bluuebunny/crossref_metadata_2025 huggingface dataset:
Determining the Coefficient of Discharge for a Draining Container
Authors: Hicks Ashley , Slaton William
Published: December 2013

The flow of fluids through open containers is a topic studied frequently in introductory physics classes. A fluid mechanics class delves deeper into the topic of fluid flow through open containers with holes or barriers. The flow of a fluid jet out of a sharp-edged orifice rarely has the same area as the orifice due to a fluid flow phenomenon known as the vena contracta. The area of a fluid jet out of an orifice is related to the actual area of the orifice by a value known as the coefficient of discharge, Cd. The purpose of this paper is to develop a mathematical model for a draining open container and an experimental method that will efficiently determine the coefficient of discharge for such a system. Prior work in physics education literature has developed a method for measuring the flow of a fluid out of an orifice using ultrasonic motion detectors. In this paper we present data that show our method can be used to find the coefficient of discharge within the expected literature values for sharp-edged and rounded orifices.
Physics Exams that Promote Collaborative Learning
Authors: Wieman Carl E. , Rieger Georg W. , Heiner Cynthia E.
Published: December 2013

The two-stage exam is a relatively simple way to introduce collaborative learning and formative assessment into an exam. Their use is rapidly growing in the physics department at the University of British Columbia, as both students and faculty find them rewarding. In a two-stage exam students first complete and turn in the exam individually, and then, working in small groups, answer the exam questions again. During the second stage, the room is filled with spirited and effective debate with nearly every student participating. This provides students with immediate targeted feedback supplied by discussions with their peers. Furthermore, we see indications that the use of this exam format not only ensures consistency across interactive course components, but it also positively impacts how students approach the other collaborative course components. This is accomplished without losing the summative assessment of individual performance that is the expectation of exams for most instructors. In this paper we describe how to implement two-stage exams and provide arguments why they should be part of physics courses that use interactive engagement and social/collaborative learning methods.
Brood Parasitism and the Evolution of Cooperative Breeding in Birds
Authors: Feeney W. E. , Medina I. , Somveille M. , Heinsohn R. , Hall M. L. , Mulder R. A. , Stein J. A. , Kilner R. M. , Langmore N. E.
Published: December 2013

Power in Numbers

Avian brood parasites target particular bird species to raise their offspring, sometimes at great cost to the foster family.

Feeney
et al.

(p.
1506
; see the Perspective by

Spottiswoode

) analyzed the global distribution of brood parasitism and found a correlation with the occurrence of cooperative breeders across multiple taxa. For example, Australian fairy wrens breed both singly and in cooperative groups, but the group breeders are better able to resist parasites than lone pairs, indicating that the prevalence of cooperative breeding may be a response to brood parasites.
Detection of Berry’s Phase in a Bulk Rashba Semiconductor
Authors: Murakawa H. , Bahramy M. S. , Tokunaga M. , Kohama Y. , Bell C. , Kaneko Y. , Nagaosa N. , Hwang H. Y. , Tokura Y.
Published: December 2013

Spin Berry's Phase

When a quantum mechanical system performs an adiabatic cyclic path in the space of the parameters that affect its state (such as, for example, the magnetic field) its wave function may acquire an additional phase rather than go back to its original value. This quantity, called the Berry's phase, is associated with the topological properties of the parameter space and has been observed in materials such as graphene and bismuth.

Murakawa
et al.

(p.
1490
) observe a Berry's phase equal to π in the material BiTeI in which the phenomenon is predicted to be a consequence of a very strong coupling of spin and orbital degrees of freedom realized through the so-called Rashba effect.
Constraining Exoplanet Mass from Transmission Spectroscopy
Authors: de Wit Julien , Seager Sara
Published: December 2013

Weighing Up Exoplanets

The mass of a planet is important to know, but it is difficult to determine for an exoplanet. If a transmission spectrum of an exoplanet is available,
de Wit and Seager
(p.
1473
) show that it is possible to determine its mass based on the properties of its atmosphere. The method is suited for low-density planets orbiting bright or large stars, and it is complementary to other mass-retrieval methods.
Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm
Amborella
Authors: Rice Danny W. , Alverson Andrew J. , Richardson Aaron O. , Young Gregory J. , Sanchez-Puerta M. Virginia , Munzinger Jérôme , Barry Kerrie , Boore Jeffrey L. , Zhang Yan , dePamphilis Claude W. , Knox Eric B. , Palmer Jeffrey D.
Published: December 2013

Shaping Plant Evolution

Amborella trichopoda
is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by

Adams

). To validate and assemble the sequence,

Chamala
et al.

(p.
1516
) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The
Amborella Genome Project
(p.
10.1126/science.1241089
) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and

Rice
et al.

(p.
1468
) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae.
No Barriers to Cellulose Breakdown
Authors: Berlin Alex
Published: December 2013

A bacterial enzyme efficiently breaks down cellulose and hemicellulose without the help of other enzymes.

[Also see Report by

Brunecky
et al.

]
Novel Catanionic Surfactant Vesicle Vaccines Protect against Francisella tularensis LVS and Confer Significant Partial Protection against F. tularensis Schu S4 Strain
Authors: Richard Katharina , Mann Barbara J. , Stocker Lenea , Barry Eileen M. , Qin Aiping , Cole Leah E. , Hurley Matthew T. , Ernst Robert K. , Michalek Suzanne M. , Stein Daniel C. , DeShong Philip , Vogel Stefanie N.
Published: December 2013

Francisella tularensisis a Gram-negative immune-evasive coccobacillus that causes tularemia in humans and animals. A safe and efficacious vaccine that is protective against multipleF. tularensisstrains has yet to be developed. In this study, we tested a novel vaccine approach using artificial pathogens, synthetic nanoparticles made from catanionic surfactant vesicles that are functionalized by the incorporation of eitherF. tularensistype B live vaccine strain (F. tularensisLVS [LVS-V]) orF. tularensistype A Schu S4 strain (F. tularensisSchu S4 [Schu S4-V]) components. The immunization of C57BL/6 mice with “bare” vesicles, which did not expressF. tularensiscomponents, partially protected againstF. tularensisLVS, presumably through activation of the innate immune response, and yet it failed to protect against theF. tularensisSchu S4 strain. In contrast, immunization with LVS-V fully protected mice against intraperitoneal (i.p.)F. tularensisLVS challenge, while immunization of mice with either LVS-V or Schu S4-V partially protected C57BL/6 mice against an intranasal (i.n.)F. tularensisSchu S4 challenge and significantly increased the mean time to death for nonsurvivors, particularly following the i.n. and heterologous (i.e., i.p./i.n.) routes of immunization. LVS-V immunization, but not immunization with empty vesicles, elicited high levels of IgG against nonlipopolysaccharide (non-LPS) epitopes that were increased afterF. tularensisLVS challenge and significantly increased early cytokine production. Antisera from LVS-V-immunized mice conferred passive protection against challenge withF. tularensisLVS. Together, these data indicate that functionalized catanionic surfactant vesicles represent an important and novel tool for the development of a safe and effectiveF. tularensissubunit vaccine and may be applicable for use with other pathogens.
High-Throughput Direct Fecal PCR Assay for Detection of Mycobacterium avium subsp. paratuberculosis in Sheep and Cattle
Authors: Plain Karren M. , Marsh Ian B. , Waldron Anna M. , Galea Francesca , Whittington Ann-Michele , Saunders Vanessa F. , Begg Douglas J. , de Silva Kumudika , Purdie Auriol C. , Whittington Richard J.
Published: December 2013

Johne's disease (JD) is a chronic enteric disease caused by
Mycobacterium avium
subsp.
paratuberculosis
that affects ruminants. Transmission occurs by the fecal-oral route. A commonly used antemortem diagnostic test for the detection of
M. avium
subsp.
paratuberculosis
in feces is liquid culture; however, a major constraint is the 2- to 3-month incubation period needed for this method. Rapid methods for the detection of
M. avium
subsp.
paratuberculosis
based on PCR have been reported, but comprehensive validation data are lacking. We describe here a new test, the high-throughput-Johnes (HT-J), to detect
M. avium
subsp.
paratuberculosis
in feces. Its diagnostic accuracy was compared with that of liquid radiometric (Bactec) fecal culture using samples from cattle (1,330 samples from 23 herds) and sheep (596 samples from 16 flocks). The multistage protocol involves the recovery of
M. avium
subsp.
paratuberculosis
cells from a fecal suspension, cell rupture by bead beating, extraction of DNA using magnetic beads, and IS
900
quantitative PCR. The limit of detection of the assay was 0.0005 pg, and the limit of quantification was 0.005 pg
M. avium
subsp.
paratuberculosis
genomic DNA. Only
M. avium
subsp.
paratuberculosis
was detected from a panel of 51 mycobacterial isolates, including 10 with IS
900
-like sequences. Of the 549 culture-negative fecal samples from unexposed herds and flocks, 99% were negative in the HT-J test, while 60% of the bovine- and 84% of the ovine-culture-positive samples were positive in the HT-J test. As similar total numbers of samples from
M. avium
subsp.
paratuberculosis
-exposed animals were positive in culture and HT-J tests in both species, and as the results of a McNemar's test were not significant, these methods probably have similar sensitivities, but the true diagnostic sensitivities of these tests are unknown. These validation data meet the consensus-based reporting standards for diagnostic test accuracy studies for paratuberculosis and the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines (S. A. Bustin et al., Clin. Chem. 55:611–622, 2009, doi:10.1373/clinchem.2008.112797). The HT-J assay has been approved for use in JD control programs in Australia and New Zealand.
Papillomavirus E6 PDZ Interactions Can Be Replaced by Repression of p53 To Promote Episomal Human Papillomavirus Genome Maintenance
Authors: Brimer Nicole , Vande Pol Scott B.
Published: December 2013

Cancer-associated human papillomaviruses (HPVs) express E6 oncoproteins that target the degradation of p53 and have a carboxy-terminal PDZ ligand that is required for stable episomal maintenance of the HPV genome. We find that the E6 PDZ ligand can be deleted and the HPV genome stably maintained if cellular p53 is inactivated. This indicates that the E6-PDZ interaction promotes HPV genome maintenance at least in part by neutralization of an activity that can arise from residual undegraded p53.
Adenovirus E1B 19-Kilodalton Protein Modulates Innate Immunity through Apoptotic Mimicry
Authors: Radke Jay R. , Grigera Fernando , Ucker David S. , Cook James L.
Published: December 2013

Cells that undergo apoptosis in response to chemical or physical stimuli repress inflammatory reactions, but cells that undergo nonapoptotic death in response to such stimuli lack this activity. Whether cells dying from viral infection exhibit a cell death-type modulatory effect on inflammatory reactions is unknown. We compared the effects on macrophage inflammatory responses of cells dying an apoptotic or a nonapoptotic death as a result of adenoviral infection. The results were exactly opposite to the predictions from the conventional paradigm. Cells dying by apoptosis induced by infection with an adenovirus type 5 (Ad5) E1B 19-kilodalton (E1B 19K) gene deletion mutant did not repress macrophage NF-κB activation or cytokine responses to proinflammatory stimuli, whereas cells dying a nonapoptotic death from infection with E1B 19K-competent, wild-type Ad5 repressed these macrophage inflammatory responses as well as cells undergoing classical apoptosis in response to chemical injury. The immunorepressive, E1B 19K-related cell death activity depended upon direct contact of the virally infected corpses with responder macrophages. Replacement of the viral E1B 19K gene with the mammalian Bcl-2 gene in
cis
restored the nonapoptotic, immunorepressive cell death activity of virally infected cells. These results define a novel function of the antiapoptotic, adenoviral E1B 19K protein that may limit local host innate immune inflammation during accumulation of virally infected cells at sites of infection and suggest that E1B 19K-deleted, replicating adenoviral vectors might induce greater inflammatory responses to virally infected cells than E1B 19K-positive vectors, because of the net effect of their loss-of-function mutation.

IMPORTANCE
We observed that cells dying a nonapoptotic cell death induced by adenovirus infection repressed macrophage proinflammatory responses while cells dying by apoptosis induced by infection with an E1B 19K deletion mutant virus did not repress macrophage proinflammatory responses and enhanced some cytokine responses. Our results define a new function of the antiapoptotic, adenoviral protein E1B 19K, which we have termed “apoptotic mimicry.” Our studies suggest the possibility that the presence or absence of this E1B 19K function could alter the immunological outcome of both natural and therapeutic adenoviral infections. For example, emerging, highly immunopathogenic adenovirus serotypes might induce increased host inflammatory responses as a result of altered E1B 19K function or expression. It is also possible that engineered variations in E1B 19K expression/function could be created during adenovirus vector design that would increase the therapeutic efficacy of replicating adenovirus vectors for vaccines or oncolytic viral targeting of neoplastic cells.
Large-Scale Production and Structural and Biophysical Characterizations of the Human Hepatitis B Virus Polymerase
Authors: Vörös Judit , Urbanek Annika , Rautureau Gilles Jean Philippe , O'Connor Maggie , Fisher Henry C. , Ashcroft Alison E. , Ferguson Neil
Published: December 2013

Hepatitis B virus (HBV) is a major human pathogen that causes serious liver disease and 600,000 deaths annually. Approved therapies for treating chronic HBV infections usually target the multifunctional viral polymerase (hPOL). Unfortunately, these therapies—broad-spectrum antivirals—are not general cures, have side effects, and cause viral resistance. While hPOL remains an attractive therapeutic target, it is notoriously difficult to express and purify in a soluble form at yields appropriate for structural studies. Thus, no empirical structural data exist for hPOL, and this impedes medicinal chemistry and rational lead discovery efforts targeting HBV. Here, we present an efficient strategy to overexpress recombinant hPOL domains in
Escherichia coli
, purifying them at high yield and solving their known aggregation tendencies. This allowed us to perform the first structural and biophysical characterizations of hPOL domains. Apo-hPOL domains adopt mainly α-helical structures with small amounts of β-sheet structures. Our recombinant material exhibited metal-dependent, reverse transcriptase activity
in vitro
, with metal binding modulating the hPOL structure. Calcomine orange 2RS, a small molecule that inhibits duck HBV POL activity, also inhibited the
in vitro
priming activity of recombinant hPOL. Our work paves the way for structural and biophysical characterizations of hPOL and should facilitate high-throughput lead discovery for HBV.

IMPORTANCE
The viral polymerase from human hepatitis B virus (hPOL) is a well-validated therapeutic target. However, recombinant hPOL has a well-deserved reputation for being extremely difficult to express in a soluble, active form in yields appropriate to the structural studies that usually play an important role in drug discovery programs. This has hindered the development of much-needed new antivirals for HBV. However, we have solved this problem and report here procedures for expressing recombinant hPOL domains in
Escherichia coli
and also methods for purifying them in soluble forms that have activity
in vitro
. We also present the first structural and biophysical characterizations of hPOL. Our work paves the way for new insights into hPOL structure and function, which should assist the discovery of novel antivirals for HBV.
Immunogenicity of Novel Mumps Vaccine Candidates Generated by Genetic Modification
Authors: Xu Pei , Chen Zhenhai , Phan Shannon , Pickar Adrian , He Biao
Published: December 2013

Mumps is a highly contagious human disease, characterized by lateral or bilateral nonsuppurative swelling of the parotid glands and neurological complications that can result in aseptic meningitis or encephalitis. A mumps vaccination program implemented since the 1960s reduced mumps incidence by more than 99% and kept the mumps case numbers as low as hundreds of cases per year in the United States before 2006. However, a large mumps outbreak occurred in vaccinated populations in 2006 and again in 2009 in the United States, raising concerns about the efficacy of the vaccination program. Previously, we have shown that clinical isolate-based recombinant mumps viruses lacking expression of either the V protein (rMuVΔV) or the SH protein (rMuVΔSH) are attenuated in a neurovirulence test using newborn rat brains (P. Xu et al., Virology 417:126–136, 2011,http://dx.doi.org/10.1016/j.virol.2011.05.003; P. Xu et al., J. Virol. 86:1768–1776, 2012,http://dx.doi.org/10.1128/JVI.06019-11) and may be good candidates for vaccine development. In this study, we examined immunity induced by rMuVΔSH and rMuVΔV in mice. Furthermore, we generated recombinant mumps viruses lacking expression of both the V protein and the SH protein (rMuVΔSHΔV). Analysis of rMuVΔSHΔV indicated that it was stable in tissue culture cell lines. Importantly, rMuVΔSHΔV was immunogenic in mice, indicating that it is a promising candidate for mumps vaccine development.
Kaposi's Sarcoma-Associated Herpesvirus Induces the ATM and H2AX DNA Damage Response Early during
De Novo
Infection of Primary Endothelial Cells, Which Play Roles in Latency Establishment
Authors: Singh Vivek Vikram , Dutta Dipanjan , Ansari Mairaj Ahmed , Dutta Sujoy , Chandran Bala
Published: December 2013

The DNA damage response (DDR) that evolved to repair host cell DNA damage also recognizes viral DNA entering the nucleus during infections. Here, we investigated the modulation of DDR signaling during
de novo
infection of primary endothelial cells by Kaposi's sarcoma-associated herpesvirus (KSHV). Phosphorylation of representative DDR-associated proteins, such as ataxia telangiectasia mutated (ATM) and H2AX, was induced as early as 30 min (0.5 h) postinfection and persisted during
in vitro
KSHV latency. Phosphorylated H2AX (γH2AX) colocalized at 30 min (0.5 h) with the KSHV genome entering the nuclei. Total H2AX protein levels also increased, and the increase was attributed to a decrease in degradative H2AX Lys48-linked polyubiquitination with a concomitant increase in Lys63-linked polyubiquitination that was shown to increase protein stability. ATM and H2AX phosphorylation and γH2AX nuclear foci were also induced by UV-inactivated KSHV, which ceased at later times of infection. Inhibition of ATM kinase activity by KU-55933 and H2AX knockdown by small interfering RNA significantly reduced the expression of the KSHV latency-associated nuclear antigen 1 (LANA-1; ORF73) and LANA-1 nuclear puncta. Knockdown of H2AX also resulted in a >80% reduction in the nuclear KSHV DNA copy numbers. Similar results were also observed in ATM-negative cells, although comparable levels of viral DNA entered ATM-negative and ATM-positive cell nuclei. In contrast, knockdown of CHK1 and CHK2 did not affect ORF73 expression. Collectively, these results demonstrate that KSHV induces ATM and H2AX, a selective arm of the DDR, for the establishment and maintenance of its latency during
de novo
infection of primary endothelial cells.

IMPORTANCE
Eukaryotic cells mount a DNA damage response (DDR) to sense and repair different types of cellular DNA damage. In addition, DDR also recognizes exogenous genetic material, such as the viral DNA genome entering the nucleus during infections. The present study was undertaken to determine whether
de novo
Kaposi's sarcoma-associated herpesvirus (KSHV) infection modulates DDR. Our results demonstrate that early during
de novo
infection of primary endothelial cells, KSHV induces a selective arm of DDR signaling, such as the ATM kinase and its downstream target, H2AX, which are essential for KSHV's latent gene expression and the establishment of latency. These studies suggest that targeting ATM and H2AX could serve as an attractive strategy to block the establishment of KSHV latent infection and the associated malignancies.
Divergent Antibody Subclass and Specificity Profiles but Not Protective HLA-B Alleles Are Associated with Variable Antibody Effector Function among HIV-1 Controllers
Authors: Lai Jennifer I. , Licht Anna F. , Dugast Anne-Sophie , Suscovich Todd , Choi Ickwon , Bailey-Kellogg Chris , Alter Galit , Ackerman Margaret E.
Published: December 2013

Understanding the coordination between humoral and cellular immune responses may be the key to developing protective vaccines, and because genetic studies of long-term HIV-1 nonprogressors have associated specific HLA-B alleles with spontaneous control of viral replication, this subject group presents an opportunity to investigate relationships between arms of the adaptive immune system. Given evidence suggesting that cellular immunity may play a role in viral suppression, we sought to determine whether and how the humoral immune response might vary among controllers. Significantly, Fc-mediated antibody effector functions have likewise been associated with durable viral control. In this study, we compared the effector function and biophysical features of HIV-specific antibodies in a cohort of controllers with and without protective HLA-B alleles in order to investigate whether there was evidence for multiple paths to HIV-1 control, or whether cellular and humoral arms of immunity might exhibit coordinated profiles. However, with the exception of IgG2 antibodies to gp41, HLA status was not associated with divergent humoral responses. This finding did not result from uniform antibody responses across subjects, as controllers could be regrouped according to strong differences in their HIV-specific antibody subclass specificity profiles. These divergent antibody profiles were further associated with significant differences in nonneutralizing antibody effector function, with levels of HIV-specific IgG1 acting as the major distinguishing factor. Thus, while HLA background among controllers was associated with minimal differences in humoral function, antibody subclass and specificity profiles were associated with divergent effector function, suggesting that these features could be used to make functional predictions. Because these nonneutralizing antibody activities have been associated with spontaneous viral control, reduced viral load, and nonprogression in infected subjects and protection in vaccinated subjects, understanding the specific features of IgGs with potentiated effector function may be critical to vaccine and therapeutic antibody development.

IMPORTANCEIn this study, we investigated whether the humoral and cellular arms of adaptive immunity exhibit coordinated or compensatory activity by studying the antibody response among HIV-1 controllers with different genetic backgrounds.
Diverse Recombinant HIV-1 Envs Fail To Activate B Cells Expressing the Germline B Cell Receptors of the Broadly Neutralizing Anti-HIV-1 Antibodies PG9 and 447-52D
Authors: McGuire Andrew T. , Glenn Jolene A. , Lippy Adriana , Stamatatos Leonidas
Published: December 2013

Broadly neutralizing antibodies (bNAbs) against HIV-1 are generated during HIV-1-infection but have not yet been elicited by immunization with recombinant forms of the viral envelope glycoprotein (Env; the target of anti-HIV-1 neutralizing antibodies). A particular type of bNAb targets the CD4-binding site (CD4-BS) region of Env. These antibodies are derived from a limited number of VH/VL genes and can bind to and neutralize diverse HIV-1 strains. Recent reports have demonstrated the limited potential of Env to activate B cells expressing the germline B cell receptor (BCR) forms of anti-CD4-BS bNAbs. A potential reason for the lack of elicitation of anti-CD4-BS bNAbs by Env immunogens is the absence of stimulation of naive B cells expressing the germline BCRs of such antibodies. Several bNAbs have been isolated from HIV-1-infected subjects that target other structurally conserved regions of Env. How frequently Env immunogens stimulate the germline BCRs that give rise to bNAbs that target Env regions other than the CD4-BS is not well understood. Here, we investigated the interactions between diverse Envs and the BCRs of known bNAbs targeting not only the CD4-BS but also conserved elements of the second and third variable Env regions. Our results indicate that Env is generally ineffective in engaging germline BCRs of bNAbs irrespective of their epitope target. Potentially, this is the result of viral evolutionary mechanisms adopted to escape broadly neutralizing antibody responses. Our results also suggest that a single Env capable of activating germline BCRs that target distinct Env epitopes will be very difficult to identify or to design.

IMPORTANCEBroadly neutralizing antibodies against HIV-1 are thought to be an important component of the immune responses that a successful vaccine should elicit. Broadly neutralizing antibodies are generated by a subset of those infected by HIV-1, but so far, they have not been generated by immunization with recombinant Envelope (Env, the target of anti-HIV-1 neutralizing antibodies). Here, we provide evidence that the inability of Env to elicit the production of broadly neutralizing antibodies is due to the inability of diverse Envs to engage the germline B cell receptor forms of known broadly neutralizing antibodies.
Morphogenesis of Pestiviruses: New Insights from Ultrastructural Studies of Strain Giraffe-1
Authors: Schmeiser Stefanie , Mast Jan , Thiel Heinz-Jürgen , König Matthias
Published: December 2013

Knowledge on the morphogenesis of pestiviruses is limited due to low virus production in infected cells. In order to localize virion morphogenesis and replication sites of pestiviruses and to examine intracellular virion transport, a cell culture model was established to facilitate ultrastructural studies. Based on results of virus growth kinetic analysis and quantification of viral RNA, pestivirus strain Giraffe-1 turned out to be a suitable candidate for studies on virion generation and export from culture cells. Using conventional transmission electron microscopy and single-tilt electron tomography, we found virions located predominately in the lumen of the endoplasmic reticulum (ER) in infected cells and were able to depict the budding process of virions at ER membranes. Colocalization of the viral core protein and the envelope glycoprotein E2 with the ER marker protein disulfide isomerase (PDI) was demonstrated by immunogold labeling of cryosections. Moreover, pestivirions could be shown in transport vesicles and the Golgi complex and during exocytosis. Interestingly, viral capsid protein and double-stranded RNA (dsRNA) were detected in multivesicular bodies (MVBs), which implies that the endosomal compartment plays a role in pestiviral replication. Significant cellular membrane alterations such as those described for members of the
Flavivirus
and
Hepacivirus
genera were not found. Based on the gained morphological data, we present a consistent model of pestivirus morphogenesis.
Involvement of Viral MicroRNA in the Regulation of Antiviral Apoptosis in Shrimp
Authors: Huang Tianzhi , Cui Yalei , Zhang Xiaobo
Published: December 2013

Viruses, in particular DNA viruses, generate microRNAs (miRNAs) to control the expression of host and viral genes. Due to their essential roles in virus-host interactions, viral miRNAs have attracted extensive investigations in recent years. To date, however, most studies on viral miRNAs have been conducted in cell lines. In this study, the viral miRNAs from white spot syndrome virus (WSSV) were characterized in shrimp
in vivo
. On the basis of our previous study and small RNA sequencing in this study, a total of 89 putative WSSV miRNAs were identified. As revealed by miRNA microarray analysis and Northern blotting, the expression of viral miRNAs was tissue specific
in vivo
. The results indicated that the viral miRNA WSSV-miR-N24 could target the shrimp caspase 8 gene, and this miRNA further repressed the apoptosis of shrimp hemocytes
in vivo
. As a result, the number of WSSV copies in shrimp
in vivo
was significantly increased compared with the control level (WSSV only). Therefore, our study presents the first report on the
in vivo
molecular events of viral miRNA in antiviral apoptosis.
A gastrointestinal stromal tumour with pulmonary metastases mimicking unilateral gynaecomastia
Authors: Guler Cimen Sanem , MacDonald Frank , Cimen Sertac , Molinari Michele
Published: December 2013

Gastrointestinal stromal tumours (GISTs) represent 1% of primary gastrointestinal cancers. These neoplasms most frequently metastasise to the liver and peritoneum and rarely to the lungs and bones. Treatment of unresectable GISTs involves systemic chemotherapy with tyrosine kinase inhibitors, imatinib and sunitinib being first-line and second-line drugs. We report the case of a 52-year-old man with GIST who developed a right-sided subareolar breast swelling and subsequently discovered to be an invasive metastatic pulmonary GIST. Given that gynaecomastia is a known adverse effect of imatinib and sunitinib, this case report illustrates the importance of including metastatic disease in the differential diagnosis of patients with GIST and with the new onset of soft tissue masses.
How familiar are clinician teammates in the emergency department?
Authors: Patterson P Daniel , Pfeiffer Anthony J , Lave Judith R , Weaver Matthew D , Abebe Kaleab , Krackhardt David , Arnold Robert M , Yealy Donald M
Published: December 2013

Objectives

Lack of familiarity between teammates is linked to worsened safety in high risk settings. The emergency department (ED) is a high risk healthcare setting where unfamiliar teams are created by diversity in clinician shift schedules and flexibility in clinician movement across the department. We sought to characterise familiarity between clinician teammates in one urban teaching hospital ED over a 22 week study period.

Methods

We used a retrospective study design of shift scheduling data to calculate the mean weekly hours of familiarity between teammates at the dyadic level, and the proportion of clinicians with a minimum of 2, 5, 10 and 20 h of familiarity at any given hour during the study period.

Results

Mean weekly hours of familiarity between ED clinician dyads was 2 h (SD 1.5). At any given hour over the study period, the proportions of clinicians with a minimum of 2, 5, 10 and 20 h of familiarity were 80%, 51%, 27% and 0.8%, respectively.

Conclusions

In our study, few clinicians could be described as having a high level of familiarity with teammates. The limited familiarity between ED clinicians identified in this study may be a natural feature of ED care delivery in academic settings. We provide a template for measurement of ED team familiarity.
Cerebral arteriopathy associated with Arg179His ACTA2 mutation
Authors: Amans Matthew R , Stout Charles , Fox Christine , Narvid Jared , Hetts Steven W , Cooke Daniel L , Higashida Randall T , Dowd Christopher F , McSwain Hugh , Halbach Van V
Published: December 2013

ACTA2 mutations have recently been shown to cause a multisystem smooth muscle dysfunction syndrome that may result in pediatric stroke. We report a case of ACTA2 mutation in a 3-year-old girl presenting with acute ischemic stroke and provide high resolution imaging of the cerebral arteries demonstrating novel findings of multiple tiny aneurysms (particularly in the posterior circulation), as well as the more characteristic imaging phenotype of straightened and narrowed proximal intracranial vessels, dilated cervical vessels and occlusion of the M1 MCA segment without lenticulostriate collateral formation. This newly identified disease should be added to the differential diagnosis of pediatric stroke and cerebral vasculopathy. Neuroradiologists, interventionalists, surgeons and neurologists should become familiar with this rare disease and its clinical sequelae.
Investigation of the solvent influence on polymer–fullerene solar cells by low frequency noise spectroscopy
Authors: Landi G. , Barone C. , Pagano S. , De Sio A. , Neitzert H.C.
Published: December 2013

The electron density of states and recombination kinetics of bulk heterojunction solar cells have been determined by means of low-frequency noise spectroscopy at room temperature and in dark conditions. The observed differences in the disorder parameter and electron lifetime are attributed to a different film ordering of the active layer because of the influence of a solvent additive. Blends prepared with the reference solvent resulted in the lowest electron lifetime and density of states population, while blends prepared with the addition of a high boiling point solvent resulted in a more efficient charge carrier separation and a higher electron lifetime.
Multiphoton Laguerre polynomial state as minimum uncertainty states of intensity-dependent squeezing
Authors: Chen Qian-Fan , Fan Hong-Yi
Published: December 2013

For a general multiphoton annihilation operator, F = f(N)ap, where N = a†a, we find the explicit form of an operator, G†, which satisfies [F, G†] = 1. Based on the nonlinear realization of the SU(1,1) Lie algebra whose generators are [Formula: see text], [Formula: see text], and R0 = [N/p] + 1/2. We introduce the concept of intensity-dependent multiphoton squeezing and find that the state Lm(–yR†)|j⟩, 0 ≤ j ≤ p, where Lm(x) is a Laguerre polynomial, is a minimum uncertainty state for intensity-dependent multiphoton squeezing. We also construct the phase states for multiphoton operator, which turn out to be SU(1,1) generalized coherent states. Additionally, we show that the photon-added coherent state |α, m⟩ (m is a non-negative integer), which can be interpreted as a nonlinear coherent state, can be expressed as [Formula: see text] in the whole Fock space.
A SEARCH GAME WITH UNKNOWN EXAMINATION COSTS AND TRAVEL TIMES
Authors: KIKUTA KENSAKU
Published: December 2013

A search game on a finite and complete graph is studied between a (immobile) hider and a seeker. A strategy for the hider is to choose a node where he hides, except for a specified node. A strategy for the seeker is an ordering of nodes in which the seeker starts at the specified node, examines each node in that order until he finds the hider, traveling along edges. Associated with an examination of a node is the examination cost, and associated with a movement from a node to a node is a traveling cost. These costs are unknown for both players when they choose strategies. They know only probability laws of them. While the hider wishes to maximize the expectation of the sum of these costs which are required to find the hider, the seeker wishes to minimize it. The game is solved when the nodes are classified into two groups depending on the examination costs, and the edges are classified into three groups depending on both costs.
IMAGE FUSION BASED ON MULTI-OBJECTIVE OPTIMIZATION
Authors: XIE QIWEI , LONG QIAN , MITA SEIICHI , GUO CHUNZHAO , JIANG AN
Published: December 2013

This paper solves the image fusion problem by using a multi-object optimization strategy and a key energy function. The energy function mainly consists of two components. One ensures injection of more correlated detailed spatial information. The detailed information is extracted from gradient representation of the image to be fused. The other one guarantees that the spectral information is preserved by a data fitting term. By minimizing the proposed energy function, the fusion result can be obtained. Moreover, a key parameter is used in the energy function to adjust the weights of the spectral and spatial information during the image fusion. In this paper, a multi-object optimization is constructed to determine such a key parameter. The image fusion performance is evaluated through visional perception and some fusion indexes. Experimental results further demonstrate advantages of the proposed technique over the conventional fusion techniques.
PERTURBED FRAME SEQUENCES: CANONICAL DUAL SYSTEMS, APPROXIMATE RECONSTRUCTIONS AND APPLICATIONS
Authors: HEINEKEN SIGRID , MATUSIAK EWA , PATERNOSTRO VICTORIA
Published: December 2013

We consider perturbation of frames and frame sequences in a Hilbert space ℋ. It is known that small perturbations of a frame give rise to another frame. We show that the canonical dual of the perturbed sequence is a perturbation of the canonical dual of the original one and estimate the error in the approximation of functions belonging to the perturbed space. We then construct perturbations of irregular translates of a bandlimited function in L2(ℝd). We give conditions for the perturbed sequence to inherit the property of being Riesz or frame sequence. For this case we again calculate the error in the approximation of functions that belong to the perturbed space and compare it with our previous estimation error for general Hilbert spaces.
Stability analysis of n-species Lotka–Volterra almost periodic competition models with grazing rates and diffusions
Authors: Zhang Yi-Jin , Wang Chang-You
Published: December 2013

In this paper, almost periodic solution of a n-species Lotka–Volterra competition system with grazing rates and diffusions is investigated. By using the method of upper and lower solutions and Schauder fixed point theorem as well as Lyapunov stability theory, we give sufficient conditions under which the strictly positive space homogeneous almost periodic solution of the system is globally asymptotically stable. Moreover, some numerical simulations are given to validate our theoretical analysis.
ESTABLISHMENT OF TRACEABILITY OF REFERENCE GRADE HYDROMETERS AT NATIONAL PHYSICAL LABORATORY, INDIA (NPLI)
Authors: KUMAR ANIL , KUMAR HARISH , MANDAL GOUTAM , DAS M B , SHARMA D C
Published: December 2013

The present paper discusses the establishment of traceability of reference grade hydrometers at National Physical Laboratory, India (NPLI). The reference grade hydrometers are calibrated and traceable to the primary solid density standard. The calibration has been done according to standard procedure based on Cuckow's Method and the reference grade hydrometers calibrated covers a wide range. The uncertainty of the reference grade hydrometers has been computed and corrections are also calculated for the scale readings, at which observations are taken.
THE DESIGN OF 1 N•M TORQUE STANDARD MACHINE AT NIM
Authors: ZHANG ZHIMIN , ZHANG YUE , LI TAO , JI HONGLEI
Published: December 2013

A 1 N•m torque standard machine has been designed and developed at National Institute of Metrology (NIM) since 2011. The torque standard machine adopts the moment arm-deadweight type, the air bearing with low friction is adopted to support the moment-arm at the fulcrum, the invar with the low expansion coefficient is used as the material of the moment-arm, the weight suspension part and weight loading system are specially designed to ensure the applied force by small weights accurately and reliably. This paper introduces the mechanical structures of the machine, the electrical control system is described. 1 N•m torque standard machine is capable of realizing the torque from 1 mN•m to 1 N•m both in clockwise and anti-clockwise directions.
ESTABLISHMENT OF CLASS E1 MASS STANDARD OF 50 kg
Authors: YAO HONG , WANG JIAN , DING JINGAN , ZHONG RUILIN , REN XIAOPING
Published: December 2013

Because of the equipment limit, the dissemination of large mass has been realized by a large amount of higher class of 20 kg weights since 1950s in China. But with improvement of the technique and customer's requirements, it is necessary to establish the mass standard of 50 kg weight. In 1990s, mass standard laboratory has set up Class E1 weight sets from 20 kg to 1 mg. To extend the mass capacity up to 50 kg of Class E1, it is not only to produce Class E1 50 kg weight and import a mass comparator, but also need to lift the heavy weight from weight box to balance receptor safely.

Up to now, the mass comparator has been installed in Hepingli campus of NIM. Two pieces of Class E1 50 kg weights are determined by combination weighing method. A lifting device has been mounted close to the mass comparator in order to move the 50 kg easily.
CHARACTERIZING THE MASS/FORCE MEASUREMENT CAPABILITY OF A MICROBALANCE
Authors: YEH YU-SHAN , CHEN SHENG-JUI , TUAN CHIN-FEN , LIN YI-CHING , PAN SHEAU-SHI
Published: December 2013

Specifying and reducing the uncertainty is very important to all kinds of measurements. In order to have a better understanding of the noise mechanism responsible for lowering the quality of mass/force measurements, the Allan variation method is applied to investigate the noise performance of a commercial ultra-microbalance installed on different noise reduction platforms. It turns out that the marble table provides a better noise isolation environment for mass measurements than an optical table. The optimal integration time is found to be 100 sec ~ 200 sec, with a lowest deviation of 0.07 μg. A different data treatment simulating the ABA load/unload cycle is also applied with or without a delay time for signal integration. The consistency between Allan deviation and the ABA simulation plots points out that the optimal integration time is applicable either in single or cyclic mass measurements.
A new appraisal of the Ancona landslide based on geotechnical investigations and stability modelling
Authors: Agostini Andrea , Tofani Veronica , Nolesini Teresa , Gigli Giovanni , Tanteri Luca , Rosi Ascanio , Cardellini Stefano , Casagli Nicola
Published: December 2013

On the night of 13 December 1982, Ancona experienced the catastrophic reactivation of an old and large landslide located along the coast to the west of the city. The outcomes of past and new geotechnical investigations and the data from the 30 year readings of the monitoring instruments have been integrated to redefine and update the actual location of the sliding surfaces. According to the new analysis, the landslide involves four main sliding surfaces with different extents and depths. The deepest surfaces converge at depth in a shear band and their toes are positioned near or beyond the coast. Numerical and analytical modelling of the landslide has been carried out using the newly derived sliding surface geometries. The numerical modelling has allowed a qualitative assessment of the deformation pattern, confirming the geometry of the sliding surfaces derived from the geotechnical investigations. The stability analyses have been performed applying the limit equilibrium method to quantify the instability conditions of the landside. The analyses have been carried out for five stratigraphic–geotechnical scenarios. All of these scenarios show a stability condition near the limit equilibrium.
Detection of differentially regulated subsarcolemmal calcium signals activated by vasoactive agonists in rat pulmonary artery smooth muscle cells
Authors: Subedi Krishna P. , Paudel Omkar , Sham James S. K.
Published: December 2013

Intracellular calcium (Ca2+) plays pivotal roles in distinct cellular functions through global and local signaling in various subcellular compartments, and subcellular Ca2+ signal is the key factor for independent regulation of different cellular functions. In vascular smooth muscle cells, subsarcolemmal Ca2+ is an important regulator of excitation-contraction coupling, and nucleoplasmic Ca2+ is crucial for excitation-transcription coupling. However, information on Ca2+ signals in these subcellular compartments is limited. To study the regulation of the subcellular Ca2+ signals, genetically encoded Ca2+ indicators (cameleon), D3cpv, targeting the plasma membrane (PM), cytoplasm, and nucleoplasm were transfected into rat pulmonary arterial smooth muscle cells (PASMCs) and Ca2+ signals were monitored using laser scanning confocal microscopy. In situ calibration showed that the Kd for Ca2+ of D3cpv was comparable in the cytoplasm and nucleoplasm, but it was slightly higher in the PM. Stimulation of digitonin-permeabilized cells with 1,4,5-trisphosphate (IP3) elicited a transient elevation of Ca2+ concentration with similar amplitude and kinetics in the nucleoplasm and cytoplasm. Activation of G protein-coupled receptors by endothelin-1 and angiotensin II preferentially elevated the subsarcolemmal Ca2+ signal with higher amplitude in the PM region than the nucleoplasm and cytoplasm. In contrast, the receptor tyrosine kinase activator, platelet-derived growth factor, elicited Ca2+ signals with similar amplitudes in all three regions, except that the rise-time and decay-time were slightly slower in the PM region. These data clearly revealed compartmentalization of Ca2+ signals in the subsarcolemmal regions and provide the basis for further investigations of differential regulation of subcellular Ca2+ signals in PASMCs.
Sulfonamide Basedβ-Carbonic Anhydrase Inhibitors: 2D QSAR Study
Authors: Deodhar Meenakshi N. , Khopade Priyanka L. , Varat Mahesh G.
Published: December 2013

The carbonic anhydrases (CAs) (or carbonate dehydratases) form a family of metalloenzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate and protons (or vice versa), a reversible reaction that occurs rather slowly in the absence of a catalyst. Theβ-CAs have been characterized in a high number of human pathogens, such as the fungi/yeastsCandida albicans, Candida glabrata, Cryptococcus neoformans, andSaccharomyces cerevisiaeand the bacteriaHelicobacter pylori, Mycobacterium tuberculosis, Haemophilus influenzae, Brucella suis, andStreptococcus pneumonia. Theβ-CAs in microorganisms provide physiological concentration of carbon dioxide and bicarbonate (CO2/HCO3-) for their growth. Inhibition ofβ-CAs from the pathogenic microorganism is recently being explored as a novel pharmacological target to treat infections caused by the these organisms. The present study aimed to establish a relationship between theβ-CAs inhibitory activity for structurally related sulphonamide derivatives and the physicochemical descriptors in quantitative terms. The statistically validated two-dimensional quantitative structure activity relationship (2D QSAR) model was obtained through multiple linear regression (MLR) analysis method using Vlife molecular design suits (MDS). Five descriptors showing positive and negative correlation with theβ-CAs inhibitory activity have been included in the model. This validated 2D QSAR model may be used to design sulfonamide derivatives with better inhibitory properties.