched. Bone mineral density, calcium and phosphorus balance, acid-base status, and markers of bone turnover were assessed at different time points for 14 wk after surgery. Bone mineral density decreased for several weeks after RYGB. Intestinal calcium absorption was reduced early after surgery, but plasma calcium and parathyroid hormone levels were normal. 25-hydroxyvitamin D levels decreased, while levels of active 1,25-dihydroxyvitamin D increased after surgery. RYGB rats displayed metabolic acidosis due to increased plasma lactate levels and increased urinary calcium loss throughout the study. These results suggest that initial calcium malabsorption may play a key role in bone loss early after RYGB in rats, but other factors, including chronic metabolic acidosis, contribute to insufficient bone restoration after normalization of intestinal calcium absorption. Secondary hyperparathyroidism is not involved in postoperative bone loss. Upregulated vitamin D activation may compensate for any vitamin D malabsorption.
Early postweaning exercise improves central leptin sensitivity in offspring of rat dams fed high-fat diet during pregnancy and lactation
Authors: Sun Bo , Liang Nu-Chu , Ewald Erin R. , Purcell Ryan H. , Boersma Gretha J. , Yan Jianqun , Moran Timothy H. , Tamashiro Kellie L. K.
Published: September 2013

Maternal high-fat (HF) diet has long-term consequences on the metabolic phenotype of the offspring. Here, we determined the effects of postweaning exercise in offspring of rat dams fed HF diet during gestation and lactation. Pregnant Sprague-Dawley rats were maintained on chow or HF diet throughout gestation and lactation. All pups were weaned onto chow diet on postnatal day (PND) 21. At 4 wk of age, male pups were given free access to running wheels (RW) or remained sedentary (SED) for 3 wk, after which all rats remained sedentary, resulting in four groups: CHOW-SED, CHOW-RW, HF-SED, and HF-RW. Male HF offspring gained more body weight by PND7 compared with CHOW pups and maintained this weight difference through the entire experiment. Three weeks of postweaning exercise did not affect body weight gain in either CHOW or HF offspring, but reduced adiposity in HF offspring. Plasma leptin was decreased at the end of the 3-wk running period in HF-RW rats but was not different from HF-SED 9 wk after the exercise period ended. At 14 wk of age, intracerebroventricular injection of leptin suppressed food intake in CHOW-SED, CHOW-RW, and HF-RW, while it did not affect food intake in HF-SED group. At death, HF-RW rats also had higher leptin-induced phospho-STAT3 level in the arcuate nucleus than HF-SED rats. Both maternal HF diet and postweaning exercise had effects on hypothalamic neuropeptide and receptor mRNA expression in adult offspring. Our data suggest that postweaning exercise improves central leptin sensitivity and signaling in this model.
CD44v3-v10 reduces the profibrotic effects of TGF-β1 and attenuates tubular injury in the early stage of chronic obstructive nephropathy
Authors: Rampanelli Elena , Rouschop Kasper , Teske Gwendoline J. D. , Claessen Nike , Leemans Jaklien C. , Florquin Sandrine
Published: September 2013

CD44 family members are cell surface glycoproteins, which are expressed on tubular epithelial cells (TEC) solely upon kidney injury and are involved in renal fibrosis development. Renal interstitial fibrosis is the final manifestation of chronic kidney diseases and is regulated by a complex network of cytokines, including the profibrotic factor transforming growth factor-β1 (TGF-β1) and the two antifibrotic cytokines bone morphogenic protein-7 (BMP-7) and hepatocyte growth factor (HGF). The present study investigates the potential role of CD44 standard (CD44s) and CD44v3-v10 (CD44v3) isoforms as modulators of the balance between TGF-β1 and HGF/BMP-7. CD44s is the shortest and most common isoform. CD44v3-v10 (CD44v3) has heparan sulfate moieties, which enable the binding to HGF/BMP-7, and hence, might exert renoprotective effects. Using transgenic mice overexpressing either CD44s or CD44v3 specifically on proximal TEC, we found that in vitro the overexpression of CD44v3 on primary TEC renders cells less susceptible to TGF-β1 profibrotic actions and more sensitive to BMP-7 and HGF compared with TEC overexpressing CD44s. One day after unilateral ureteric obstruction, obstructed kidneys from CD44v3 transgenic mice showed less tubular damage and myofibroblasts accumulation, which was associated with decreased TGF-β1 signaling and increased BMP-7 synthesis and signaling compared with kidneys from wild-type and CD44s transgenic mice. These data suggest that CD44v3 plays a renoprotective role in early stage of chronic obstructive nephropathy.
Impact of inhibitory constraint of interneurons on neuronal excitability
Authors: Lee Vallent , Maguire Jamie
Published: September 2013

Tonic inhibition is thought to dampen the excitability of principal neurons; however, little is known about the role of tonic GABAergic inhibition in interneurons and the impact on principal neuron excitability. In many brain regions, tonic GABAergic inhibition is mediated by extrasynaptic, δ-subunit-containing GABAA receptors (GABAARs). In the present study we demonstrate the importance of GABAAR δ-subunit-mediated tonic inhibition in interneurons. Selective elimination of the GABAAR δ-subunit from interneurons was achieved by crossing a novel floxed Gabrd mouse model with GAD65-Cre mice ( Gabrd/Gad mice). Deficits in GABAAR δ-subunit expression in GAD65-positive neurons result in a decrease in tonic GABAergic inhibition and increased excitability of both molecular layer (ML) and stratum radiatum (SR) interneurons. Disinhibition of interneurons results in robust alterations in the neuronal excitability of principal neurons and decreased seizure susceptibility. Gabrd/Gad mice have enhanced tonic and phasic GABAergic inhibition in both CA1 pyramidal neurons and dentate gyrus granule cells (DGGCs). Consistent with alterations in hippocampal excitability, CA1 pyramidal neurons and DGGCs from Gabrd/Gad mice exhibit a shift in the input-output relationship toward decreased excitability compared with those from Cre−/− littermates. Furthermore, seizure susceptibility, in response to 20 mg/kg kainic acid, is significantly decreased in Gabrd/Gad mice compared with Cre−/− controls. These data demonstrate a critical role for GABAAR δ-subunit-mediated tonic GABAergic inhibition of interneurons on principal neuronal excitability and seizure susceptibility.