bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal weighting of binaural cues revealed by detection of dynamic interaural differences in high-rate Gabor click trains
Authors: Stecker G. Christopher , Brown Andrew D.
Published: May 2010

Listeners detected interaural differences of time (ITDs) or level (ILDs) carried by single 4000-Hz Gabor clicks (Gaussian-windowed tone bursts) and trains of 16 such clicks repeating at an interclick interval (ICI) of 2, 5, or 10 ms. In separate conditions, target interaural differences favored the right ear by a constant amount for all clicks (condition RR), attained their peak value at onset and diminished linearly to 0 at offset (condition R0), or grew linearly from 0 at onset to a peak value at offset (condition 0R). Threshold ITDs and ILDs were determined adaptively in separate experiments for each of these conditions and for single clicks. ITD thresholds were found to be lower for 16-click trains than for single clicks at 10-ms ICI, regardless of stimulus condition. At 2-ms ICI, thresholds in RR and R0 conditions were similar to single click thresholds at 2-ms ICI; thresholds in the 0R condition were significantly worse than for single clicks at 2-ms ICI, consistent with strong rate-dependent onset dominance in listeners’ temporal weighting of ITD. ILD thresholds, in contrast, were predominantly unaffected by ICI, suggesting little or no onset dominance for ILD of high-rate stimuli.
Scaling for the ensemble statistics prediction of a random system subjected to harmonic excitations
Authors: Li Xianhui
Published: May 2010

This paper is concerned with the ensemble statistics of the dynamic responses of a random system subjected to harmonic excitations. Random point process theory is employed to derive general scaling laws with the Gaussian orthogonal ensemble assumption about the system natural frequencies. A scaled model is built to simulate the high-frequency vibrations of the original system. Specific forms of the scaling laws are presented for a mass-loaded plate regarding the scaling factors for the structural parameters. The ensemble statistics predicted from the scaled model are compared favorably with those obtained from the original system.
A scaling approach for the prediction of high-frequency mean responses of vibrating systems
Authors: Li Xianhui
Published: May 2010

This analysis presents a scaling approach to predict high-frequency mean responses of vibrating systems. The basis of the approach lies in the dynamic similitude between the original systems and the scaled models. A general scaling law is formulated using Skudrzyk’s mean-value theorem and its specific form is derived for the case of a flexural plate. Modal density is scaled down to reduce the computational cost in the high-frequency mean response prediction. Different scaling procedures are numerically experimented and some insights are given about the accuracy of the scaling approach as compared with a dense finite element analysis.
Comment on “Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome”
Authors: Sudlow Cathie , Macleod Malcolm , Salman Rustam Al-Shahi , Stone Jon
Published: May 2010

Lombardi
et al
. (Reports, 23 October 2009, p. 585) reported an association between the
human gammaretrovirus XMRV and chronic fatigue syndrome. However, their results may be misleading because of various potential sources of bias and confounding. If real, the association may lack generalizability because of the specific characteristics of the cases studied and could
be due to reverse causality.
Comment on “Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome”
Authors: van der Meer Jos W. M. , Netea Mihai G. , Galama Jochem M. D. , van Kuppeveld Frank J. M.
Published: May 2010

Lombardi
et al
. (Reports, 23 October 2009, p. 585) reported detection of the human gammaretrovirus XMRV in the blood cells of patients with chronic fatigue syndrome (CFS). However, the patient description provided was incomplete. The inclusion of patients from a “CFS outbreak” previously linked with a viral infection, without confirmation in sporadic CFS cases, casts doubt on the role of XMRV in the pathogenesis of CFS.
The Population Dynamics and Control of Tuberculosis
Authors: Dye Christopher , Williams Brian G.
Published: May 2010

More than 36 million patients have been successfully treated via the World Health Organization’s strategy for tuberculosis (TB) control since 1995. Despite predictions of a decline in global incidence, the number of new cases continues to grow, approaching 10 million in 2010. Here we review the changing relationship between the causative agent,
Mycobacterium tuberculosis
, and its human host and examine a range of factors that could explain the persistence of TB. Although there are ways to reduce susceptibility to infection and disease, and a high-efficacy vaccine would boost TB prevention, early diagnosis and drug treatment to interrupt transmission remain the top priorities for control. Whatever the technology used, success depends critically on the social, institutional, and epidemiological context in which it is applied.
Molecular Identity of Dendritic Voltage-Gated Sodium Channels
Authors: Lorincz Andrea , Nusser Zoltan
Published: May 2010

Counting Na
+
Channels One by One

Understanding how nerve cells integrate their synaptic inputs and generate their output signals requires the identification of voltage-dependent ion channels on the axo-somato-dendritic surface of central neurons. Using improved ultrastructural immunocytochemistry techniques,
Lorincz and Nusser
(p.
906
) found that a newly described voltage-gated sodium channel, Nav1.6, was present not only at nodes of Ranvier and axon initial segments but also at much lower, but functionally significant levels, in dendrites of CA1 pyramidal cells. However, other brain Na
+
channels were not present in these dendrites, suggesting that dendritic sodium spikes result from somatic activation of this particular type of sodium channel.
A Paleoclimatic Enigma?
Authors: Ruddiman William F.
Published: May 2010

What caused the onset of major Northern Hemisphere glaciation about 2.75 million years ago?
Hydrogen Bonding Controls the Dynamics of Catechol Adsorbed on a TiO
2
(110) Surface
Authors: Li Shao-Chun , Chu Li-Na , Gong Xue-Qing , Diebold Ulrike
Published: May 2010

Stop or Go on Oxide Surfaces

Direct studies of surface diffusion with instruments such as the scanning tunneling microscope (STM) have often focused on species on metal surfaces, but surface diffusion can play an important role for reactions on metal oxide surfaces.

Li
et al.

(p.
882
) used STM and density functional theory calculations to study how catechol (a benzene ring bearing two −OH groups) diffuses on the surface of the rutile phase of titanium dioxide. Both mobile and immobile species were observed on the time scale of minutes while making repeated STM scans. Hydrogen atom transfers between surface OH groups and the molecule changed the interaction energy between the molecule and the surface, and hence the barrier for diffusion.
Small RNA Makes Its Move
Authors: Martienssen Rob
Published: May 2010

Mobile small RNA in plants provides cell-to-cell communication that affects gene expression during development.
Phylogeny of Methylomes
Authors: Jeltsch Albert
Published: May 2010

The patterns of DNA methylation across the genomes of 20 eukaryotes reveal conserved features and specific roles during evolution.
ITER Cost Estimates Leave Europe Struggling to Find Ways to Pay
Authors: Clery Daniel
Published: May 2010

Last week, it was announced that Europe's contribution to building the ITER fusion reactor project would amount to €7.2 billion, 2.7 times the original estimate. Senior fusion researchers were astonished that the European Commission proposed no solution to the problem apart from asking E.U. member states for more money.
Bioethicists Assail a Celebrated TB/HIV Treatment Trial
Authors: Cohen Jon
Published: May 2010

A heralded clinical study in South Africa that assessed the best treatment strategy for people infected with HIV who are receiving drugs for tuberculosis should never have been done, two bioethicists argue.
Panel Finds Environmental Risks Neglected
Authors: Kaiser Jocelyn
Published: May 2010

A flap has erupted among health experts over a report last week from a presidential advisory group that concludes environmental pollutants are an underappreciated cause of cancer that is inflicting "grievous harm" on Americans.
Ever-Smaller Lasers Pave the Way for Data Highways Made of Light
Authors: Service Robert F.
Published: May 2010

New materials and techniques are bringing researchers close to a once-unthinkable goal: optical devices tiny enough to work hand in hand with electronic circuits.
As Challenges Change, So Does Science
Authors: Enserink Martin
Published: May 2010

Although nobody believes that it is possible in the next 10, 20, or even 30 years, the call to eradicate malaria, combined with the plummeting disease burden, are already reshaping the scientific agenda.
If Artemisinin Drugs Fail, What's Plan B?
Authors: Enserink Martin
Published: May 2010

If the current generation of artemisinin-based combination therapies should fail, does the world have a solid backup plan? The short answer: No.
The ‘Do Unto Others’ Malaria Vaccine
Authors: Vogel Gretchen
Published: May 2010

Once neglected, research on transmission-blocking vaccines for malaria is gaining new prominence.
Shrinking the Malaria Map From the Outside In
Authors: Roberts Leslie
Published: May 2010

A debate is brewing over how best to fight malaria: Go for the quick wins, or the worst places first, or both?
LIFE SCIENCE TECHNOLOGIES: Mass Spectrometry Raises the Bar
Authors: Dove Alan
Published: May 2010

Mass spectrometry is clearly having its moment in the sun. Once restricted to a handful of well-equipped research laboratories, mass spectrometers have now become almost ubiquitous. Even modestly funded scientists can usually get their samples analyzed in a core mass spectrometry facility, and user-friendly spectrometers are becoming a fixture of forensic and clinical labs worldwide.
Strong HIV-Specific CD4
+
and CD8
+
T-Lymphocyte Proliferative Responses in Healthy Individuals Immunized with an HIV-1 DNA Vaccine and Boosted with Recombinant Modified Vaccinia Virus Ankara Expressing HIV-1 Genes
Authors: Aboud Said , Nilsson Charlotta , Karlén Katarina , Marovich Mary , Wahren Britta , Sandström Eric , Gaines Hans , Biberfeld Gunnel , Godoy-Ramirez Karina
Published: May 2010

We investigated HIV-1 vaccine-induced lymphoproliferative responses in healthy volunteers immunized intradermally or intramuscularly (with or without adjuvant granulocyte-macrophage colony-stimulating factor [GM-CSF] protein) with DNA expressing HIV-1
gag
,
env
,
rev
, and
rt
at months 0, 1, and 3 using a Biojector and boosted at 9 months with modified vaccinia virus Ankara (MVA) expressing heterologous HIV-1
gag
,
env
, and
pol
(HIV-MVA). Lymphoproliferative responses to aldrithiol-2 (AT-2)-inactivated-HIV-1 antigen were tested by a [
3
H]thymidine uptake assay and a flow-cytometric assay of specific cell-mediated immune response in activated whole blood (FASCIA-WB) 2 weeks after the HIV-MVA boost (
n
= 38). A FASCIA using peripheral blood mononuclear cells (FASCIA-PBMC) was also employed (
n
= 14). Thirty-five of 38 (92%) vaccinees were reactive by the [
3
H]thymidine uptake assay. Thirty-two of 38 (84%) vaccinees were reactive by the CD4
+
T-cell FASCIA-WB, and 7 of 38 (18%) also exhibited CD8
+
T-cell responses. There was strong correlation between the proliferative responses measured by the [
3
H]thymidine uptake assay and CD4
+
T-cell FASCIA-WB (
r
= 0.68;
P
< 0.01). Fourteen vaccinees were analyzed using all three assays. Ten of 14 (71%) and 11/14 (79%) demonstrated CD4
+
T-cell responses in FASCIA-WB and FASCIA-PBMC, respectively. CD8
+
T-cell reactivity was observed in 3/14 (21%) and 7/14 (50%) using the FASCIA-WB and FASCIA-PBMC, respectively. All 14 were reactive by the [
3
H]thymidine uptake assay. The overall HIV-specific T-cell proliferative response in the vaccinees employing any of the assays was 100% (38/38). A standardized FASCIA-PBMC, which allows simultaneous phenotyping, may be an option to the [
3
H]thymidine uptake assay for assessment of vaccine-induced T-cell proliferation, especially in isotope-restricted settings.
Dendritic Cells in Uninfected Infants Born to Hepatitis B Virus-Positive Mothers
Authors: Koumbi Lemonica J. , Papadopoulos Nikolaos G. , Anastassiadou Vassiliki , Machaira Maria , Kafetzis Dimitris A. , Papaevangelou Vassiliki
Published: May 2010

Plasmacytoid dendritic cells (pDCs) play a central role in antiviral immunity, detecting viruses via Toll-like receptors (TLR) and producing in response vast amounts of type I interferons (IFNs). Hepatitis B virus (HBV) causes chronic infection after vertical transmission. This study investigated whether an HBV-infected maternal environment might influence DC numbers and pDC function in uninfected infants. Blood was collected from inactive HBsAg carrier and control mothers and their infants at birth and 1 and 6 months of age. HBV DNA was measured in maternal and neonatal perinatal sera using real-time PCR. The circulating frequencies of myeloid DCs (mDCs) and pDCs were determined in the babies by flow cytometry. Peripheral blood mononuclear cells (PBMCs) and cord blood pDCs were stimulated with resiquimod, and alpha interferon (IFN-α) production and the pDC phenotype were assessed. The effect of the common-cold virus, rhinovirus (RV), on resiquimod stimulation was also determined. HBV DNA was detected in 62.3% of the mothers and 41% of their infants. DC numbers and pDC functions were similar between subjects and controls and were not correlated with maternal or neonatal viremia. RV infection did not induce pDC maturation until the age of 6 months, and it reduced TLR7-dependent resiquimod-induced IFN-α production similarly in both groups. Although the DC system is immature at birth, DCs of uninfected neonates of HBV-positive mothers are competent to initiate and maintain T-cell responses. RV is a weak inducer of IFN-α production until the age of 6 months and inhibits IFN-α responses triggered by the TLR7 pathway.
Functional T-Cell Deficiency in Adolescents Who Experience Serogroup C Meningococcal Disease despite Receiving the Meningococcal Serogroup C Conjugate Vaccine
Authors: Foster Rachel A. , Carlring Jennifer , Lees Andrew , Borrow Ray , Ramsay Mary , Kacsmarski Ed , Miller Elizabeth , McKendrick Michael W. , Heath Andrew W. , Read Robert C.
Published: May 2010

Some individuals have experienced meningococcal disease despite receiving the meningococcal serogroup C conjugate (MCC) vaccine in adolescence. We sought to determine whether this is due to subclinical functional B- or T-cell immunodeficiency. Of 53 vaccine failures identified by enhanced surveillance of England and Wales from 1999 to 2004, 15 received MCC vaccine in adolescence, 9 of whom were recruited 2 to 6 years following convalescence from meningococcal disease. Their peripheral blood mononuclear cells (PBMCs) were incubated with polyclonal activators designed to mimic T-cell-independent B-cell stimulation by bacterial polysaccharides and the T-cell stimulation provided by the protein component of the conjugate vaccine. Subsequent proliferation and activation of T and B lymphocytes were measured, along with T-cell help to B cells. Compared to age-, sex-, geographically, and ethnicity-matched controls, CD4 T-cell proliferation rates in response to both anti-CD3 (T-cell receptor [TCR]) stimulation and anti-CD3 in the presence of B cells activated through anti-IgD conjugated to dextran (α-δ-dex) were lower in PBMCs derived from vaccine failures (P= 0.044 andP= 0.029, respectively). There was reduced CD4 cell activation of the patient cells compared to controls following stimulation by CD3 (P= 0.048). B-cell activation during incubation of PBMCs with the T-cell stimuli, anti-CD3 (P= 0.044), or anti-CD3 plus anti-CD28 (P= 0.018) was relatively impaired in patients. Anti-tetanus toxoid IgG concentrations were lower in the vaccine failure group (P= 0.0385). There was a relative defect of T-cell responsiveness to T-cell-dependent antigen stimulation in MCC vaccine failures, which was manifested in reduced T-cell help to B cells.
Analytical and Biological Considerations in the Measurement of Cell-Associated CCR5 and CXCR4 mRNA and Protein
Authors: Campbell D. E. , Lai J. P. , Tustin N. B. , Riedel E. , Tustin R. , Taylor J. , Murray J. , Douglas S. D.
Published: May 2010

The accurate measurement of T cell-associated CC chemokine receptor type 5 (CCR5) and CXC chemokine receptor type 4 (CXCR4) expression, including expression of CCR5 and CXCR4 mRNA as an immune measure of immunologic response to highly active antiretroviral therapy (HAART) and newer agents, including entry inhibitors, is essential. Previous studies have reported alterations in lymphocyte cell membrane CCR5 expression that were related to blood collection and cell separation media. Clinical trials often require the transport of specimens to central laboratories for evaluation, resulting in significant time delays between specimen procurement and analysis. This study shows that CCR5 expression on naïve and memory T cells is influenced by blood collection media and specimen age. Peripheral blood collected in Streck Vacutainer tubes containing a cell stabilizer and fixative was found to improve detection of CCR5 expression compared to specimens collected in K2 EDTA anticoagulant. The selection of flow cytometry gating strategies for the identification of naïve and memory T-helper cells can also significantly influence the sensitivity of detection of CCR5 expression. Procedural methods are described that allow for the optimal measurement of naïve and memory T-helper cell CCR5 and CXCR4 expression as well as the quantitation of CCR5 and CXCR4 mRNA.
Multicenter Study of Clinical Performance of the 3M Rapid Detection RSV Test
Authors: Ginocchio Christine C. , Swierkosz Ella , McAdam Alexander J. , Marcon Mario , Storch Gregory A. , Valsamakis Alexandra , Juretschko Stefan , Romero José , Yen-Lieberman Belinda
Published: May 2010

This multicenter study evaluated the clinical performance of the 3M Rapid Detection RSV test (3MRSV) compared to a composite reference standard of R-Mix culture and direct specimen immunofluorescence for detection of respiratory syncytial virus (RSV). The performance of the BinaxNOW RSV test was also evaluated using this reference standard. In a secondary analysis, discordant results were arbitrated using the Gen-Probe/Prodesse ProFlu+ reverse transcription-PCR (RT-PCR) assay. Subjects were stratified into three groups as follows: group 1 (G1), all ages; G2, subjects <22 years old (FDA-cleared ages for 3MRSV testing); and G3, subjects <5 years old (FDA-cleared ages for BinaxNOW RSV testing). A total of 1,306 specimens (G1,
n
= 1,306; G2,
n
= 1,140; G3,
n
= 953) from subjects of all ages presenting with respiratory symptoms met study criteria for analysis. Sensitivities, specificities, positive predictive values, and negative predictive values of 3MRSV for G1 were 86.5%, 95.8%, 91.4%, and 93.2%, respectively, and those for G2 were 87.3%, 95.6%, 92.4%, and 92.5%, respectively. For those samples analyzed by both 3MRSV and BinaxNOW, the 3MRSV was more sensitive (G1, 86.3%; G2, 87.2%; and G3, 89.9%) than was BinaxNOW (G1, 70.84%; G2, 72.0%; and G3, 72.4%) (
P
< 0.05). Specificities for RSV detection from nasopharyngeal (NP) aspirates and NP swabs for all groups were comparable for 3MRSV and BinaxNOW, but 3MRSV was less specific than BinaxNOW when nasal washes/aspirates were tested (
P
< 0.05). The 3MRSV assay performed well for the detection of RSV, and the overall assay performance was superior to that of BinaxNOW. The 3MRSV reader eliminated user misinterpretation and provided test result and quality control documentation.
Phylogenetic Analysis of Rubella Viruses Involved in Congenital Rubella Infections in France between 1995 and 2009
Authors: Vauloup-Fellous Christelle , Hübschen Judith M. , Abernathy Emily S. , Icenogle Joseph , Gaidot Nicolas , Dubreuil Pascal , Parent-du-Châtelet Isabelle , Grangeot-Keros Liliane , Muller Claude P.
Published: May 2010

Rubella is an acute infectious disease that normally has a mild clinical course. However, infections during pregnancy, especially before week 12 of gestation (WG), can cause severe birth defects known as congenital rubella syndrome (CRS). The aim of this study was to perform genotyping and molecular characterization of rubella viruses involved in congenital infections in France over the past 15 years (1995 to 2009). Amniotic fluid (AF) specimens (
n
= 80) from pregnant women with congenital rubella infections (CRI) before week 20 of gestation, and a few other samples available from children/newborns with CRS (
n
= 26), were analyzed. The coding region of the rubella virus E1 gene was amplified directly from clinical specimens by reverse transcriptase PCR, and the resulting DNA fragments were sequenced. Sequences were assigned to genotypes by phylogenetic analysis with rubella virus reference sequences. Sufficient E1 gene sequences were obtained from 56 cases. Phylogenetic analysis of the sequences showed that at least five different genotypes (1E, 1G, 1B, 2B, and 1h) were present in France and were involved in congenital infections, with a strong predominance of genotype 1E (87%). This is one of the very few comprehensive studies of rubella viruses involved in CRI. The results indicated that over the past 15 years, multiple introductions of the dominant genotype E caused most of the CRI cases in France. A few sporadic cases were due to other genotypes (1B, 1G, 1h, 2B).
Salmonella enterica
Serovar Virchow Bacteremia Presenting as Typhoid-Like Illness in an Immunocompetent Patient
Authors: Eckerle Isabella , Zimmermann Stefan , Kapaun Annette , Junghanss Thomas
Published: May 2010

We report a typhoid-like illness with fever and altered consciousness in a 22-year-old man with growth of
Salmonella enterica
serovar Virchow in blood and stool culture. Bacteremia and invasive disease due to non-typhoid salmonellae (NTS) are known in severely immunocompromised patients, but so far have not been described in immunocompetent adults.
Correlation of Parasite Load Determined by Quantitative PCR to Clinical Outcome in a Heart Transplant Patient with Disseminated Toxoplasmosis
Authors: Patrat-Delon Solène , Gangneux Jean-Pierre , Lavoué Sylvain , Lelong Bernard , Guiguen Claude , le Tulzo Yves , Robert-Gangneux Florence
Published: May 2010

Disseminated toxoplasmosis is a life-threatening infection in transplant recipients, which results either from reactivation of latent infection or from organ-transmitted primary infection. Preventive measures and diagnostic screening methods differ between countries and are related to the seroprevalence ofToxoplasmaspp. in the general population. Here we report a case of disseminated toxoplasmosis in a heart transplant recipient with previous immunity that occurred after cotrimoxazole prophylaxis for the prevention ofPneumocystis jiroveciipneumonia was stopped. Quantitative PCR proved useful for the diagnosis and monitoring ofToxoplasmainfection. Decreasing parasitic burdens in sequential samples of cerebrospinal fluid, blood, and bronchoalveolar lavage fluid correlated with a favorable outcome and allowed modulation of the immunosuppressive drug regimen. The duration of anti-Toxoplasmatreatment and the need for maintenance prophylaxis are discussed, as well as prophylaxis for solid-organ transplant recipients. Although a rare event in heart transplant recipients,Toxoplasmareactivation must be investigated promptly, since early treatment improves the prognosis.
In Vivo
Acquisition of a Plasmid-Mediated
bla
KPC-2
Gene among Clonal Isolates of
Serratia marcescens
Authors: Tsakris Athanassios , Voulgari Evangelia , Poulou Aggeliki , Kimouli Maria , Pournaras Spyros , Ranellou Kyriaki , Kosmopoulou Olga , Petropoulou Dimitra
Published: May 2010

Three patients admitted to a Greek hospital were infected with
Serratia marcescens
isolates that exhibited reduced susceptibility to carbapenems and harbored
Klebsiella pneumoniae
carbapenemase (KPC) enzymes. In two of these cases, the patients were initially infected by carbapenem-susceptible
S. marcescens
isolates. Molecular typing and plasmid analysis suggested that all three patients had clonally indistinguishable isolates of
S. marcescens
that acquired a plasmid-mediated
bla
KPC-2
gene during the hospitalization.
Pepscan Mapping of Viral Hemorrhagic Septicemia Virus Glycoprotein G Major Lineal Determinants Implicated in Triggering Host Cell Antiviral Responses Mediated by Type I Interferon
Authors: Chico V. , Martinez-Lopez A. , Ortega-Villaizan M. , Falco A. , Perez L. , Coll J. M. , Estepa A.
Published: May 2010

Surface glycoproteins of enveloped virus are potent elicitors of type I interferon (IFN)-mediated antiviral responses in a way that may be independent of the well-studied genome-mediated route. However, the viral glycoprotein determinants responsible for initiating the IFN response remain unidentified. In this study, we have used a collection of 60 synthetic 20-mer overlapping peptides (pepscan) spanning the full length of glycoprotein G (gpG) of viral hemorrhagic septicemia virus (VHSV) to investigate what regions of this protein are implicated in triggering the type I IFN-associated immune responses. Briefly, two regions with ability to increase severalfold the basal expression level of the IFN-stimulated
mx
gene and to restrict the spread of virus among responder cells were mapped to amino acid residues 280 to 310 and 340 to 370 of the gpG protein of VHSV. In addition, the results obtained suggest that an interaction between VHSV gpG and integrins might trigger the host IFN-mediated antiviral response after VHSV infection. Since it is known that type I IFN plays an important role in determining/modulating the protective-antigen-specific immune responses, the identification of viral glycoprotein determinants directly implicated in the type I IFN induction might be of special interest for designing new adjuvants and/or more-efficient and cost-effective viral vaccines as well as for improving our knowledge on how to stimulate the innate immune system.
The T=1 Capsid Protein of
Penicillium chrysogenum
Virus Is Formed by a Repeated Helix-Rich Core Indicative of Gene Duplication
Authors: Luque Daniel , González José M. , Garriga Damiá , Ghabrial Said A. , Havens Wendy M. , Trus Benes , Verdaguer Nuria , Carrascosa José L. , Castón José R.
Published: May 2010

Penicillium chrysogenum
virus (PcV), a member of the
Chrysoviridae
family, is a double-stranded RNA (dsRNA) fungal virus with a multipartite genome, with each RNA molecule encapsidated in a separate particle. Chrysoviruses lack an extracellular route and are transmitted during sporogenesis and cell fusion. The PcV capsid, based on a T=1 lattice containing 60 subunits of the 982-amino-acid capsid protein, remains structurally undisturbed throughout the viral cycle, participates in genome metabolism, and isolates the virus genome from host defense mechanisms. Using three-dimensional cryoelectron microscopy, we determined the structure of the PcV virion at 8.0 Å resolution. The capsid protein has a high content of rod-like densities characteristic of α-helices, forming a repeated α-helical core indicative of gene duplication. Whereas the PcV capsid protein has two motifs with the same fold, most dsRNA virus capsid subunits consist of dimers of a single protein with similar folds. The spatial arrangement of the α-helical core resembles that found in the capsid protein of the L-A virus, a fungal totivirus with an undivided genome, suggesting a conserved basic fold. The encapsidated genome is organized in concentric shells; whereas the inner dsRNA shells are well defined, the outermost layer is dense due to numerous interactions with the inner capsid surface, specifically, six interacting areas per monomer. The outermost genome layer is arranged in an icosahedral cage, sufficiently well ordered to allow for modeling of an A-form dsRNA. The genome ordering might constitute a framework for dsRNA transcription at the capsid interior and/or have a structural role for capsid stability.
Deep Sequencing Reveals Highly Complex Dynamics of Human Cytomegalovirus Genotypes in Transplant Patients over Time
Authors: Görzer Irene , Guelly Christian , Trajanoski Slave , Puchhammer-Stöckl Elisabeth
Published: May 2010

In lung transplant patients undergoing immunosuppression, more than one human cytomegalovirus (HCMV) genotype may emerge during follow-up, and this could be critical for the outcome of HCMV infection. Up to now, many cases of infection with multiple HCMV genotypes were probably overlooked due to the limitations of the current genotyping approaches. We have now analyzed mixed-genotype infections in 17 clinical samples from 9 lung transplant patients using the highly sensitive ultradeep-pyrosequencing (UDPS) technology. UDPS genotyping was performed at three variable HCMV genes, coding for glycoprotein N (gN), glycoprotein O (gO), and UL139. Simultaneous analysis of a mean of 10,430 sequence reads per amplicon allowed the relative amounts of distinct genotypes in the samples to be determined down to 0.1% to 1% abundance. Complex mixtures of up to six different HCMV genotypes per sample were observed. In all samples, no more than two major genotypes accounted for at least 88% of the HCMV DNA load, and these were often accompanied by up to four low-abundance genotypes at frequencies of 0.1% to 8.6%. No evidence for the emergence of new genotypes or sequence changes over time was observed. However, analysis of different samples withdrawn from the same patients at different time points revealed that the relative levels of replication of the individual HCMV genotypes changed within a mixed-genotype population upon reemergence of the virus. Our data show for the first time that, similar to what has been hypothesized for the murine model, HCMV reactivation in humans seems to occur stochastically.
Productive Replication of
vif
-Chimeric HIV-1 in Feline Cells
Authors: Stern Melissa A. , Hu Chunling , Saenz Dyana T. , Fadel Hind J. , Sims Olivia , Peretz Mary , Poeschla Eric M.
Published: May 2010

Nonprimate animal models of HIV-1 infection are prevented by missing cellular cofactors and by antiviral actions of species-specific host defense factors. These blocks are profound in rodents but may be less abundant in certain Carnivora. Here, we enabled productive, spreading replication and passage of HIV-1 in feline cells. Feline fibroblasts, T-cell lines, and primary peripheral blood mononuclear cells supported early and late HIV-1 life cycle phases in a manner equivalent to that of human cells, except that produced virions had low infectivity. Stable expression of feline immunodeficiency virus (FIV) Vif-green fluorescent protein (GFP) in HIV-1 entry receptor-complemented feline (CrFK) cells enabled robust spreading HIV-1 replication. FIV Vif colocalized with feline APOBEC3 (fA3) proteins, targeted them for degradation, and prevented G→A hypermutation of the HIV-1 cDNA by fA3CH and fA3H. HIV-1 Vif was inactive against fA3s as expected and even paradoxically augmented restriction in some assays. In an interesting contrast, simian immunodeficiency virus SIVmac Vif had substantial anti-fA3 activities, which were complete against fA3CH and partial against fA3H. Moreover, both primate lentiviral Vifs colocalized with fA3s and could be pulled down from cell lysates by fA3CH. HIV-1 molecular clones that encode FIV Vif or SIVmac Vif (HIV-1
VF
and HIV-1
VS
) were then constructed. These viruses replicated productively in HIV-1 receptor-expressing CrFK cells and could be passaged serially to uninfected cells. Thus, with the exception of entry receptors, the cat genome can supply the dependency factors needed by HIV-1, and a main restriction can be countered by
vif
chimerism. The results raise the possibility that the domestic cat could yield an animal model of HIV-1 infection.
Oligomerization of Ebola Virus VP40 Is Essential for Particle Morphogenesis and Regulation of Viral Transcription
Authors: Hoenen T. , Biedenkopf N. , Zielecki F. , Jung S. , Groseth A. , Feldmann H. , Becker S.
Published: May 2010

The morphogenesis and budding of virus particles represent an important stage in the life cycle of viruses. For Ebola virus, this process is driven by its major matrix protein, VP40. Like the matrix proteins of many other nonsegmented, negative-strand RNA viruses, VP40 has been demonstrated to oligomerize and to occur in at least two distinct oligomeric states: hexamers and octamers, which are composed of antiparallel dimers. While it has been shown that VP40 oligomers are essential for the viral life cycle, their function is completely unknown. Here we have identified two amino acids essential for oligomerization of VP40, the mutation of which blocked virus-like particle production. Consistent with this observation, oligomerization-deficient VP40 also showed impaired intracellular transport to budding sites and reduced binding to cellular membranes. However, other biological functions, such as the interaction of VP40 with the nucleoprotein, NP, remained undisturbed. Furthermore, both wild-type VP40 and oligomerization-deficient VP40 were found to negatively regulate viral genome replication, a novel function of VP40, which we have recently reported. Interestingly, while wild-type VP40 was also able to negatively regulate viral genome transcription, oligomerization-deficient VP40 was no longer able to fulfill this function, indicating that regulation of viral replication and transcription by VP40 are mechanistically distinct processes. These data indicate that VP40 oligomerization not only is a prerequisite for intracellular transport of VP40 and efficient membrane binding, and as a consequence virion morphogenesis, but also plays a critical role in the regulation of viral transcription by VP40.
Interferon Regulatory Factor 3 Attenuates Reovirus Myocarditis and Contributes to Viral Clearance
Authors: Holm Geoffrey H. , Pruijssers Andrea J. , Li Lianna , Danthi Pranav , Sherry Barbara , Dermody Terence S.
Published: May 2010

Apoptosis is a pathological hallmark of encephalitis and myocarditis caused by reovirus in newborn mice. In cell culture models, the antiviral transcription factor interferon regulatory factor 3 (IRF-3) enhances reovirus-induced apoptosis following activation via retinoic acid inducible gene I and interferon promoter-stimulating factor 1. To determine the role of IRF-3 in reovirus disease, we infected newborn IRF-3+/+and IRF-3−/−mice perorally with mildly virulent strain type 1 Lang (T1L) and fully virulent strain type 3 SA+ (T3SA+) and monitored infected animals for survival. Both wild-type and IRF-3−/−mice succumbed with equivalent frequencies to infection with T3SA+. However, the absence of IRF-3 was associated with significantly decreased survival rates following infection with T1L. The two virus strains achieved similar peak titers in IRF-3+/+and IRF-3−/−mice in the intestine, brain, heart, liver, and spleen. However, by day 12 postinoculation, titers in all organs examined were 10- to 100-fold higher in IRF-3−/−mice than those in wild-type mice. Increased titers were associated with marked pathological changes in all organs examined, especially in the heart, where absence of IRF-3 resulted in severe myocarditis. Cellular and humoral immune responses were equivalent in wild-type and IRF-3−/−animals, suggesting that IRF-3 functions independently of the adaptive immune response to enhance reovirus clearance. Thus, IRF-3 serves to facilitate virus clearance and prevent tissue injury in response to reovirus infection.
Opposing Effects of a Tyrosine-Based Sorting Motif and a PDZ-Binding Motif Regulate Human T-Lymphotropic Virus Type 1 Envelope Trafficking
Authors: Ilinskaya Anna , Heidecker Gisela , Derse David
Published: May 2010

Human T-lymphotropic virus type 1 (HTLV-1) envelope (Env) glycoprotein mediates binding of the virus to its receptor on the surface of target cells and subsequent fusion of virus and cell membranes. To better understand the mechanisms that control HTLV-1 Env trafficking and activity, we have examined two protein-protein interaction motifs in the cytoplasmic domain of Env. One is the sequence YSLI, which matches the consensus YXXΦ motifs that are known to interact with various adaptor protein complexes; the other is the sequence ESSL at the C terminus of Env, which matches the consensus PDZ-binding motif. We show here that mutations that destroy the YXXΦ motif increased Env expression on the cell surface and increased cell-cell fusion activity. In contrast, mutation of the PDZ-binding motif greatly diminished Env expression in cells, which could be restored to wild-type levels either by mutating the YXXΦ motif or by silencing AP2 and AP3, suggesting that interactions with PDZ proteins oppose an Env degradation pathway mediated by AP2 and AP3. Silencing of the PDZ protein hDlg1 did not affect Env expression, suggesting that hDlg1 is not a binding partner for Env. Substitution of the YSLI sequence in HTLV-1 Env with YXXΦ elements from other cell or virus membrane-spanning proteins resulted in alterations in Env accumulation in cells, incorporation into virions, and virion infectivity. Env variants containing YXXΦ motifs that are predicted to have high-affinity interaction with AP2 accumulated to lower steady-state levels. Interestingly, mutations that destroy the YXXΦ motif resulted in viruses that were not infectious by cell-free or cell-associated routes of infection. Unlike YXXΦ, the function of the PDZ-binding motif manifests itself only in the producer cells; AP2 silencing restored the incorporation of PDZ-deficient Env into virus-like particles (VLPs) and the infectivity of these VLPs to wild-type levels.
APOBEC3G Generates Nonsense Mutations in Human T-Cell Leukemia Virus Type 1 Proviral Genomes
In Vivo
Authors: Fan Jun , Ma Guangyong , Nosaka Kisato , Tanabe Junko , Satou Yorifumi , Koito Atsushi , Wain-Hobson Simon , Vartanian Jean-Pierre , Matsuoka Masao
Published: May 2010

Human T-cell leukemia virus type 1 (HTLV-1) induces cell proliferation after infection, leading to efficient transmission by cell-to-cell contact. After a long latent period, a fraction of carriers develop adult T-cell leukemia (ATL). Genetic changes in the
tax
gene in ATL cells were reported in about 10% of ATL cases. To determine genetic changes that may occur throughout the provirus, we determined the entire sequence of the HTLV-1 provirus in 60 ATL cases. Abortive genetic changes, including deletions, insertions, and nonsense mutations, were frequent in all viral genes except the
HBZ
gene, which is transcribed from the minus strand of the virus. G-to-A base substitutions were the most frequent mutations in ATL cells. The sequence context of G-to-A mutations was in accordance with the preferred target sequence of human APOBEC3G (hA3G). The target sequences of hA3G were less frequent in the plus strand of the
HBZ
coding region than in other coding regions of the HTLV-1 provirus. Nonsense mutations in viral genes including
tax
were also observed in proviruses from asymptomatic carriers, indicating that these mutations were generated during reverse transcription and prior to oncogenesis. The fact that hA3G targets the minus strand during reverse transcription explains why the
HBZ
gene is not susceptible to such nonsense mutations. HTLV-1-infected cells likely take advantage of hA3G to escape from the host immune system by losing expression of viral proteins.
Narratives of melancholy: a humanities approach to depression
Authors: Flynn Deborah
Published: May 2010

This paper explores narrative literature as a means of inquiry into the sense of self in depression. Described as a disease, an identity and a way of life, depression is influenced by both internal and external factors. Although brain research has provided new insight into the relationship between neurotransmitter function and depression, the symptoms are experienced by individuals whose lives are intertwined with historical and sociocultural interpretations of illness and its manifestations. At the intersection of science and the humanities, narratives aid in the interpretation of lived experiences, provide a window to that experience, and a public medium that engages writers and readers as they interpret the world. Engaging narratives to interpret both experience and medical jargon may reveal for both those experiencing depression and those engaged in their care, a way of mediating that experience. Narratives can help dissect and thus illuminate the official language of medicine and psychiatry and the personal language of depression. Such a window can enhance the opportunities for empathy and care.
Historical and contemporary perspectives on children's diets: is choice always in the patients' best interest?
Authors: Denny G , Sundvall P , Thornton S J , Reinarz J , Williams A N
Published: May 2010

On 29 March 1744, Thomasin Grace, a 13-year-old girl, was the first inpatient admitted to the Northampton General Infirmary (later the Northampton General Hospital). Inpatient hospital diets, then and now, are mainstays of effective patient treatment. In the mid-18th century there were four prescribed diets at Northampton: ‘full’, ‘milk’, ‘dry’ and ‘low’. Previous opinions concerning these four diets were unfavourable, but had not been based upon an individual dietetic assessment. Thomasin would most likely have been given the milk diet, but use of the full diet cannot be excluded.

‘Grace Everyman’ is Thomasin's modern equivalent. Under current NHS guidelines Thomasin would be considered a paediatric patient, but in 1744 she would have been considered as an adult. This study undertakes a full dietetic analysis of all the prescribed diets available for Thomasin in 1744 and compares this against random choices for Grace from the 2009 inpatient menu from the paediatric (Paddington) ward, and the adult ward inpatient menu at the Northampton General Hospital. The results show that, for Thomasin, the 1744 milk and full diets met the current advised nutritional requirements for adequate dietary intake. However, for Grace, the present 2009 Paddington and adult ward menu, although generally meeting nutritional requirements, could, if Grace or her carer consistently chose poorly during a prolonged inpatient stay, lead to inadequate nutrition. This challenges assumptions that hospital diets were historically inadequate, and that choice in present day equates with satisfactory nutritional intake.
Perivitelline Fluid pH of Rainbow Trout (Oncorhynchus mykiss) Eggs in Relation to Ambient pH
Authors: Kügel B. , Peterson R. H.
Published: May 2010

In soft water of various pH levels, the perivitelline fluid of late eyed rainbow trout (Oncorhynchus mykiss) eggs showed significant pH buffering: final perivitelline pH was higher than ambient by 0.7–0.85 pH unit in acidified water but was lower by 0.3–1.0 pH unit in weak acidified or basic water. No significant difference between the pH of an external buffer solution and that of the perivitelline fluid could be observed after 24 h. Most rapid perivitelline pH change occurred in the first 2 h and in the first 10–20 min, when eggs were transferred from acidified to weak acid or basic water and buffer, respectively. Final pH of the perivitelline fluid was reached after 48 h in unbuffered water and 24 h or less in buffer.
Identification of Sockeye Salmon (Oncorhynehus nerka) Stocks in Mixed-stock Fisheries in British Columbia and Southeast Alaska using Biological Markers
Authors: Wood Chris C. , Rutherford Dennis T. , McKinnell Skip
Published: May 2010

We demonstrate the present analytical capability and the potential for coast-wide stock identification of sockeye salmon (Oncorhynchus nerka) using reference sampling data from 51 principal stocks in British Columbia and Southeast Alaska situated between the Fraser and Taku Rivers. We evaluate the relative accuracy and precision of stock composition estimates from maximum likelihood mixture analysis with four types of biological markers, either alone or in combination; these include freshwater age, six scale pattern variables, the prevalence of the brain parasite Myxobolus neurobius, and five biochemical genetic (electrophoretic) traits. Using all markers in combination, estimates of mixing proportions for all test mixtures are acceptable for most purposes (roughly ± 10% with 95% confidence) providing all samples are representative and mixture samples are large ([Formula: see text] fish). The reliability of these estimates is greatly reduced when reference samples are corrupted to simulate observed annual variation in scale pattern markers. Annual variation may preclude the use of scale pattern markers for complicated stock identification problems where representative reference samples cannot be obtained annually, or until after the fishing period. In contrast, no significant annual variation is detectable for biochemical genetic and brain parasite markers in stocks that have been sampled repeatedly. Using only these stable markers, contributions from about 15 different groups of the 51 stocks can be estimated with acceptable precision, but in general, estimates for individual stocks are unreliable.
Thyroid Hormone Content of Eggs and Early Developmental Stages of Five Oncorhynchus Species
Authors: Leatherland J. F. , Lin L. , Down N. E. , Donaldson E. M.
Published: May 2010

Measurements were made of thyroxine (T4) and triiodothyronine (T3) levels in the embryos and larvae of five species of the genus Oncorhynchus. Pink salmon (O. gorbuscha) embryos and larvae contained relatively low levels of both T4 and T3 throughout the early developmental stages. Sockeye salmon (O. nerka) had the highest levels of T4, with coho (O. kisutch), chum (O. keta), and chinook salmon (O. tshawytscha) having similar total T4 content. The chinook salmon embryos contained the highest T3 content of the five species studied, pink, sockeye, and chum salmon embryos had relatively low levels, and coho salmon embryos had intermediate levels of T3. In the pink salmon, there was little evidence of significant change in either T4 or T3 during development. In the other four species, the T4 content changed little between fertilization and hatch, but fell thereafter to stabilize at levels close to the lower detectable range of the assay used, except in the sockeye salmon larvae in which the values were considerably higher. The T3 content of chinook and coho salmon changed with development in a manner comparable with that observed for T4, but there was little evidence of a comparable posthatch decline in T3 levels in chum, sockeye, or pink salmon.
Thyroid Hormone Content of Eggs and Early Developmental Stages of Three Stocks of Goitred Coho Salmon (Oncorhynchus kisutch) from the Great Lakes of North America, and a Comparison with a Stock from British Columbia
Authors: Leatheland J. F. , Lin L. , Down N. E. , Donaldson E. M.
Published: May 2010

The thyroxine (T4) and triiodothyronine (T3) concentrations in embryos and larvae of two stocks of markedly goitred Lake Erie coho salmon (Oncorhynchus kisutch) were lower than in comparable developmental stages of a mildly goitred Lake Michigan and a nongoitred British Columbia stock. There was no apparent correlation between fecundity, egg weight, embryo mortality rates, or developmental rates of the three Great Lakes stocks and the egg yolk reserves of thyroid hormone, indicating that the reserves may not ipso facto affect developmental success. The low thyroid hormone levels of the embryos of the two Lake Erie stocks were probably related to the dysfunction in hormone uptake from the maternal blood during the period of oocyte growth, and not to low maternal blood thyroid hormone levels per se.