bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic trajectory‐based couch motion for improvement of radiation therapy trajectories in cranial SRT
Authors: Lee MacDonald R. , Thomas Christopher G. 
Published: April 2015

Purpose:To investigate potential improvement in external beam stereotactic radiation therapy plan quality for cranial cases using an optimized dynamic gantry and patient support couch motion trajectory, which could minimize exposure to sensitive healthy tissue.Methods:Anonymized patient anatomy and treatment plans of cranial cancer patients were used to quantify the geometric overlap between planning target volumes and organs‐at‐risk (OARs) based on their two‐dimensional projection from source to a plane at isocenter as a function of gantry and couch angle. Published dose constraints were then used as weighting factors for the OARs to generate a map of couch‐gantry coordinate space, indicating degree of overlap at each point in space. A couch‐gantry collision space was generated by direct measurement on a linear accelerator and couch using an anthropomorphic solid‐water phantom. A dynamic, fully customizable algorithm was written to generate a navigable ideal trajectory for the patient specific couch‐gantry space. The advanced algorithm can be used to balance the implementation of absolute minimum values of overlap with the clinical practicality of large‐scale couch motion and delivery time. Optimized cranial cancer treatment trajectories were compared to conventional treatment trajectories.Results:Comparison of optimized treatment trajectories with conventional treatment trajectories indicated an average decrease in mean dose to the OARs of 19% and an average decrease in maximum dose to the OARs of 12%. Degradation was seen for homogeneity index (6.14% ± 0.67%–5.48% ± 0.76%) and conformation number (0.82 ± 0.02–0.79 ± 0.02), but neither was statistically significant. Removal of OAR constraints from volumetric modulated arc therapy optimization reveals that reduction in dose to OARs is almost exclusively due to the optimized trajectory and not the OAR constraints.Conclusions:The authors’ study indicated that simultaneous couch and gantry motion during radiation therapy to minimize the geometrical overlap in the beams‐eye‐view of target volumes and the organs‐at‐risk can have an appreciable dose reduction to organs‐at‐risk.
Technical Note: Experimental carbon ion range verification in inhomogeneous phantoms using prompt gammas
Authors: Pinto M. , De Rydt M. , Dauvergne D. , Dedes G. , Freud N. , Krimmer J. , Létang J. M. , Ray C. , Testa E. , Testa M. 
Published: April 2015

Purpose:The purpose of this study was to experimentally assess the possibility to monitor carbon ion range variations—due to tumor shift and/or elongation or shrinking—using prompt‐gamma (PG) emission with inhomogeneous phantoms. Such a study is related to the development of PG monitoring techniques to be used in a carbon ion therapy context.Methods:A 95 MeV/u carbon ion beam was used to irradiate phantoms with a variable density along the ion path to mimic the presence of bone and lung in homogeneous humanlike tissue. PG profiles were obtained after a longitudinal scan of the phantoms. A setup comprising a narrow single‐slit collimator and two detectors placed at 90° with respect to the beam axis was used. The time of flight technique was applied to allow the selection between PG and background events.Results:Using the positions at 50% entrance and 50% falloff of the PG profiles, a quantity called prompt‐gamma profile length (PGPL) is defined. It is possible to observe shifts in the PGPL when there are absolute ion range shifts as small as 1–2 mm. Quantitatively, for an ion range shift of −1.33 ± 0.46 mm (insertion of a Teflon slab), a PGPL difference of −1.93 ± 0.58 mm and −1.84 ± 1.27 mm is obtained using a BaF2 and a NaI(Tl) detector, respectively. In turn, when an ion range shift of 4.59 ± 0.42 mm (insertion of a lung‐equivalent material slab) is considered, the difference is of 4.10 ± 0.54 and 4.39 ± 0.80 mm for the same detectors.Conclusions:Herein, experimental evidence of the usefulness of employing PG to monitor carbon ion range using inhomogeneous phantoms is presented. Considering the homogeneous phantom as reference, the results show that the information provided by the PG emission allows for detecting ion range shifts as small as 1–2 mm. When considering the expected PG emission from an energy slice in a carbon ion therapy scenario, the experimental setup would allow to retrieve the same PGPL as the high statistics of the full experimental dataset in 58% of the times. However, this success rate increases to 93% when using a better optimized setup by means of Monte Carlo simulations.
Improved Standardization of the Bio-Rad Platelia Aspergillus Galactomannan Antigen Sandwich Enzyme Immunoassay Using the DS2 (Dynex) Enzyme-Linked Immunosorbent Assay (ELISA) Processing System
Authors: Gorton R. L. , White P. L. , Bagkeris E. , Cotterall D. , Desai R. , McHugh T. , Kibbler C. C. 
Published: April 2015

ABSTRACT

The galactomannan enzyme immunoassay (GM-EIA) is widely utilized for the diagnosis of invasive aspergillosis (IA). There is inconsistent reproducibility of results between centers when the assay is processed manually. Automation of EIAs can reduce variation. This study investigated the semiautomation of the GM-EIA on the DS2 (Dynex) platform in the following three stages: (i) DS2 GM-EIA method validation with experimental samples, (ii) DS2 retesting of case-defined clinical samples, and (iii) a 12-month audit of DS2 GM-EIA performance. In stage i, Bland-Altman analysis demonstrated a reduced variance between optical density index (ODI) values for samples processed on two DS2 platforms (mean difference, −0.02; limits of agreement [LOA], −0.19 to 0.14) compared with the variance between samples processed manually and on a DS2 platform (mean difference, 0.02; LOA, −0.25 to 0.3). In stage ii, 100% (14/14 samples) qualitative agreement was observed for serum samples from patients with IA, with no significant change in the ODI values when samples were processed on the DS2 platform. A significant decrease in ODI values was observed for control serum samples on the DS2 platform (difference, 0.01;
P
= 0.042). In stage iii, a significant reduction in the frequency of equivocal results, from 5.56% (136/2,443 samples) to 1.56% (15/961 samples), was observed after DS2 automation (difference, 4.0%; 95% confidence interval [CI], 2.7 to 5.2%;
P
< 0.01), with an equivalent increase in negative results. This study demonstrates that GM-EIA automation may reduce intersite variability. Automation does not have an impact on the repeatability of truly positive results but contributes to a reduction in false-positive (equivocal) GM-EIA results, reducing the need to retest a significant proportion of samples.
Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus
Authors: Hedskog Charlotte , Chodavarapu Krishna , Ku Karin S. , Xu Simin , Martin Ross , Miller Michael D. , Mo Hongmei , Svarovskaia Evguenia 
Published: April 2015

ABSTRACT

Hepatitis C virus (HCV) exhibits a high genetic diversity and is classified into 6 genotypes, which are further divided into 66 subtypes. Current sequencing strategies require prior knowledge of the HCV genotype and subtype for efficient amplification, making it difficult to sequence samples with a rare or unknown genotype and/or subtype. Here, we describe a subtype-independent full-genome sequencing assay based on a random amplification strategy coupled with next-generation sequencing. HCV genomes from 17 patient samples with both common subtypes (1a, 1b, 2a, 2b, and 3a) and rare subtypes (2c, 2j, 3i, 4a, 4d, 5a, 6a, 6e, and 6j) were successfully sequenced. On average, 3.7 million reads were generated per sample, with 15% showing HCV specificity. The assembled consensus sequences covered 99.3% to 100% of the HCV coding region, and the average coverage was 6,070 reads/position. The accuracy of the generated consensus sequence was estimated to be >99% based on results from
in vitro
HCV replicon amplification, with the same extrapolated amount of input RNA molecules as that for the patient samples. Taken together, the HCV genomes from 17 patient samples were successfully sequenced, including samples with subtypes that have limited sequence information. This method has the potential to sequence any HCV patient sample, independent of genotype or subtype. It may be especially useful in confounding cases, like those with rare subtypes, intergenotypic recombination, or multiple genotype infections, and may allow greater insight into HCV evolution, its genetic diversity, and drug resistance development.
Human Cytomegalovirus
UL135
and
UL136
Genes Are Required for Postentry Tropism in Endothelial Cells
Authors: Bughio Farah , Umashankar Mahadevaiah , Wilson Jean , Goodrum Felicia 
Published: April 2015

ABSTRACT

Endothelial cells (ECs) are a critical target of viruses, and infection of the endothelium represents a defining point in viral pathogenesis. Human cytomegalovirus (HCMV), the prototypical betaherpesvirus, encodes proteins specialized for entry into ECs and delivery of the genome to the nuclei of ECs. Virus strains competent to enter ECs replicate with differing efficiencies, suggesting that the virus encodes genes for postentry tropism in ECs. We previously reported a specific requirement for the
UL133/8
locus of HCMV for replication in ECs. The
UL133/8
locus harbors four genes:
UL133
,
UL135
,
UL136
, and
UL138
. In this study, we find that while
UL133
and
UL138
are dispensable for replication in ECs, both
UL135
and
UL136
are important. These genes are not required for virus entry or the expression of viral genes. The phenotypes associated with disruption of either gene reflect phenotypes observed for the
UL133/8
NULL
virus, which lacks the entire
UL133/8
locus, but are largely distinct from one another. Viruses lacking
UL135
fail to properly envelop capsids in the cytoplasm, produce fewer dense bodies (DB) than the wild-type (WT) virus, and are unable to incorporate viral products into multivesicular bodies (MVB). Viruses lacking
UL136
also fail to properly envelop virions and produce larger dense bodies than the WT virus. Our results indicate roles for the
UL135
and
UL136
proteins in commandeering host membrane-trafficking pathways for virus maturation.
UL135
and
UL136
represent the first HCMV genes crucial for early- to late-stage tropism in ECs.

IMPORTANCE
Human cytomegalovirus (HCMV) persists in the majority of the world's population. While typically asymptomatic in healthy hosts, HCMV can cause significant morbidity and mortality in immunocompromised or naïve individuals, particularly transplant patients and patients with congenital infections, respectively. Lifelong persistence of the virus may also contribute to age-related pathologies, such as vascular disease. One aspect of HCMV infection contributing to complex and varied pathogenesis is the diverse array of cell types that this virus infects in the host. The vascular endothelium is a particularly important target of infection, contributing to viral dissemination and likely leading to CMV complications following transplantation. In this work, we identify two viral gene products required for postentry tropism in endothelial cells. Identifying tropism factors required for replication in critical cell targets of infection is important for the development of strategies to restrict virus replication.
Novel CD4-Based Bispecific Chimeric Antigen Receptor Designed for Enhanced Anti-HIV Potency and Absence of HIV Entry Receptor Activity
Authors: Liu Li , Patel Bhavik , Ghanem Mustafa H. , Bundoc Virgilio , Zheng Zhili , Morgan Richard A. , Rosenberg Steven A. , Dey Barna , Berger Edward A. 
Published: April 2015

ABSTRACT

Adoptive transfer of CD8 T cells genetically engineered to express “chimeric antigen receptors” (CARs) represents a potential approach toward an HIV infection “functional cure” whereby durable virologic suppression is sustained after discontinuation of antiretroviral therapy. We describe a novel bispecific CAR in which a CD4 segment is linked to a single-chain variable fragment of the 17b human monoclonal antibody recognizing a highly conserved CD4-induced epitope on gp120 involved in coreceptor binding. We compared a standard CD4 CAR with CD4-17b CARs where the polypeptide linker between the CD4 and 17b moieties is sufficiently long (CD4-35-17b CAR) versus too short (CD4-10-17b) to permit simultaneous binding of the two moieties to a single gp120 subunit. When transduced into a peripheral blood mononuclear cell (PBMC) or T cells thereof, all three CD4-based CARs displayed specific functional activities against HIV-1 Env-expressing target cells, including stimulation of gamma interferon (IFN-γ) release, specific target cell killing, and suppression of HIV-1 pseudovirus production. In assays of spreading infection of PBMCs with genetically diverse HIV-1 primary isolates, the CD4-10-17b CAR displayed enhanced potency compared to the CD4 CAR whereas the CD4-35-17b CAR displayed diminished potency. Importantly, both CD4-17b CARs were devoid of a major undesired activity observed with the CD4 CAR, namely, rendering the transduced CD8
+
T cells susceptible to HIV-1 infection. Likely mechanisms for the superior potency of the CD4-10-17b CAR over the CD4-35-17b CAR include the greater potential of the former to engage in the serial antigen binding required for efficient T cell activation and the ability of two CD4-10-17b molecules to simultaneously bind a single gp120 subunit.

IMPORTANCE
HIV research has been energized by prospects for a cure for HIV infection or, at least, for a “functional cure” whereby antiretroviral therapy can be discontinued without virus rebound. This report describes a novel CD4-based “chimeric antigen receptor” (CAR) which, when genetically engineered into T cells, gives them the capability to selectively respond to and kill HIV-infected cells. This CAR displays enhanced features compared to previously described CD4-based CARs, namely, increased potency and avoidance of the undesired rendering of the genetically modified CD8 T cells susceptible to HIV infection. When adoptively transferred back to the individual, the genetically modified T cells will hopefully provide durable killing of infected cells and sustained virus suppression without continued antiretroviral therapy, i.e., a functional cure.
The Vesicle-Forming 6K
2
Protein of Turnip Mosaic Virus Interacts with the COPII Coatomer Sec24a for Viral Systemic Infection
Authors: Jiang Jun , Patarroyo Camilo , Garcia Cabanillas Daniel , Zheng Huanquan , Laliberté Jean-François 
Published: April 2015

ABSTRACT

Positive-sense RNA viruses remodel host cell endomembranes to generate quasi-organelles known as “viral factories” to coordinate diverse viral processes, such as genome translation and replication. It is also becoming clear that enclosing viral RNA (vRNA) complexes within membranous structures is important for virus cell-to-cell spread throughout the host. In plant cells infected by turnip mosaic virus (TuMV), a member of the family
Potyviridae
, peripheral motile endoplasmic reticulum (ER)-derived viral vesicles are produced that carry the vRNA to plasmodesmata for delivery into adjacent noninfected cells. The viral protein 6K
2
is responsible for the formation of these vesicles, but how 6K
2
is involved in their biogenesis is unknown. We show here that 6K
2
is associated with cellular membranes. Deletion mapping and site-directed mutagenesis experiments defined a soluble N-terminal 12-amino-acid stretch, in particular a potyviral highly conserved tryptophan residue and two lysine residues that were important for vesicle formation. When the tryptophan residue was changed into an alanine in the viral polyprotein, virus replication still took place, albeit at a reduced level, but cell-to-cell movement of the virus was abolished. Yeast (
Saccharomyces cerevisiae
) two-hybrid and coimmunoprecipitation experiments showed that 6K
2
interacted with Sec24a, a COPII coatomer component. Appropriately, TuMV systemic movement was delayed in an
Arabidopsis thaliana
mutant line defective in Sec24a. Intercellular movement of TuMV replication vesicles thus requires ER export of 6K
2
, which is mediated by the interaction of the N-terminal domain of the viral protein with Sec24a.

IMPORTANCE
Many plant viruses remodel the endoplasmic reticulum (ER) to generate vesicles that are associated with the virus replication complex. The viral protein 6K
2
of turnip mosaic virus (TuMV) is known to induce ER-derived vesicles that contain vRNA as well as viral and host proteins required for vRNA synthesis. These vesicles not only sustain vRNA synthesis, they are also involved in the intercellular trafficking of vRNA. In this investigation, we found that the N-terminal soluble domain of 6K
2
is required for ER export of the protein and for the formation of vesicles. ER export is not absolutely required for vRNA replication but is necessary for virus cell-to-cell movement. Furthermore, we found that 6K
2
physically interacts with the COPII coatomer Sec24a and that an
Arabidopsis thaliana
mutant line with a defective Sec24a shows a delay in the systemic infection by TuMV.
Immunogenic Display of Purified Chemically Cross-Linked HIV-1 Spikes
Authors: Leaman Daniel P. , Lee Jeong Hyun , Ward Andrew B. , Zwick Michael B. 
Published: April 2015

ABSTRACT
HIV-1 envelope glycoprotein (Env) spikes are prime vaccine candidates, at least in principle, but suffer from instability, molecular heterogeneity and a low copy number on virions. We anticipated that chemical cross-linking of HIV-1 would allow purification and molecular characterization of trimeric Env spikes, as well as high copy number immunization. Broadly neutralizing antibodies bound tightly to all major quaternary epitopes on cross-linked spikes. Covalent cross-linking of the trimer also stabilized broadly neutralizing epitopes, although surprisingly some individual epitopes were still somewhat sensitive to heat or reducing agent. Immunodepletion using non-neutralizing antibodies to gp120 and gp41 was an effective method for removing non-native-like Env. Cross-linked spikes, purified via an engineered C-terminal tag, were shown by negative stain EM to have well-ordered, trilobed structure. An immunization was performed comparing a boost with Env spikes on virions to spikes cross-linked and captured onto nanoparticles, each following a gp160 DNA prime. Although differences in neutralization did not reach statistical significance, cross-linked Env spikes elicited a more diverse and sporadically neutralizing antibody response against Tier 1b and 2 isolates when displayed on nanoparticles, despite attenuated binding titers to gp120 and V3 crown peptides. Our study demonstrates display of cross-linked trimeric Env spikes on nanoparticles, while showing a level of control over antigenicity, purity and density of virion-associated Env, which may have relevance for Env based vaccine strategies for HIV-1.

IMPORTANCE
The envelope spike (Env) is the target of HIV-1 neutralizing antibodies, which a successful vaccine will need to elicit. However, native Env on virions is innately labile, as well as heterogeneously and sparsely displayed. We therefore stabilized Env spikes using a chemical cross-linker and removed non-native Env by immunodepletion with non-neutralizing antibodies. Fixed native spikes were recognized by all classes of known broadly neutralizing antibodies but not by non-neutralizing antibodies and displayed on nanoparticles in high copy number. An immunization experiment in rabbits revealed that cross-linking Env reduced its overall immunogenicity; however, high-copy display on nanoparticles enabled boosting of antibodies that sporadically neutralized some relatively resistant HIV-1 isolates, albeit at a low titer. This study describes the purification of stable and antigenically correct Env spikes from virions that can be used as immunogens.
Chronic comorbidities in children with type 1 diabetes: a population-based cohort study
Authors: Fazeli Farsani Soulmaz , Souverein Patrick C , van der Vorst Marja M J , Knibbe Catherijne A J , de Boer Anthonius , Mantel-Teeuwisse Aukje K 
Published: April 2015

ObjectiveTo determine the incidence of chronic comorbidities among children with type 1 diabetes (T1D) and to compare incidences with a group of children without diabetes.DesignPopulation-based cohort study.SettingDutch PHARMO database (1998–2010).PatientsAll patients (<19 years old) with T1D between 1999 and 2009 (T1D cohort) and a group of age- and sex-matched (ratio: 1–4) children without diabetes (reference cohort).Main outcome measureThe incidence of nine common chronic comorbidities was assessed on the basis that they were treated pharmacologically and/or resulted in hospital admission. Cox proportional hazard analysis was used to estimate the strength of the association between T1D and comorbidities, expressed as HRs and 95% CIs.ResultsA total of 915 patients with T1D and 3590 children in the reference cohort (51% boys, mean age of 10.1 (SD 4.5) years) were included. T1D was associated with an increased risk (HR; 95% CI) of hospitalisation for any comorbidity (3.7; 2.5 to 5.5), thyroid disease (14.2; 6.7 to 31.0), non-infectious enteritis and colitis (5.9; 3.0 to 11.5), cardiovascular disorders (3.1; 2.3 to 4.2), mental disorders (2.0; 1.4 to 3.1), epilepsy (2.0; 1.1 to 3.7) and (obstructive) pulmonary disease (1.5; 1.2 to 2.0). There was no significant difference in the incidences of other comorbidities (malignant disorders, anaemia and migraine) between the two cohorts.ConclusionsOur longitudinal study showed that incidences of six chronic diseases were significantly higher in T1D children during the early years of developing this disease compared with the reference children.
Clarifying life lost due to cold and heat: a new approach using annual time series
Authors: Rehill Nirandeep , Armstrong Ben , Wilkinson Paul 
Published: April 2015

ObjectiveTo clarify whether deaths associated with hot and cold days are among the frail who would have died anyway in the next few weeks or months.DesignTime series regression analysis of annual deaths in relation to annual summaries of cold and heat.SettingLondon, UK.Participants3 530 280 deaths from all natural causes among London residents between October 1949 and September 2006.Main outcome measuresChange in annual risk of death (all natural cause, cardiovascular and respiratory) associated with each additional 1°C of average cold (or heat) below (above) the threshold (18°C) across each year.ResultsCold years were associated with increased deaths from all causes. For each additional 1° of cold across the year, all-cause mortality increased by 2.3% (95% CI 0.7% to 3.8%), after adjustment for influenza and secular trends. The estimated association between hot years and all-cause mortality was very imprecise and thus inconclusive (effect estimate 1.7%, −2.9% to 6.5%). These estimates were broadly robust to changes in the way temperature and trend were modelled. Estimated risk increments using weekly data but otherwise comparable were cold: 2.0% (2.0% to 2.1%) and heat: 3.9% (3.4% to 3.8%).ConclusionsIn this London annual series, we saw an association of cold with mortality which was broadly similar in magnitude to that found in published daily studies and our own weekly analysis, suggesting that most deaths due to cold were among individuals who would not have died in the next 6 months. The estimated association with heat was imprecise, with the CI including magnitudes found in daily studies but also including zero.