bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics of an OSLD in the diagnostic energy range
Authors: Al‐Senan Rani M. , Hatab Mustapha R. 
Published: June 2011

Purpose:Optically stimulated luminescence (OSL) dosimetry has been recently introduced in radiation therapy as a potential alternative to the thermoluminescent dosimeter (TLD) system. The aim of this study was to investigate the feasibility of using OSL point dosimeters in the energy range used in diagnostic imaging.Methods:NanoDot OSL dosimeters (OSLDs) were used in this study, which started with testing the homogeneity of a new packet of nanoDots. Reproducibility and the effect of optical treatment (bleaching) were then examined, followed by an investigation of the effect of accumulated dose on the OSLD indicated doses. OSLD linearity, angular dependence, and energy dependence were also studied. Furthermore, comparison with LiF:Mg,Ti TLD chips using standard CT dose phantoms at 80 and 120 kVp settings was performed.Results:Batch homogeneity showed a coefficient of variation of <5%. Single‐irradiation measurements with bleaching after each OSL readout was found to be associated with a 3.3% reproducibility (one standard deviation measured with a 8 mGy test dose), and no systematic change in OSLDs sensitivity could be noted from measurement to measurement. In contrast, the multiple‐irradiation readout without bleaching in between measurements was found to be associated with an uncertainty (using a 6 mGy test dose) that systematically increased with accumulated dose, reaching 42% at 82 mGy. Good linearity was shown by nanoDots under general x‐ray, CT, and mammography units with anR2 > 0.99. The angular dependence test showed a drop of approximately 70% in the OSLD response at 90° in mammography (25 kVp). With the general radiography unit, the maximum drop was 40% at 80 kVp and 20% at 120 kVp, and it was only 10% with CT at both 80 and 120 kVp. The energy dependence study showed a range of ion chamber‐to‐OSLDs ratios between 0.81 and 1.56, at the energies investigated (29–62 keV). A paired t‐test for comparing the OSLDs and TLDs showed no significant variation (p > 0.1).Conclusions:OSLDs exhibited good batch homogeneity (<5%) and reproducibility (3.3%), as well as a linear response. In addition, they showed no statistically significant difference with TLDs in CT measurements (p > 0.1). However, high uncertainty (42%) in the dose estimate was found as a result of relatively high accumulated dose. Furthermore, nanoDots showed high angular dependence (up to 70%) in low kVp techniques. Energy dependence of about 60% was found, and correction factors were suggested for the range of energies investigated. Therefore, if angular and energy dependences are taken into consideration and the uncertainty associated with accumulated dose is avoided, OSLDs (nanoDots) can be suitable for use as point dosimeters in diagnostic settings.
Pulmonary nodule registration: Rigid or nonrigid?
Authors: Gu Suicheng , Wilson David , Tan Jun , Pu Jiantao 
Published: June 2011

Purpose:The primary aim of this study is to investigate the performance difference of rigid and nonrigid registration schemes in matching corresponding pulmonary nodules depicted on sequential chest computed tomography (CT) examinations.Methods:A gradient descent based rigid registration algorithm with scaling was developed and it handled the involved geometric transformations (i.e., translation, rescaling, shearing, and rotation) separately instead of optimizing them in a single pass. Given two lung CT examinations, the scaling and translation parameters were simply estimated from the lung volume dimensions (e.g., size and mass center), while the rotation parameters were optimized progressively using gradient descent. To investigate the performance difference of rigid and nonrigid schemes in pulmonary nodule registration, the well‐known nonrigid Demons algorithm was implemented and tested along with the developed schemes against 60 diverse low‐dose clinical lung CT examinations with average 2‐yr follow‐up scans. A verified cancer and its correspondence in the follow‐up scan as well as their spatial locations (mass center) were identified in each examination. In addition to the computational efficiency, the accuracy of these registration procedures was assessed by computing the Euclidean distances between the corresponding nodules after the registration. To demonstrate the advantage of the developed algorithm, the authors also implemented a fast iterative closest point (ICP) based rigid algorithm and compared their performance.Results:Our experiments on the collected chest CT examinations showed that the nodule registration errors in 3D Euclidean distance for the developed rigid affine approach, the traditional ICP algorithm, and the refining nonrigid Demons algorithm were 9.6, 9.8, and 10.0 mm, respectively, and the corresponding computational costs in time were 5, 300, and 55 s, respectively.Conclusions:A rigid solution may be preferred in practice for the pulmonary nodule registration in longitudinal studies because of its relatively high efficiency and sufficient accuracy for the clinical need.
Reference‐free ground truth metric for metal artifact evaluation in CT images
Authors: Kratz Bärbel , Ens Svitlana , Müller Jan , Buzug Thorsten M. 
Published: June 2011

Purpose:In computed tomography (CT), metal objects in the region of interest introduce data inconsistencies during acquisition. Reconstructing these data results in an image with star shaped artifacts induced by the metal inconsistencies. To enhance image quality, the influence of the metal objects can be reduced by different metal artifact reduction (MAR) strategies. For an adequate evaluation of new MAR approaches a ground truth reference data set is needed. In technical evaluations, where phantoms can be measured with and without metal inserts, ground truth data can easily be obtained by a second reference data acquisition. Obviously, this is not possible for clinical data. Here, an alternative evaluation method is presented without the need of an additionally acquired reference data set.Methods:The proposed metric is based on an inherent ground truth for metal artifacts as well as MAR methods comparison, where no reference information in terms of a second acquisition is needed. The method is based on the forward projection of a reconstructed image, which is compared to the actually measured projection data.Results:The new evaluation technique is performed on phantom and on clinical CT data with and without MAR. The metric results are then compared with methods using a reference data set as well as an expert‐based classification. It is shown that the new approach is an adequate quantification technique for artifact strength in reconstructed metal or MAR CT images.Conclusions:The presented method works solely on the original projection data itself, which yields some advantages compared to distance measures in image domain using two data sets. Beside this, no parameters have to be manually chosen. The new metric is a useful evaluation alternative when no reference data are available.
Immunogenicity of Inactivated Polio Vaccine with Concurrent Antiviral V-073 Administration in Mice
Authors: Kouiavskaia Diana , Collett Marc S. , Dragunsky Eugenia M. , Sarafanov Andrey , Chumakov Konstantin M. 
Published: June 2011

ABSTRACT
Immunization of mice with inactivated polio vaccine (IPV) with concurrent dosing of poliovirus antiviral V-073 showed no detrimental impact on the elicitation of serum-neutralizing antibodies. A strategy involving coadministration of antiviral V-073 and IPV can be considered for the management of poliovirus incidents.
Diagnostic Issues, Clinical Characteristics, and Outcomes for Patients with Fungemia
Authors: Arendrup Maiken Cavling , Sulim Sofia , Holm Anette , Nielsen Lene , Nielsen Susanne Dam , Knudsen Jenny Dahl , Drenck Niels Erik , Christensen Jens Jørgen , Johansen Helle Krogh 
Published: June 2011

ABSTRACT

This study investigated microbiological, clinical, and management issues and outcomes for Danish fungemia patients. Isolates and clinical information were collected at six centers. A total of 334 isolates, 316 episodes, and 305 patients were included, corresponding to 2/3 of the national episodes. Blood culture positivity varied by system, species, and procedure. Thus, cases with concomitant bacteremia were reported less commonly by BacT/Alert than by the Bactec system (9% [11/124 cases] versus 28% [53/192 cases];
P
< 0.0001), and cultures with
Candida glabrata
or those drawn via arterial lines needed longer incubation. Species distribution varied by age, prior antifungal treatment (57% occurrence of
C. glabrata
,
Saccharomyces cerevisiae
, or
C. krusei
in patients with prior antifungal treatment versus 28% occurrence in those without it;
P
= 0.007), and clinical specialty (61% occurrence of
C. glabrata
or
C. krusei
in hematology wards versus 27% occurrence in other wards;
P
= 0.002). Colonization samples were not predictive for the invasive species in 11/100 cases. Fifty-six percent of the patients had undergone surgery, 51% were intensive care unit (ICU) patients, and 33% had malignant disease. Mortality increased by age (
P
= 0.009) and varied by species (36% for
C. krusei
, 25% for
C. parapsilosis
, and 14% for other
Candida
species), severity of underlying disease (47% for ICU patients versus 24% for others;
P
= 0.0001), and choice but not timing of initial therapy (12% versus 48% for patients with
C. glabrata
infection receiving caspofungin versus fluconazole;
P
= 0.023). The initial antifungal agent was deemed suboptimal upon species identification in 15% of the cases, which would have been 6.5% if current guidelines had been followed. A large proportion of Danish fungemia patients were severely ill and received suboptimal initial antifungal treatment. Optimization of diagnosis and therapy is possible.
Mycobacterium haemophilum and Histoplasma capsulatum Coinfection in a Renal Transplant Patient
Authors: Clement Cecilia G. , Loeffelholz Michael J. , Eltorky Mahmoud A. , Tang Yi-Wei , Williams-Bouyer Natalie 
Published: June 2011

ABSTRACT

We report the case of a 22-year-old man who presented with a
Mycobacterium haemophilum
and
Histoplasma capsulatum
coinfection occurring 21 years after a living-donor-related renal transplant.
Evaluation of Commercial Universal rRNA Gene PCR plus Sequencing Tests for Identification of Bacteria and Fungi Associated with Infectious Endocarditis
Authors: Kühn Christian , Disqué Claudia , Mühl Helge , Orszag Peter , Stiesch Meike , Haverich Axel 
Published: June 2011

ABSTRACT

Two new commercially available universal rRNA gene PCR plus sequencing tests, SepsiTest and universal microbe detection (UMD; Molzym, Bremen, Germany), were evaluated using blood specimens and heart valves from 30 patients with suspected infectious endocarditis (IE). The sensitivity of PCR (85%) was nearly twice as high as that of culture (45%), which in 10/20 IE cases presumably stayed negative as a consequence of growth inhibition of the pathogens by antibiotics. Further, PCR provided the basis for reclassification of 5/10 non-IE cases into IE cases. Culture-negative infections were identified by PCR, including single infections due to streptococci and Gram-negative bacteria (
Escherichia coli
,
Haemophilus parainfluenzae
) and mixed infections involving two Gram-positive bacteria or
Candida
spp. with Gram-positive bacteria. The new commercial tests proved to be of value for the rapid diagnosis of IE, particularly in cases of culture-negative infections. Issues regarding the feasibility of these tests for routine use are discussed.
Evaluation of High-Throughput Sequencing for Identifying Known and Unknown Viruses in Biological Samples
Authors: Cheval Justine , Sauvage Virginie , Frangeul Lionel , Dacheux Laurent , Guigon Ghislaine , Dumey Nicolas , Pariente Kevin , Rousseaux Claudine , Dorange Fabien , Berthet Nicolas , Brisse Sylvain , Moszer Ivan , Bourhy Hervé , Manuguerra Claude Jean , Lecuit Marc , Burguiere Ana , Caro Valérie , Eloit Marc 
Published: June 2011

ABSTRACT

High-throughput sequencing furnishes a large number of short sequence reads from uncloned DNA and has rapidly become a major tool for identifying viruses in biological samples, and in particular when the target sequence is undefined. In this study, we assessed the analytical sensitivity of a pipeline for detection of viruses in biological samples based on either the Roche-454 genome sequencer or Illumina genome analyzer platforms. We sequenced biological samples artificially spiked with a wide range of viruses with genomes composed of single or double-stranded DNA or RNA, including linear or circular single-stranded DNA. Viruses were added at a very low concentration most often corresponding to 3 or 0.8 times the validated level of detection of quantitative reverse transcriptase PCRs (RT-PCRs). For the viruses represented, or resembling those represented, in public nucleotide sequence databases, we show that the higher output of Illumina is associated with a much greater sensitivity, approaching that of optimized quantitative (RT-)PCRs. In this blind study, identification of viruses was achieved without incorrect identification. Nevertheless, at these low concentrations, the number of reads generated by the Illumina platform was too small to facilitate assembly of contigs without the use of a reference sequence, thus precluding detection of unknown viruses. When the virus load was sufficiently high,
de novo
assembly permitted the generation of long contigs corresponding to nearly full-length genomes and thus should facilitate the identification of novel viruses.
NF-κB Protects Human Papillomavirus Type 38 E6/E7-Immortalized Human Keratinocytes against Tumor Necrosis Factor Alpha and UV-Mediated Apoptosis
Authors: Hussain Ishraq , Fathallah Ikbal , Accardi Rosita , Yue Jiping , Saidj Djamel , Shukla Ruchi , Hasan Uzma , Gheit Tarik , Niu Yamei , Tommasino Massimo , Sylla Bakary S. 
Published: June 2011

ABSTRACT

Constitutive activation of NF-κB signaling is a key event in virus- and non-virus-induced carcinogenesis. We have previously reported that cutaneous human papillomavirus type 38 (HPV38) displays transforming properties in
in vitro
and
in vivo
experimental models. However, the involvement of NF-κB signaling in HPV38-induced cell growth transformation remains to be determined. In this study, we showed that HPV38 E6 and E7 activate NF-κB and that inhibition of the pathway with the IκBα superrepressor sensitizes HPV38E6E7-immortalized human keratinocytes to tumor necrosis factor alpha (TNF-α)- and UVB radiation-mediated apoptosis. Accordingly, inhibition of NF-κB signaling resulted in the downregulation of NF-κB-regulated antiapoptotic genes, including cIAP1, cIAP2, and xIAP genes. These findings demonstrate a critical role of NF-κB activity in the survival of HPV38E6E7-immortalized human keratinocytes exposed to cytokine or UV radiation. Our data provide additional evidence for cooperation between beta HPV infection and UV irradiation in skin carcinogenesis.
Passive Immunotherapies Protect WRvFire and IHD-J-Luc Vaccinia Virus-Infected Mice from Lethality by Reducing Viral Loads in the Upper Respiratory Tract and Internal Organs
Authors: Zaitseva Marina , Kapnick Senta M. , Meseda Clement A. , Shotwell Elisabeth , King Lisa R. , Manischewitz Jody , Scott John , Kodihalli Shantha , Merchlinsky Michael , Nielsen Henriette , Lantto Johan , Weir Jerry P. , Golding Hana 
Published: June 2011

ABSTRACT

Whole-body bioimaging was employed to study the effects of passive immunotherapies on lethality and viral dissemination in BALB/c mice challenged with recombinant vaccinia viruses expressing luciferase. WRvFire and IHD-J-Luc vaccinia viruses induced lethality with similar times to death following intranasal infection, but WRvFire replicated at higher levels than IHD-J-Luc in the upper and lower respiratory tracts. Three types of therapies were tested: licensed human anti-vaccinia virus immunoglobulin intravenous (VIGIV); recombinant anti-vaccinia virus immunoglobulin (rVIG; Symphogen, Denmark), an investigational product containing a mixture of 26 human monoclonal antibodies (HuMAbs) against mature virion (MV) and enveloped virion (EV); and HuMAb compositions targeting subsets of MV or EV proteins. Bioluminescence recorded daily showed that pretreatment with VIGIV (30 mg) or with rVIG (100 μg) on day −2 protected mice from death but did not prevent viral replication at the site of inoculation and dissemination to internal organs. Compositions containing HuMAbs against MV or EV proteins were protective in both infection models at 100 μg per animal, but at 30 μg, only anti-EV antibodies conferred protection. Importantly, the
t
statistic of the mean total fluxes revealed that viral loads in surviving mice were significantly reduced in at least 3 sites for 3 consecutive days (days 3 to 5) postchallenge, while significant reduction for 1 or 2 days in any individual site did not confer protection. Our data suggest that reduction of viral replication at multiple sites, including respiratory tract, spleen, and liver, as monitored by whole-body bioluminescence can be used to predict the effectiveness of passive immunotherapies in mouse models.
Gouléako Virus Isolated from West African Mosquitoes Constitutes a Proposed Novel Genus in the Family Bunyaviridae
Authors: Marklewitz M. , Handrick S. , Grasse W. , Kurth A. , Lukashev A. , Drosten C. , Ellerbrok H. , Leendertz F. H. , Pauli G. , Junglen S. 
Published: June 2011

ABSTRACT

The family
Bunyaviridae
is the most diversified family of RNA viruses. We describe a novel prototypic bunyavirus, tentatively named Gouléako virus, isolated from various mosquito species trapped in Côte d'Ivoire. The S segment comprised 1,087 nucleotides (nt), the M segment 3,188 nt, and the L segment 6,358 nt, constituting the shortest bunyavirus genome known so far. The virus had shorter genome termini than phleboviruses and showed no evidence of encoded NSs and NSm proteins. An uncharacterized 105-amino-acid (aa) putative open reading frame (ORF) was detected in the S segment. Genetic equidistance to other bunyaviruses (74 to 88% aa identity) and absence of serological cross-reactivity with phleboviruses suggested a proposed novel
Bunyaviridae
genus.
Replication-Competent Simian Immunodeficiency Virus (SIV) Gag Escape Mutations Archived in Latent Reservoirs during Antiretroviral Treatment of SIV-Infected Macaques
Authors: Queen Suzanne E. , Mears Brian M. , Kelly Kathleen M. , Dorsey Jamie L. , Liao Zhaohao , Dinoso Jason B. , Gama Lucio , Adams Robert J. , Zink M. Christine , Clements Janice E. , Kent Stephen J. , Mankowski Joseph L. 
Published: June 2011

ABSTRACT

In response to pressure exerted by major histocompatibility complex (MHC) class I-mediated CD8
+
T cell control, human immunodeficiency virus (HIV) escape mutations often arise in immunodominant epitopes recognized by MHC class I alleles. While the current standard of care for HIV-infected patients is treatment with highly active antiretroviral therapy (HAART), suppression of viral replication in these patients is not absolute and latently infected cells persist as lifelong reservoirs. To determine whether HIV escape from MHC class I-restricted CD8
+
T cell control develops during HAART treatment and then enters latent reservoirs in the periphery and central nervous system (CNS), with the potential to emerge as replication-competent virus, we tracked the longitudinal development of the simian immunodeficiency virus (SIV) Gag escape mutation K165R in HAART-treated SIV-infected pigtailed macaques. Key findings of these studies included: (i) SIV Gag K165R escape mutations emerged in both plasma and cerebrospinal fluid (CSF) during the decaying phase of viremia after HAART initiation before suppression of viral replication, (ii) SIV K165R Gag escape mutations were archived in latent proviral DNA reservoirs, including the brain in animals receiving HAART that suppressed viral replication, and (iii) replication-competent SIV Gag K165R escape mutations were present in the resting CD4
+
T cell reservoir in HAART-treated SIV-infected macaques. Despite early administration of aggressive antiretroviral treatment, HIV immune escape from CD8
+
T cell control can still develop during the decaying phases of viremia and then persist in latent reservoirs, including the brain, with the potential to emerge if HAART therapy is interrupted.
Human Leukocyte Antigen Variants B*44 and B*57 Are Consistently Favorable during Two Distinct Phases of Primary HIV-1 Infection in Sub-Saharan Africans with Several Viral Subtypes
Authors: Tang Jianming , Cormier Emmanuel , Gilmour Jill , Price Matthew A. , Prentice Heather A. , Song Wei , Kamali Anatoli , Karita Etienne , Lakhi Shabir , Sanders Eduard J. , Anzala Omu , Amornkul Pauli N. , Allen Susan , Hunter Eric , Kaslow Richard A. ,   for the IAVI African HIV Research Network
Published: June 2011

ABSTRACT

As part of an ongoing study of early human immunodeficiency virus type 1 (HIV-1) infection in sub-Saharan African countries, we have identified 134 seroconverters (SCs) with distinct acute-phase (peak) and early chronic-phase (set-point) viremias. SCs with class I human leukocyte antigen (HLA) variants B*44 and B*57 had much lower peak viral loads (VLs) than SCs without these variants (adjusted linear regression beta values of −1.08 ± 0.26 log
10
[mean ± standard error] and −0.83 ± 0.27 log
10
, respectively;
P
< 0.005 for both), after accounting for several nongenetic factors, including gender, age at estimated date of infection, duration of infection, and country of origin. These findings were confirmed by alternative models in which major viral subtypes (A1, C, and others) in the same SCs replaced country of origin as a covariate (
P
≤ 0.03). Both B*44 and B*57 were also highly favorable (
P
≤ 0.03) in analyses of set-point VLs. Moreover, B*44 was associated with relatively high CD4
+
T-cell counts during early chronic infection (
P
= 0.02). Thus, at least two common
HLA-B
variants showed strong influences on acute-phase as well as early chronic-phase VL, regardless of the infecting viral subtype. If confirmed, the identification of B*44 as another favorable marker in primary HIV-1 infection should help dissect mechanisms of early immune protection against HIV-1 infection.