bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calculation of strain images of a breast‐mimicking phantom from 3D CT image data
Authors: Kim Jae G. , Aowlad Hossain A. B. M. , Shin Jong H. , Lee Soo Y. 
Published: August 2012

Purpose:Elastography is a medical imaging modality to visualize the elasticity of soft tissues. Ultrasound and MRI have been exclusively used for elastography of soft tissues since they can sensitize the tissues’ minute displacements of an order ofμm. It is known that ultrasound and MRI elastography show cancerous tissues with much higher contrast than conventional ultrasound and MRI. To evaluate possibility of combining elastography with x‐ray imaging, we have calculated strain images of a breast‐mimicking phantom from its 3D CT image data.Methods:We first simulated the x‐ray elastography using a FEM model which incorporated both the elasticity and x‐ray attenuation behaviors of breast tissues. After validating the x‐ray elastography scheme by simulation, we made a breast‐mimicking phantom that contained a hard inclusion against soft background. With a micro‐CT, we took 3D images of the phantom twice, changing the compressing force to the phantom. From the two 3D phantom images taken with two different compression ratios, we calculated the displacement vector maps that represented the compression‐induced pixel displacements. In calculating the displacement vectors, we tracked the movements of image feature patterns from the less‐compressed‐phantom images to the more‐compressed‐phantom images using the 3D image correlation technique. We obtained strain images of the phantom by differentiating the displacement vector maps.Results:The FEM simulation has shown that x‐ray strain imaging is possible by tracking image feature patterns in the 3D CT images of the breast‐mimicking phantom. The experimental displacement and strain images of a breast‐mimicking phantom, obtained from the 3D micro‐CT images taken with 0%–3% compression ratios, show behaviors similar to the FEM simulation results. The contrast and noise performance of the strain images improves as the phantom compression ratio increases.Conclusions:We have experimentally shown that we can improve x‐ray strain image quality by applying 3D image correlation to the two sets of 3D CT images taken with different compression ratios. But, we need further investigations to evaluate the strain imaging performance considering the noise and decorrelation effects as well as the extra dose caused by two scans.
Effects on Immunogenicity by Formulations of Emulsion-Based Adjuvants for Malaria Vaccines
Authors: Fox Christopher B. , Baldwin Susan L. , Vedvick Thomas S. , Angov Evelina , Reed Steven G. 
Published: August 2012

ABSTRACTNew malaria vaccines are urgently needed to improve vaccine protective efficacy. PfCelTOS is a recombinant malaria vaccine antigen that has shown protective efficacy in a small-animal challenge model when combined with a water-in-oil emulsion adjuvant (Montanide ISA 720). In this report, we show that PfCelTOS vaccines containing GLA-SE (a stable oil-in-water emulsion combined with a Toll-like receptor 4 [TLR4] agonist) elicit strong Th1-type immune responses in BALB/c mice. These responses include higher antigen-specific IgG2a antibody titers and more gamma interferon (IFN-γ) production than those seen with a PfCelTOS vaccine containing Montanide ISA 720. Furthermore, reducing the emulsion dose from 2% to 1% or 0.5% (vol/vol) squalene in GLA-SE did not compromise immunogenicity. Emulsion dose titration in the absence of formulated GLA caused some reduction in humoral and cellular immune responses compared to those with the 2% squalene emulsion dose.
Prosthetic Joint Infection Diagnosis Using Broad-Range PCR of Biofilms Dislodged from Knee and Hip Arthroplasty Surfaces Using Sonication
Authors: Gomez Eric , Cazanave Charles , Cunningham Scott A. , Greenwood-Quaintance Kerryl E. , Steckelberg James M. , Uhl James R. , Hanssen Arlen D. , Karau Melissa J. , Schmidt Suzannah M. , Osmon Douglas R. , Berbari Elie F. , Mandrekar Jayawant , Patel Robin 
Published: August 2012

ABSTRACT

Periprosthetic tissue and/or synovial fluid PCR has been previously studied for prosthetic joint infection (PJI) diagnosis; however, few studies have assessed the utility of PCR on biofilms dislodged from the surface of explanted arthroplasties using vortexing and sonication (i.e., sonicate fluid PCR). We compared sonicate fluid 16S rRNA gene real-time PCR and sequencing to culture of synovial fluid, tissue, and sonicate fluid for the microbiologic diagnosis of PJI. PCR sequences generating mixed chromatograms were decatenated using RipSeq Mixed. We studied sonicate fluids from 135 and 231 subjects with PJI and aseptic failure, respectively. Synovial fluid, tissue, and sonicate fluid culture and sonicate fluid PCR had similar sensitivities (64.7, 70.4, 72.6, and 70.4%, respectively;
P
> 0.05) and specificities (96.9, 98.7, 98.3, and 97.8%, respectively;
P
> 0.05). Combining sonicate fluid culture and PCR, the sensitivity was higher (78.5%,
P
< 0.05) than those of individual tests, with similar specificity (97.0%). Thirteen subjects had positive sonicate fluid culture but negative PCR, and 11 had negative sonicate fluid culture but positive PCR (among which 7 had prior use of antimicrobials). Broad-range PCR and culture of sonicate fluid have equivalent performance for PJI diagnosis.
Echinocandin Resistance in Two Candida haemulonii Isolates from Pediatric Patients
Authors: Dominguez Muro Marisol , Motta Fábio de Araújo , Burger Marion , Melo Analy Salles de Azevedo , Dalla-Costa Líbera Maria 
Published: August 2012

ABSTRACT

We report 3 cases of patients with
Candida haemulonii
isolates that were obtained from hemocultures. In 2 of the 3 cases, isolates exhibited resistance to echinocandins and fluconazole. This is the first report of an echinocandin-resistant species of this fungus in pediatric patients.
Molecular Epidemiological Study of Enteroviruses Associated with Encephalitis in Children from India
Authors: Kumar Arvind , Shukla Deepti , Kumar Rashmi , Idris Mohammad Z. , Misra Usha K. , Dhole Tapan N. 
Published: August 2012

ABSTRACT
Enteroviruses have been reported in encephalitis cases. However, clinical and epidemiological characteristics of enteroviruses in encephalitis are not fully established. We prospectively investigated 204 children with encephalitis over a period of 2 years (2009 to 2010) for enterovirus. Enterovirus was detected in 45 specimens (22.1%); of these, 40 were typed by seminested reverse transcription-PCR (RT-PCR) and sequencing of the VP1 gene. Molecular typing of enterovirus revealed the predominance of echovirus 21 associated with an epidemic during the rainy seasons of 2010 and the circulation of echovirus 1, coxsackievirus B1, enterovirus 75, enterovirus 76, coxsackievirus B5, and echovirus 19. The nucleotide divergence among echovirus 21 strains was 0 to 2% at the nucleotide level. This study suggests that enterovirus is an important cause of encephalitis in children from India. To our knowledge, this is the first report of echovirus 21 in encephalitis cases worldwide.
Prospective Genotyping of Hospital-Acquired Methicillin-Resistant Staphylococcus aureus Isolates by Use of a Novel, Highly Discriminatory Binary Typing System
Authors: O'Sullivan Matthew V. N. , Zhou Fei , Sintchenko Vitali , Gilbert Gwendolyn L. 
Published: August 2012

ABSTRACT

In settings of high methicillin-resistant
Staphylococcus aureus
(MRSA) prevalence, detection of nosocomial transmission events can be difficult without strain typing. Prospective typing of all MRSA isolates could potentially identify transmission in a timely fashion, making infection control responses to outbreaks more effective. We describe the development and evaluation of a novel 19-target binary typing system for MRSA using the multiplex-PCR/reverse line blot hybridization platform. Pulse-field gel electrophoresis (PFGE),
spa
typing, and phage-derived open reading frame (PDORF) typing were performed for comparison. The system was utilized to identify transmission events in three general surgical wards over a 12-month period. Initial MRSA isolates from 273 patients were differentiated into 55 unique binary types. One or more potential contacts colonized with the same MRSA strain were identified in 69 of 87 cases (79%) in which definite or possible nosocomial MRSA acquisition had occurred. The discriminatory power of the typing system was similar to that of PFGE (Simpson's index of diversity [
D
] = 0.994, versus 0.987) and higher than that of
spa
typing (
D
= 0.926). Strain typing reduced the total number of potential MRSA-colonized source contacts from 859 to 212 and revealed temporal clustering of transmission events. Prospective MRSA typing using this novel binary typing method can rapidly identify nosocomial transmission events, even in high-prevalence settings, which allows timely infection control interventions. The system is rapid, inexpensive, discriminatory, and suitable for routine, high-throughput use in the hospital microbiology laboratory.
Molecular Epidemiology of Acinetobacter baumannii Bloodstream Isolates Obtained in the United States from 1995 to 2004 Using rep-PCR and Multilocus Sequence Typing
Authors: Higgins Paul G. , Janßen Katharina , Fresen Maximilian M. , Wisplinghoff Hilmar , Seifert Harald 
Published: August 2012

ABSTRACT

Using a repetitive-sequence-based (rep)-PCR (DiversiLab), we have molecularly typed
Acinetobacter
nosocomial bloodstream isolates (
Acinetobacter
baumannii
[
n
= 187],
Acinetobacter
pittii
[
n
= 23], and
Acinetobacter
nosocomialis
[
n
= 61]) obtained from patients hospitalized in U.S. hospitals over a 10-year period (1995-2004) during a nationwide surveillance study (Surveillance and Control of Pathogens of Epidemiological Importance [SCOPE]). Patterns of
A. baumannii
rep-PCR were compared to those of previously identified international clonal lineages (ICs) and were further investigated by multilocus sequence typing (MLST) to compare the two typing methods. Forty-seven of the
A. baumannii
isolates clustered with the previously defined IC 2. ICs 1, 3, 6, and 7 were also detected. The remaining 81 isolates were unrelated to the described ICs. In contrast,
A. pittii
and
A. nosocomialis
isolates were more heterogeneous, as determined by rep-PCR. Our MLST results were in good correlation with the rep-PCR clusters. Our study confirms previous data indicating the predominance of a few major clonal
A. baumannii
lineages in the United States, particularly IC 2. The presence in the United States of
A. baumannii
ICs 1, 2, and 3 from as early as 1995 suggests that global dissemination of these lineages was an early event.
First Human Case of Pulmonary Fungal Ball Due to a Perenniporia Species (a Basidiomycete)
Authors: Chowdhary Anuradha , Agarwal Kshitij , Kathuria Shallu , Singh Pradeep Kumar , Roy P. , Gaur S. N. , Rodrigues Anderson M. , de Hoog G. S. , Meis Jacques F. 
Published: August 2012

ABSTRACT

Perenniporia
species are basidiomycetes, resupinate shelf fungi responsible for white rot decay of wood. Here, we report for the first time an intracavitary pulmonary fungal ball due to a species of
Perenniporia
that has not been recognized so far as a human pathogen. The fungus was identified by sequencing of the partial ribosomal operon of a culture from a clinical specimen.
Proteomic Characterization of Bovine Herpesvirus 4 Extracellular Virions
Authors: Lété Céline , Palmeira Leonor , Leroy Baptiste , Mast Jan , Machiels Bénédicte , Wattiez Ruddy , Vanderplasschen Alain , Gillet Laurent 
Published: August 2012

ABSTRACT
Gammaherpesviruses are important pathogens in human and animal populations. During early events of infection, these viruses manipulate preexisting host cell signaling pathways to allow successful infection. The different proteins that compose viral particles are therefore likely to have critical functions not only in viral structures and in entry into target cell but also in evasion of the host's antiviral response. In this study, we analyzed the protein composition of bovine herpesvirus 4 (BoHV-4), a close relative of the human Kaposi's sarcoma-associated herpesvirus. Using mass spectrometry-based approaches, we identified 37 viral proteins associated with extracellular virions, among which 24 were resistant to proteinase K treatment of intact virions. Analysis of proteins associated with purified capsid-tegument preparations allowed us to define protein localization. In parallel, in order to identify some previously undefined open reading frames, we mapped peptides detected in whole virion lysates onto the six frames of the BoHV-4 genome to generate a proteogenomic map of BoHV-4 virions. Furthermore, we detected important glycosylation of three envelope proteins: gB, gH, and gp180. Finally, we identified 38 host proteins associated with BoHV-4 virions; 15 of these proteins were resistant to proteinase K treatment of intact virions. Many of these have important functions in different cellular pathways involved in virus infection. This study extends our knowledge of gammaherpesvirus virions composition and provides new insights for understanding the life cycle of these viruses.
HIV Control through a Single Nucleotide on the HLA-B Locus
Authors: Kløverpris Henrik N. , Harndahl Mikkel , Leslie Alasdair J. , Carlson Jonathan M. , Ismail Nasreen , van der Stok Mary , Huang Kuan-Hsiang Gary , Chen Fabian , Riddell Lynn , Steyn Dewald , Goedhals Dominique , van Vuuren Cloete , Frater John , Walker Bruce D. , Carrington Mary , Ndung'u Thumbi , Buus Søren , Goulder Philip 
Published: August 2012

ABSTRACTGenetic variation within the HLA-B locus has the strongest impact on HIV disease progression of any polymorphisms within the human genome. However, identifying the exact mechanism involved is complicated by several factors. HLA-Bw4 alleles provide ligands for NK cells and for CD8 T cells, and strong linkage disequilibrium between HLA class I alleles complicates the discrimination of individual HLA allelic effects from those of other HLA and non-HLA alleles on the same haplotype. Here, we exploit an experiment of nature involving two recently diverged HLA alleles, HLA-B*42:01 and HLA-B*42:02, which differ by only a single amino acid. Crucially, they occur primarily on identical HLA class I haplotypes and, as Bw6 alleles, do not act as NK cell ligands and are therefore largely unconfounded by other genetic factors. We show that in an outbred cohort (n= 2,093) of HIV C-clade-infected individuals, a single amino acid change at position 9 of the HLA-B molecule critically affects peptide binding and significantly alters the cytotoxic T lymphocyte (CTL) epitopes targeted, measured directlyex vivoby gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay (P= 2 × 10−10) and functionally through CTL escape mutation (P= 2 × 10−8). HLA-B*42:01, which presents multiple Gag epitopes, is associated with a 0.52 log10lower viral-load set point than HLA-B*42:02 (P= 0.02), which presents no p24 Gag epitopes. The magnitude of this effect from a single amino acid difference in the HLA-A*30:01/B*42/Cw*17:01 haplotype is equivalent to 75% of that of HLA-B*57:03, the most protective HLA class I allele in this population. This naturally controlled experiment represents perhaps the clearest demonstration of the direct impact of a particular HIV-specific CTL on disease control.
Antibody-Dependent Cellular Cytotoxicity-Mediating Antibodies from an HIV-1 Vaccine Efficacy Trial Target Multiple Epitopes and Preferentially Use the VH1 Gene Family
Authors: Bonsignori Mattia , Pollara Justin , Moody M. Anthony , Alpert Michael D. , Chen Xi , Hwang Kwan-Ki , Gilbert Peter B. , Huang Ying , Gurley Thaddeus C. , Kozink Daniel M. , Marshall Dawn J. , Whitesides John F. , Tsao Chun-Yen , Kaewkungwal Jaranit , Nitayaphan Sorachai , Pitisuttithum Punnee , Rerks-Ngarm Supachai , Kim Jerome H. , Michael Nelson L. , Tomaras Georgia D. , Montefiori David C. , Lewis George K. , DeVico Anthony , Evans David T. , Ferrari Guido , Liao Hua-Xin , Haynes Barton F. 
Published: August 2012

ABSTRACTThe ALVAC-HIV/AIDSVAX-B/E RV144 vaccine trial showed an estimated efficacy of 31%. RV144 secondary immune correlate analysis demonstrated that the combination of low plasma anti-HIV-1 Env IgA antibodies and high levels of antibody-dependent cellular cytotoxicity (ADCC) inversely correlate with infection risk. One hypothesis is that the observed protection in RV144 is partially due to ADCC-mediating antibodies. We found that the majority (73 to 90%) of a representative group of vaccinees displayed plasma ADCC activity, usually (96.2%) blocked by competition with the C1 region-specific A32 Fab fragment. Using memory B-cell cultures and antigen-specific B-cell sorting, we isolated 23 ADCC-mediating nonclonally related antibodies from 6 vaccine recipients. These antibodies targeted A32-blockable conformational epitopes (n= 19), a non-A32-blockable conformational epitope (n= 1), and the gp120 Env variable loops (n= 3). Fourteen antibodies mediated cross-clade target cell killing. ADCC-mediating antibodies displayed modest levels of V-heavy (VH) chain somatic mutation (0.5 to 1.5%) and also displayed a disproportionate usage of VH1 family genes (74%), a phenomenon recently described for CD4-binding site broadly neutralizing antibodies (bNAbs). Maximal ADCC activity of VH1 antibodies correlated with mutation frequency. The polyclonality and low mutation frequency of these VH1 antibodies reveal fundamental differences in the regulation and maturation of these ADCC-mediating responses compared to VH1 bNAbs.
Kaposi's Sarcoma-Associated Herpesvirus MicroRNAs Target IRAK1 and MYD88, Two Components of the Toll-Like Receptor/Interleukin-1R Signaling Cascade, To Reduce Inflammatory-Cytokine Expression
Authors: Abend Johanna R. , Ramalingam Dhivya , Kieffer-Kwon Philippe , Uldrick Thomas S. , Yarchoan Robert , Ziegelbauer Joseph M. 
Published: August 2012

ABSTRACTKaposi's sarcoma (KS)-associated herpesvirus (KSHV) is the causative agent of KS, an important AIDS-associated malignancy. KSHV expresses at least 18 different mature microRNAs (miRNAs). We identified interleukin-1 receptor (IL-1R)-associated kinase 1 (IRAK1) as a potential target of miR-K12-9 (miR-K9) in an array data set examining changes in cellular gene expression levels in the presence of KSHV miRNAs. Using 3′-untranslated region (3′UTR) luciferase reporter assays, we confirmed that miR-K9 and other miRNAs inhibit IRAK1 expression. In addition, IRAK1 expression is downregulated in cells transfected with miR-K9 and duringde novoKSHV infection. IRAK1 is an important component of the Toll-like receptor (TLR)/IL-1R signaling cascade. The downregulation of IRAK1 by miR-K9 resulted in the decreased stimulation of NF-κB activity in endothelial cells treated with IL-1α and in B cells treated with a TLR7/8 agonist. Interestingly, miR-K9 had a greater effect on NF-κB activity than did a small interfering RNA (siRNA) targeting IRAK1 despite the more efficient downregulation of IRAK1 expression with the siRNA. We hypothesized that KSHV miRNAs may also be regulating a second component of the TLR/IL-1R signaling cascade, resulting in a stronger phenotype. Reanalysis of the array data set identified myeloid differentiation primary response protein 88 (MYD88) as an additional potential target. 3′UTR luciferase reporter assays and Western blot analysis confirmed the targeting of MYD88 by miR-K5. The presence of miR-K9 and miR-K5 inhibited the production of IL-6 and IL-8 upon the IL-1α stimulation of endothelial cells. These results demonstrate KSHV-encoded miRNAs regulating the TLR/IL-1R signaling cascade at two distinct points and suggest the importance of these pathways during viral infection.
Identification of the HIV-1 NC Binding Interface in Alix Bro1 Reveals a Role for RNA
Authors: Sette Paola , Dussupt Vincent , Bouamr Fadila 
Published: August 2012

ABSTRACT
HIV-1 recruits members of ESCRT, the cell membrane fission machinery that promotes virus exit. HIV-1 Gag protein gains access to ESCRT directly by binding Alix, an ESCRT-associated protein that promotes budding. The Alix Bro1 and V domains bind Gag NC and p6 regions, respectively. Whereas V-p6 binding and function are well characterized, residues in Bro1 that interact with NC and their functional contribution to Alix-mediated HIV-1 budding are unknown. We mapped Bro1 residues that constitute the NC binding interface and found that they are critical for function. Intriguingly, residues involved in interactions on both sides of the Bro1-NC interface are positively charged, suggesting the involvement of a negatively charged cellular factor serving as a bridge. Nuclease treatment eliminated Bro1-NC interactions, revealing the involvement of RNA. These findings establish a direct role for NC in mediating interactions with ESCRT necessary for virus release and report the first evidence of RNA involvement in such recruitments.
Packaging Accessory Protein P7 and Polymerase P2 Have Mutually Occluding Binding Sites inside the Bacteriophage ϕ6 Procapsid
Authors: Nemecek Daniel , Qiao Jian , Mindich Leonard , Steven Alasdair C. , Heymann J. Bernard 
Published: August 2012

ABSTRACT

Bacteriophage ϕ6 is a double-stranded RNA (dsRNA) virus whose genome is packaged sequentially as three single-stranded RNA (ssRNA) segments into an icosahedral procapsid which serves as a compartment for genome replication and transcription. The procapsid shell consists of 60 copies each of P1
A
and P1
B
, two nonequivalent conformers of the P1 protein. Hexamers of the packaging ATPase P4 are mounted over the 5-fold vertices, and monomers of the RNA-dependent RNA polymerase (P2) attach to the inner surface, near the 3-fold axes. A fourth protein, P7, is needed for packaging and also promotes assembly. We used cryo-electron microscopy to localize P7 by difference mapping of procapsids with different protein compositions. We found that P7 resides on the interior surface of the P1 shell and appears to be monomeric. Its binding sites are arranged around the 3-fold axes, straddling the interface between two P1
A
subunits. Thus, P7 may promote assembly by stabilizing an initiation complex. Only about 20% of the 60 P7 binding sites were occupied in our preparations. P7 density overlaps P2 density similarly mapped, implying mutual occlusion. The known structure of the ϕ12 homolog fits snugly into the P7 density. Both termini—which have been implicated in RNA binding—are oriented toward the adjacent 5-fold vertex, the entry pathway of ssRNA segments. Thus, P7 may promote packaging either by interacting directly with incoming RNA or by modulating the structure of the translocation pore.
Memory CD4
+
T Lymphocytes in the Gastrointestinal Tract Are a Major Source of Cell-Associated Simian Immunodeficiency Virus in Chronic Nonpathogenic Infection of African Green Monkeys
Authors: Schmitz Joern E. , Ma Zhong-Min , Hagan Emily A. , Wilks Andrew B. , Furr Kathryn L. , Linde Caitlyn H. , Zahn Roland C. , Brenchley Jason M. , Miller Christopher J. , Permar Sallie R. 
Published: August 2012

ABSTRACT

Simian immunodeficiency virus (SIV) infection of natural hosts is characterized by nonpathogenic chronic viremia, maintenance of gastrointestinal epithelial barrier integrity, and low numbers of target cells. Assessment of cell-associated virus load in T cell subsets in multiple anatomic compartments of chronically SIV-infected sabeus African green monkeys (AGMs) revealed that gastrointestinal memory CD4
+
T lymphocytes are a major source of cell-associated virus and a significant contributor to SIV viremia in AGMs.