The role/s of T lymphocytes in the foreign body response has not been thoroughly elucidated. Lymphocytes are known to augment macrophage adhesion and fusion in vitro. Furthermore T lymphocytes are a possible source of the cytokines, IL-4 and IL-13 which induce macrophage fusion. In this study we used BALB/c mice and BALB/c (nu/nu) nude mice to investgate foreign body giant cell (FBGC) formation in a T cell deficient setting. Mice were implanted with Elasthane 80A (PEU), silicone rubber (SR) or poly(ethylene terephthalate) (PET) for 7, 14, or 21 days using the cage implant system. Exudate cells and IL-4 and IL-13 levels in exudate supernatants were analyzed by flow cytometry and a multiplex immunoassay, respectively, at days 7, 14, and 21. Macrophage adhesion and fusion on material surfaces were analyzed using optical microscopy. T cell deficient mice had lower total leukocyte concentrations at the biomaterial implant site at all time points. Adherent cell density was comparable between normal and T cell deficient mice except in the PEU group at day 21. However, percent fusion, average nuclei per FBGC, and FBGC morphology was comparable between normal and T cell deficient mice. IL-4 was not detected in any samples, but IL-13 levels were also comparable between normal and T cell deficient mice indicating Th2 polarized T cells are not the sole source of this cytokine. We have shown that there are pathways that do not require thymus-matured T lymphocytes which lead to a normal foreign body response to biomaterials in a murine model.
foreign body response; IL-4; IL-13; T lymphocyte; biomaterials
Lymphocytes have been shown to be involved in modulating monocyte and macrophage behavior in the foreign body reaction. Lymphocyte effects on biomaterial-adherent macrophage and foreign body giant cell (FBGC) behavior were further investigated by culturing monocytes alone or together with lymphocytes, either in direct co-cultures or indirectly in transwells, on a series of polyethylene terephthalate (PET)-based photograft co-polymerized material surfaces displaying distinct hydrophobic, hydrophilic/neutral, hydrophilic/anionic, and hydrophilic/cationic chemistries. After periods of 3, 7, and 10 days, cytokine production was quantified by ELISA and normalized to adherent macrophage/FBGC density to yield a measure of adherent macrophage/FBGC activation. Interactions with lymphocytes enhanced adherent macrophage and FBGC production of pro-inflammatory IL-1β, TNF-α, IL-6, IL-8, and MIP-1β on the hydrophobic and hydrophilic/cationic surfaces but had no effect on anti-inflammatory IL-10 production indicating lymphocytes promote a pro-inflammatory response to biomaterials. Lymphocytes also did not significantly influence MMP-9, TIMP-1, and TIMP-2 production. Interactions through indirect (paracrine) signaling showed a significant effect in enhancing adherent macrophage/FBGC activation at early time points while interactions via direct (juxtacrine) mechanisms dominated at later time points. Biomaterial surface chemistries differentially affected the observed responses as hydrophilic/neutral and hydrophilic/anionic surfaces evoked the highest levels of activation relative to the other surfaces but did not facilitate lymphocyte enhancement of adherent macrophage/FBGC activation.
biomaterials; foreign body reaction; lymphocytes; macrophages; activation
In order to further elucidate the foreign body reaction, investigation of cytokines at biomaterial implant sites was carried out using a multiplex immunoassay and ELISA. Macrophage activation cytokines (IL-1β, IL-6, TNFα), cytokines important for macrophage fusion (IL-4, IL-13), anti-inflammatory cytokines (IL-10, TGFβ), chemokines (GRO/KC, MCP-1), and the T cell activation cytokine IL-2 were quantified at biomaterial implant sites. Empty cages (controls) or cages containing synthetic biomedical polymer (Elasthane 80A (PEU), Silicone rubber (SR), or polyethylene terephthalate (PET)) were implanted subcutaneously in Sprague Dawley rats for 4, 7, or 14 days, and cytokines in exudate supernatants and macrophage surface adhesion and fusion were quantified. The presence of a polymer implant did not affect the levels of IL-1β, TGFβ, and MCP-1 in comparison to the control group. IL-2 was not detected in virtually any of the samples. Although the levels of IL-4, IL-13, IL-10, and GRO/KC were affected by polymer implantation, but not dependent on a specific polymer, IL-6 and TNFα were significantly greater in those animals implanted with PEU and SR, materials that do not promote fusion. The results indicate differential material dependent cytokine profiles are produced by surface adherent macrophages and foreign body giant cells in vivo.
cage implant system; multiplex immunoassay; cytokines; synthetic biomaterials
Dulaglutide (dula, LY2189265), a long-acting glucagon-like peptide-1 analog, is being developed to treat type 2 diabetes mellitus.
To foster the development of dula, we designed a two-stage adaptive, dose-finding, inferentially seamless phase 2/3 study. The Bayesian theoretical framework is used to adaptively randomize patients in stage 1 to 7 dula doses and, at the decision point, to either stop for futility or to select up to 2 dula doses for stage 2. After dose selection, patients continue to be randomized to the selected dula doses or comparator arms. Data from patients assigned the selected doses will be pooled across both stages and analyzed with an analysis of covariance model, using baseline hemoglobin A1c and country as covariates. The operating characteristics of the trial were assessed by extensive simulation studies.
Simulations demonstrated that the adaptive design would identify the correct doses 88% of the time, compared to as low as 6% for a fixed-dose design (the latter value based on frequentist decision rules analogous to the Bayesian decision rules for adaptive design).
This article discusses the decision rules used to select the dula dose(s); the mathematical details of the adaptive algorithm—including a description of the clinical utility index used to mathematically quantify the desirability of a dose based on safety and efficacy measurements; and a description of the simulation process and results that quantify the operating characteristics of the design.
adaptive dose finding; dulaglutide; GLP-1; seamless design
Dulaglutide (dula, LY2189265) is a once-weekly glucagon-like peptide-1 analog in development for the treatment of type 2 diabetes mellitus. An adaptive, dose-finding, inferentially seamless phase 2/3 study was designed to support the development of this novel diabetes therapeutic. The study is divided into two stages based on two randomization schemes: a Bayesian adaptive scheme (stage 1) and a fixed scheme (stage 2). Stage 1 of the trial employs an adaptive, dose-finding design to lead to a dula dose-selection decision or early study termination due to futility. If dose selection occurs, the study proceeds to stage 2 to allow continued evaluation of the selected dula doses. At completion, the entire study will serve as a confirmatory phase 3 trial. The final study design is discussed, along with specifics pertaining to the actual execution of this study and selected baseline characteristics of the participants.
adaptive dose finding; dulaglutide; GLP-1; inferentially seamless
Neisseria gonorrhoeae PilC1 is a member of the PilC family of type IV pilus-associated adhesins found in Neisseria species and other type IV pilus-producing genera. Previously, a calcium-binding domain was described in the C-terminal domains of PilY1 of Pseudomonas aeruginosa and in PilC1 and PilC2 of Kingella kingae. Genetic analysis of N. gonorrhoeae revealed a similar calcium-binding motif in PilC1. To evaluate the potential significance of this calcium-binding region in N. gonorrhoeae, we produced recombinant full-length PilC1 and a PilC1 C-terminal domain fragment. We show that, while alterations of the calcium-binding motif disrupted the ability of PilC1 to bind calcium, they did not grossly affect the secondary structure of the protein. Furthermore, we demonstrate that both full-length wild-type PilC1 and full-length calcium-binding-deficient PilC1 inhibited gonococcal adherence to cultured human cervical epithelial cells, unlike the truncated PilC1 C-terminal domain. Similar to PilC1 in K. kingae, but in contrast to the calcium-binding mutant of P. aeruginosa PilY1, an equivalent mutation in N. gonorrhoeae PilC1 produced normal amounts of pili. However, the N. gonorrhoeae PilC1 calcium-binding mutant still had partial defects in gonococcal adhesion to ME180 cells and genetic transformation, which are both essential virulence factors in this human pathogen. Thus, we conclude that calcium binding to PilC1 plays a critical role in pilus function in N. gonorrhoeae.
Metastatic lung disease in Wilms tumor (WT) patients was traditionally identified by chest radiograph (CXR). It is unclear whether patients with small lesions, detectable only by computed tomography (“CT-only” lesions), require the more intensive therapy, including doxorubicin and lung irradiation, given to patients with metastases detectable by CXR.
This study involved 417 patients with favorable histology WT and isolated lung metastases (detected by CXR or CT) who were registered on National Wilms Tumor Study (NWTS)-4 or -5. Outcomes by method of detection (CXR vs. CT only), use of lung radiation, and 2- or 3-drug chemotherapy (dactinomycin and vincristine +/− doxorubicin) were determined and compared using the log-rank test.
There were 231 patients with lung lesions detected by CXR and 186 by CT only. Of the patients with CT-only nodules, 37 received only 2 drugs and 101 did not receive lung radiation. Five-year event-free survival (EFS) was greater for patients receiving 3 drugs (including doxorubicin) with or without lung radiation than for those receiving 2 drugs (80% vs. 56%; p=0.004). There was no difference seen in 5-year overall survival (OS) between the 3-drug and 2-drug subsets (87% vs 86%; p=0.91). There were no significant differences in EFS (82% vs. 72%; p=0.13) or OS (91% vs. 83%; p = 0.46) for patients with CT-only nodules whether they received lung radiation or not.
Our results suggest that patients with CT-only lung lesions may have improved EFS but not OS from the addition of doxorubicin but do not appear to benefit from pulmonary radiation.
Wilms tumor; CT scans; pulmonary metastases; doxorubicin; lung radiation
The integrity of the tight junction barrier in epithelial and endothelial cells is critical to human health, but we still lack a detailed mechanistic knowledge of how the barrier is formed during development or responds to pathological and pharmacological insults. This limits our understanding of barrier dysfunction in disease and slows the development of therapeutic strategies. Recent studies confirm the long-maintained but previously unsupported view that the zonula occludens (ZO) proteins ZO-1 and ZO-2 are critical determinants of barrier formation. However, ZO proteins can also be components of adherens junctions, and recent studies suggest that ZO proteins may also promote the assembly and function of these junctions during epithelial morphogenesis. We review these studies and outline several recent observations that suggest that one role of ZO proteins is to regulate cytoskeletal dynamics at cell junctions. Finally, we propose a model by which the functional activities of ZO proteins in the adherens junction and tight junction are differentiated by a novel regulatory motif known as the U6 or acidic motif.
tight junction; adherens junction; zonula occludens; ZO-1; ZO-2; E-cadherin; cytoskeleton; MAGUK; PDZ; scaffold; permeability; epithelia; morphogenesis
This study reports on the use of a fibrinogen-derived peptide for the specific targeting and delivery of vancomycin to Staphylococcus epidermidis biofilms. One method by which S. epidermidis initially adheres to biomaterials uses the plasma protein fibrinogen as an intermediary, where the S. epidermidis surface protein SdrG binds to a short amino acid sequence near the amino terminus of the Bβ chain of fibrinogen. We mimicked this binding interaction and demonstrated the use of a synthetic fibrinogen-based β6-20 peptide to target and deliver vancomycin to S. epidermidis in vitro. The β6-20 peptide was synthesized and labeled with a nanogold probe, and its targeting capabilities were examined through the use of scanning electron microscopy. The Nanogold component was then replaced by vancomycin, utilizing a flexible, variable length poly(ethylene glycol) linker between the peptide and antibiotic to create the targeted vancomycin products, β6-20-PEGx-VAN. Initial binding to surface adherent S. epidermidis was increased in a concentration-dependent manner relative to vancomycin for all equivalent concentrations ≥4 μg/ml, with targeted vancomcyin content up to 22.9 times that of vancomycin alone. Retention of the targeted antibiotics was measured after an additional 24 hour incubation period, revealing levels 1.3 times that of vancomycin. The results demonstrate the improved targeting and retention of vancomycin within a biofilm due to the incorporation of a specific targeting motif.
Staphylococcus epidermidis; SdrG; β6-20 peptide; Targeted Delivery; Vancomycin
Pediatric rhabdomyosarcoma (RMS) is a morphologically and genetically heterogeneous malignancy commonly classified into three histologic subtypes, namely, alveolar, embryonal, and anaplastic. An issue that continues to challenge effective RMS patient prognosis is the dearth of molecular markers predictive of disease stage irrespective of tumor subtype. Our study involving a panel of 70 RMS tumors has identified specific alternative splice variants of the oncogenes Murine Double Minute 2 (MDM2) and MDM4 as potential biomarkers for RMS. Our results have demonstrated the strong association of genotoxic-stress inducible splice forms MDM2-ALT1 (91.6% Intergroup Rhabdomyosarcoma Study Group stage 4 tumors) and MDM4-ALT2 (90.9% MDM4-ALT2-positive T2 stage tumors) with high-risk metastatic RMS. Moreover, MDM2-ALT1-positive metastatic tumors belonged to both the alveolar (50%) and embryonal (41.6%) subtypes, making this the first known molecular marker for high-grade metastatic disease across the most common RMS subtypes. Furthermore, our results show that MDM2-ALT1 expression can function by directly contribute to metastatic behavior and promote the invasion of RMS cells through a matrigel-coated membrane. Additionally, expression of both MDM2-ALT1 and MDM4-ALT2 increased anchorage-independent cell-growth in soft agar assays. Intriguingly, we observed a unique coordination in the splicing of MDM2-ALT1 and MDM4-ALT2 in approximately 24% of tumor samples in a manner similar to genotoxic stress response in cell lines. To further explore splicing network alterations with possible relevance to RMS disease, we used an exon microarray approach to examine stress-inducible splicing in an RMS cell line (Rh30) and observed striking parallels between stress-responsive alternative splicing and constitutive splicing in RMS tumors.
The two compositionally distinct extracellular cochlear fluids, endolymph and perilymph, are separated by tight junctions that outline the scala media and reticular lamina. Mutations in TRIC (also known as MARVELD2), which encodes a tricellular tight junction protein known as tricellulin, lead to nonsyndromic hearing loss (DFNB49). We generated a knockin mouse that carries a mutation orthologous to the TRIC coding mutation linked to DFNB49 hearing loss in humans. Tricellulin was absent from the tricellular junctions in the inner ear epithelia of the mutant animals, which developed rapidly progressing hearing loss accompanied by loss of mechanosensory cochlear hair cells, while the endocochlear potential and paracellular permeability of a biotin-based tracer in the stria vascularis were unaltered. Freeze-fracture electron microscopy revealed disruption of the strands of intramembrane particles connecting bicellular and tricellular junctions in the inner ear epithelia of tricellulin-deficient mice. These ultrastructural changes may selectively affect the paracellular permeability of ions or small molecules, resulting in a toxic microenvironment for cochlear hair cells. Consistent with this hypothesis, hair cell loss was rescued in tricellulin-deficient mice when generation of normal endolymph was inhibited by a concomitant deletion of the transcription factor, Pou3f4. Finally, comprehensive phenotypic screening showed a broader pathological phenotype in the mutant mice, which highlights the non-redundant roles played by tricellulin.
Piperazirum, isolated from Arum palaestinum Boiss, was originally assigned as r-3,c-5-diisobutyl-c-6-isopropylpiperazin-2-one. The reported structure was synthesised diastereoselectively using a key nitro-Mannich reaction to set up the C5/C6 relative stereochemistry. The structure was unambiguously assigned by single crystal X-ray diffraction but the spectroscopic data did not match those reported for the natural product. The structure of the natural product must therefore be revised.
alkaloid; aza-Henry; natural products; nitro-Mannich; piperazinone; stereoselective synthesis
Functional neuroimaging is being used in clinical psychiatry today despite the vigorous objections of many in the research community over issues of readiness. To date, a systematic examination of the perspectives of key stakeholders involved in this debate has not yet been attempted. To this fill this gap, we interviewed investigators who conduct functional neuroimaging studies involving adults with mood disorders, schizophrenia, obsessive compulsive disorder, and/or attention deficit hyperactivity disorder, providers who offer clinical neuroimaging services in the open marketplace, and consumers of these services, in order to understand perspectives underlying different views and practices.
Semi-structured interviews were conducted over the telephone. Verbal consent was obtained and all interviews were audio recorded. Interviews of investigators and service providers followed the same interview guide. A separate set of questions was developed for consumers. All interviews were transcribed and made software ready. We applied the qualitative methodology of constant comparison to analyze the data, whereby two researchers independently analyzed the results into textual themes. Coding discrepancies were discussed until consensus was achieved.
Investigators, service providers, and consumers held many common perspectives about the potential or actual risks and benefits of functional neuroimaging for mental illness. However, we also found striking divergences. Service providers focused on the challenges posed by the persistence of symptoms based diagnostic categories, whereas the limitations of the science in this area was the challenge noted most frequently by investigators. The majority of consumers stated that their expectations were met.
Our findings point toward a fundamental tension between academic investigators on the one hand, and commercial service providers and their customers on the other. This scenario poses dangers to the communities directly involved, and to public trust in science and medicine more generally. We conclude with recommendations for work that needs to be done to minimize tensions and maximize the potential of neurotechnology through concerted efforts to respect its limitations while leveraging the strengths, investments, and hopes of each stakeholder group.
BACKGROUND AND OBJECTIVE:
Many thousands of patients die every year in the United States as a result of serious and largely preventable safety events or medical errors. Safety events are common in hospitalized children. We conducted a quality improvement initiative to implement cultural and system changes with the goal of reducing serious safety events (SSEs) by 80% within 4 years at our large, urban pediatric hospital.
A multidisciplinary SSE reduction team reviewed the safety literature, examined recent SSEs, interviewed internal leaders, and visited other leading organizations. Senior hospital leaders provided oversight, monitored progress, and helped to overcome barriers. Interventions focused on: (1) error prevention; (2) restructuring patient safety governance; (3) a new root cause analysis process and a common cause database; (4) a highly visible lessons learned program; and (5) specific tactical interventions for high-risk areas. Our outcome measures were the rate of SSEs and the change in patient safety culture.
SSEs per 10 000 adjusted patient-days decreased from a mean of 0.9 at baseline to 0.3 (P < .0001). The days between SSEs increased from a mean of 19.4 at baseline to 55.2 (P < .0001). After a worsening of patient safety culture outcomes in the first year of intervention, significant improvements were observed between 2007 and 2009.
Our multifaceted approach was associated with a significant and sustained reduction of SSEs and improvements in patient safety culture. Multisite studies are needed to better understand contextual factors and the significance of specific interventions.
patient safety; quality improvement; safety culture
To provide guidelines for future trials, we reviewed the outcomes of children with synchronous bilateral Wilms tumors (BWT) treated on National Wilms Tumor Study-4 (NWTS-4).
NWTS-4 enrolled 3,335 patients (pts) including 188 pts with BWT (5.6%). Treatment and outcome data were collected.
Among 188 BWT pts registered with NWTS-4, 195 kidneys in 123 patients had initial open biopsy, 44 kidneys in 31 pts had needle biopsies. Although pre-resection chemotherapy was recommended, 87 kidneys in 83 pts were managed with primary resection: Complete nephrectomy 48 in 48 pts, 31 partial/wedge nephrectomies in 27 pts, enucleations 8 in 8 pts. No initial surgery was performed in 45 kidneys in 43 pts, 5 kidneys in 3 pts not coded. Anaplasia was diagnosed after completion of the initial course of chemotherapy in 14 pts (initial surgical procedure: 9 open biopsies, 4 needle biopsies, 1 partial nephrectomy). The average number of days from the start of chemotherapy to diagnosis of anaplasia was 390 (range 44–1,925 days). Relapse or progression of disease occurred in 54 children. End stage renal failure occurred in 23 children, 6 of whom had bilateral nephrectomies. The 8 year event free survival (EFS) for BWT with favorable histology was 74%, and overall survival (OS) was 89%; while the EFS for BWT with unfavorable histology was 40%, OS was 45%.
The current analysis of patients with BWT treated on NWTS-4 shows that preservation of renal parenchyma is possible in many pts following initial preoperative chemotherapy. The incidence of end-stage renal disease remains significantly higher in children with BWT. Future studies are warranted to address the need for earlier biopsy in non-responsive tumors and earlier definitive surgery to recognize unfavorable histology in these high risk patients.
Synthetic Biology is the ‘Engineering of Biology’ – it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components, we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of ‘dials’ that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post-translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others.
SIX2 and CITED1 are transcriptional regulators that specify self-renewing nephronic progenitor cells of the embryonic kidney. We hypothesized that SIX2, which promotes and maintains this stem cell population, and CITED1 remain active in Wilms Tumor (WT).
To evaluate expression domains and the pathogenic significance of SIX2 and CITED1 across WT, the Children’s Oncology Group provided 40 WT specimens of stages I–IV (n=10/stage), which were enriched for unfavorable histology (n=20) and treatment failure (relapse or death; n=20). SIX2 and CITED1 protein expression was evaluated qualitatively (immunohistochemistry) and quantitatively (Western blot; WB). Gene transcription was estimated using qRT-PCR.
SIX2 was visualized by immunohistochemistry in 36/38 specimens (94.7%). Protein and mRNA expression of SIX2 were quantitatively similar across all stages of disease (p=0.48 WB; p=0.38 qPCR), in favorable or unfavorable histology (p=0.51 WB; p=0.58 qPCR), and in treatment failure or success (p=0.86 WB; p=0.49 qPCR). Although CITED1 expression paralleled SIX2 qualitatively, no quantitative correlation between SIX2 and CITED1 expression was observed (Spearman’s correlation coefficient 0.28, p=0.08). As in the fetal kidney, overlapping, but also distinct, WT cellular expression domains were observed between SIX2 and CITED1.
SIX2 and CITED1 remain active across all disease characteristics of WT. Activity of these genes in WT potentially identifies a population of self-renewing cancer cells that exhibit an embryonic, stem-like phenotype. Taken together, these transcriptional regulators may be fundamental to WT cellular self-renewal and may represent targets for novel therapies that promote terminal differentiation.
SIX2; CITED1; Wilms tumor; embryonic kidney
To evaluate conventional brachytherapy (BT) plans using dose-volume parameters and high resolution (3 Tesla) MRI datasets, and to quantify dosimetric benefits and limitations when MRI-guided, conformal BT (MRIG-CBT) plans are generated.
Material and methods
Fifty-five clinical high-dose-rate BT plans from 14 cervical cancer patients were retrospectively studied. All conventional plans were created using MRI with titanium tandem-and-ovoid applicator (T&O) for delivery. For each conventional plan, a MRIG-CBT plan was retrospectively generated using hybrid inverse optimization. Three categories of high risk (HR)-CTV were considered based on volume: non-bulky (< 20 cc), low-bulky (> 20 cc and < 40 cc) and bulky (≥ 40 cc). Dose-volume metrics of D90 of HR-CTV and D2cc and D0.1cc of rectum, bladder, and sigmoid colon were analyzed.
Tumor coverage (HR-CTV D90) of the conventional plans was considerably affected by the HR-CTV size. Sixteen percent of the plans covered HR-CTV D90 with the prescription dose within 5%. At least one OAR had D2cc values over the GEC-ESTRO recommended limits in 52.7% of the conventional plans. MRIG-CBT plans showed improved target coverage for HR-CTV D90 of 98 and 97% of the prescribed dose for non-bulky and low-bulky tumors, respectively. No MRIG-CBT plans surpassed the D2cc limits of any OAR. Only small improvements (D90 of 80%) were found for large targets (> 40 cc) when using T&O applicator approach.
MRIG-CBT plans displayed considerable improvement for tumor coverage and OAR sparing over conventional treatment. When the HR-CTV volume exceeded 40 cc, its improvements were diminished when using a conventional intracavitary applicator.
brachytherapy; cervical cancer; high-dose-rate brachytherapy; MRI-guided brachytherapy
Three cases of drug-induced liver injury (DILI) have been reported after desflurane anesthesia. However, no previous reports have detected serum autoantibodies such as that reported with DILI from halothane or isoflurane.
METHODS AND RESULTS
We describe the first documentation of cytochrome P450 2E1 IgG4 autoantibodies, as well as 58 kDa endoplasmic reticulum protein and trifluoroacetyl chloride hapten-specific IgG4 antibodies, in a patient who developed DILI after desflurane anesthesia.
These findings suggest that allergic and autoimmune mechanisms have critical roles in the development of desflurane DILI.
With the advancement of next-generation sequencing and transcriptomics technologies, regulatory effects involving RNA, in particular RNA structural changes are being detected. These results often rely on RNA secondary structure predictions. However, current approaches to RNA secondary structure modelling produce predictions with a high variance in predictive accuracy, and we have little quantifiable knowledge about the reasons for these variances.
In this paper we explore a number of factors which can contribute to poor RNA secondary structure prediction quality. We establish a quantified relationship between alignment quality and loss of accuracy. Furthermore, we define two new measures to quantify uncertainty in alignment-based structure predictions. One of the measures improves on the “reliability score” reported by PPfold, and considers alignment uncertainty as well as base-pair probabilities. The other measure considers the information entropy for SCFGs over a space of input alignments.
Our predictive accuracy improves on the PPfold reliability score. We can successfully characterize many of the underlying reasons for and variances in poor prediction. However, there is still variability unaccounted for, which we therefore suggest comes from the RNA secondary structure predictive model itself.
To compare dosimetric parameters of intensity modulated radiation therapy (IMRT) and three-dimensional conformal radiation therapy (3DCRT) in patients with intermediate risk rhabdomyosarcoma (RMS), and to analyze their effect on local-regional control (LRC) and failure-free survival (FFS).
Methods and Materials
The study population consisted of 375 patients enrolled on Children’s Oncology Group protocol D9803, receiving IMRT or 3DCRT. Dosimetric data was collected from 179 patients with an available composite plan. Chi-square or Fisher’s exact tests were used to compare patient characteristics and radiotherapy (RT) parameters between the two groups. Time-to- event outcomes were estimated using the Kaplan-Meier method and compared using log-rank tests. Cox analysis was used to examine the effect of RT technique on FFS after adjusting for primary site and risk group.
The median follow-up time was 5.7 and 4.2 years for patients receiving 3DCRT and IMRT respectively. No differences in 5 year failure of LRC (18% vs. 15%) and FFS (72% vs. 76%) were noted between the two groups. Multivariate analysis revealed no association between RT technique and FFS. Patients with primary tumors in parameningeal (PM) sites were more likely to receive IMRT than 3DCRT. IMRT became more common during the later years of the study. Patients receiving IMRT were more likely to receive >50Gy, photon energy of ≤6MV, and >5 RT fields than those who received 3DCRT. There was improved coverage of the IMRT planning target volume (PTV) by the prescription dose compared to the 3DCRT with similar target dose heterogeneity.
IMRT improved target dose coverage when compared to 3DCRT, though an improvement in LRC or FFS could not be demonstrated in this population. Future studies comparing integral dose to non-target tissue and late RT toxicity between the two groups is warranted.
Rhabdomyosarcoma; Intermediate risk; IMRT/3DCRT
Pre-operative assessment of intravascular extension of Wilms tumor is essential to guide management. Our aim is to evaluate the diagnostic performance of multidetector CT in detection of tumor thrombus in Wilms tumor.
The study population was drawn from the first 1015 cases in the AREN03B2 study of the Children’s Oncology Group. CT scans of children with (n=62) and without (n=111) tumor thrombus at nephrectomy were independently reviewed by two radiologists, blinded to patient information. Doppler sonography results were obtained from institutional radiology reports, as Doppler requires real-time evaluation. The diagnostic performance of CT and Doppler for detection of tumor thrombus was determined using nephrectomy findings as reference standard.
In the primary nephrectomy group, tumor thrombus detection sensitivity, specificity of CT was 65.6%, 84.8%, and Doppler was 45.8%, 95.7%, respectively. In this group, sensitivity of CT, Doppler for detection of cavoatrial thrombus was 84.6% and 70.0%, respectively. In the secondary nephrectomy group, tumor thrombus detection sensitivity, specificity of CT was 86.7%, 90.6%, and Doppler was 66.7%, 100.0%, respectively. In this group, sensitivity of CT, Doppler for detection of cavoatrial thrombus was 96.0% and 68.8%, respectively. Pre-operative Doppler evaluation performed in 108/173 cases, detected 3 cases with intravenous extension (2 in renal vein, 1 in IVC at renal vein level) that were missed at CT.
CT can accurately identify cavoatrial tumor thrombus that will impact surgical approach. Routine Doppler evaluation, after CT has already been performed, is not required in Wilms tumor.
Wilms tumor; tumor thrombus; CT; Doppler
This study describes a method for optimizing selective stimulus parameters for multi-contact peripheral electrodes. Overlap between pairs of contacts is quantified by the deviation in their combined response from linear addition of their individual responses. Mathematical models are fit to recruitment and overlap data, and a cost function is defined to maximize recruitment and minimize overlap between all contacts. Results are presented for two four-contact nerve-cuff electrodes stimulating bilateral femoral nerves of one human subject with spinal cord injury. Knee extension moments between 11.6 and 17.2 Nm are achieved through two contacts of each nerve-cuff with less than 10% overlap between each pair of contacts. These results suggest that optimization can provide an automated means of determining stimulus parameters to achieve strong, selective muscle contractions through multi-contact peripheral nerve electrodes.