Accelerating 4D image reconstruction for magnetic resonance-guided radiotherapy

Background and purpose

Physiological motion impacts the dose delivered to tumours and vital organs in external beam radiotherapy and particularly in particle therapy. The excellent soft-tissue demarcation of 4D magnetic resonance imaging (4D-MRI) could inform on intra-fractional motion, but long image reconstruction times hinder its use in online treatment adaptation. Here we employ techniques from high-performance computing to reduce 4D-MRI reconstruction times below two minutes to facilitate their use in MR-guided radiotherapy.

Material and methods

Four patients with pancreatic adenocarcinoma were scanned with a radial stack-of-stars gradient echo sequence on a 1.5T MR-Linac. Fast parallelised open-source implementations of the extra-dimensional golden-angle radial sparse parallel algorithm were developed for central processing unit (CPU) and graphics processing unit (GPU) architectures. We assessed the impact of architecture, oversampling and respiratory binning strategy on 4D-MRI reconstruction time and compared images using the structural similarity (SSIM) index against a MATLAB reference implementation. Scaling and bottlenecks for the different architectures were studied using multi-GPU systems.

Results

All reconstructed 4D-MRI were identical to the reference implementation (SSIM > 0.99). Images reconstructed with overlapping respiratory bins were sharper at the cost of longer reconstruction times. The CPU  + GPU implementation was over 17 times faster than the reference implementation, reconstructing images in 60 ± 1 s and hyper-scaled using multiple GPUs.

Conclusion

Respiratory-resolved 4D-MRI reconstruction times can be reduced using high-performance computing methods for online workflows in MR-guided radiotherapy with potential applications in particle therapy.

Institutional experience of using active breathing control for paediatric and teenage patients receiving thoraco-abdominal radiotherapy

Introduction

Active Breathing Control (ABC) is a motion management strategy that facilitates reproducible breath-hold for thoracic radiotherapy (RT), which may reduce radiation dose to organs at risk (OARs). Reduction of radiation-induced toxicity is of high importance in younger patients. However, there is little published literature on the feasibility of ABC in this group. The purpose of this study was to report our experience of using ABC for paediatric and teenage patients.

Methods

Patients ≤18 years referred for thoracic RT using ABC at our centre from 2013-2021 were identified. Electronic records were retrospectively reviewed to obtain information on diagnosis, RT dose and technique, OAR dosimetry, tolerability of ABC, post-treatment imaging and early toxicity rates.

Results

12 patients completed RT and were able to comply with ABC during planning and for the duration of RT. Median age was 15.5 years (10-18 years). Diagnoses were: Hodgkin lymphoma (n = 5), mediastinal B-cell lymphoma (n = 1), Ewing sarcoma (n = 5) and rhabdomyosarcoma (n = 1). For mediastinal RT cases (n = 6), median dose delivered was 30.6Gy(19.8-40Gy), median mean heart dose was 11.4Gy(4.8-19.4Gy), median mean lung dose was 9.9Gy(5.7-14.5Gy) and mean lung V20 was 10.9%. For ipsilateral RT cases, (n = 6), median hemithorax and total doses to primary tumour were 18Gy(15-20Gy) and 52.2Gy(36-60Gy) respectively. Median mean heart dose was 19.5Gy(10.6-33.2Gy) and median mean lung dose was 17.7Gy(16.3-30.5Gy). Mean bilateral lung V20 was 39.6%. Median mean contralateral lung dose was 5.2Gy(3.5-11.6Gy) and mean contralateral lung V20 was 1.5%. At a median follow-up of 36 months, only 1 patient had symptomatic radiation pneumonitis having received further thoracic RT following relapse.

Conclusions

ABC is feasible and well tolerated in younger patients receiving RT. Children as young as 10 years are able to comply. Use of ABC results in OAR dosimetry which is comparable to similar data in adults and can facilitate RT for extensive thoracic sarcoma.

Public and Patient Involvement in Doctoral Research During the COVID-19 Pandemic: Reflections on the Process, Challenges, Impact and Experiences From the Perspectives of Adults With Cerebral Palsy and the Doctoral Researcher

Introduction

Cerebral palsy (CP) is a lifelong condition, where people may experience complications as they age. Including the views of people with CP through Public and Patient Involvement (PPI) ensures that research into the condition is relevant and meaningful in addressing their concerns. However, there is a lack of evidence on incorporating the voices of adults with CP in the doctoral research process. Therefore, this paper aims to provide an overview of how adults with CP were involved in a doctoral research process during the pandemic.

Methods

This paper describes the PPI process and its impact at various stages of the doctoral research process and reflects on the experiences from the perspective of the doctoral researcher and adults with CP using the INVOLVE Values and Principles framework. Five adults with CP were consulted throughout the doctoral research programme. The data for this paper is a combination of reflection notes, email exchanges, meeting minutes and informal discussions with the PPI team on their experiences of being involved in the PPI process. The content of this paper is informed by GRIPP 2 checklist.

Results

The doctoral researcher and adult reflections highlighted the value of collaboration and the positive impact on research at each stage of the doctoral research process. Although meetings were adapted due to the pandemic, the values of PPI were adhered to throughout the doctoral research.

Conclusion

Involving adults with CP positively impacted the doctoral research process. It is recommended to consider individual access needs to ensure meetings and information are accessible for disabled adults. Our reflective findings and recommendations may help other researchers who plan to involve adults with CP in doctoral research.

Identical and Nonidentical Twins: Risk and Factors Involved in Development of Islet Autoimmunity and Type 1 Diabetes

OBJECTIVE

There are variable reports of risk of concordance for progression to islet autoantibodies and type 1 diabetes in identical twins after one twin is diagnosed. We examined development of positive autoantibodies and type 1 diabetes and the effects of genetic factors and common environment on autoantibody positivity in identical twins, nonidentical twins, and full siblings.

RESEARCH DESIGN AND METHODS

Subjects from the TrialNet Pathway to Prevention Study (N = 48,026) were screened from 2004 to 2015 for islet autoantibodies (GAD antibody [GADA], insulinoma-associated antigen 2 [IA-2A], and autoantibodies against insulin [IAA]). Of these subjects, 17,226 (157 identical twins, 283 nonidentical twins, and 16,786 full siblings) were followed for autoantibody positivity or type 1 diabetes for a median of 2.1 years.

RESULTS

At screening, identical twins were more likely to have positive GADA, IA-2A, and IAA than nonidentical twins or full siblings (all P < 0.0001). Younger age, male sex, and genetic factors were significant factors for expression of IA-2A, IAA, one or more positive autoantibodies, and two or more positive autoantibodies (all P ≤ 0.03). Initially autoantibody-positive identical twins had a 69% risk of diabetes by 3 years compared with 1.5% for initially autoantibody-negative identical twins. In nonidentical twins, type 1 diabetes risk by 3 years was 72% for initially multiple autoantibody-positive, 13% for single autoantibody-positive, and 0% for initially autoantibody-negative nonidentical twins. Full siblings had a 3-year type 1 diabetes risk of 47% for multiple autoantibody-positive, 12% for single autoantibody-positive, and 0.5% for initially autoantibody-negative subjects.

CONCLUSIONS

Risk of type 1 diabetes at 3 years is high for initially multiple and single autoantibody-positive identical twins and multiple autoantibody-positive nonidentical twins. Genetic predisposition, age, and male sex are significant risk factors for development of positive autoantibodies in twins.

Low-Dose Anti-Thymocyte Globulin (ATG) Preserves β-Cell Function and Improves HbA1c in New-Onset Type 1 Diabetes

OBJECTIVE

A pilot study suggested that combination therapy with low-dose anti-thymocyte globulin (ATG) and pegylated granulocyte colony-stimulating factor (GCSF) preserves C-peptide in established type 1 diabetes (T1D) (duration 4 months to 2 years). We hypothesized that 1) low-dose ATG/GCSF or 2) low-dose ATG alone would slow the decline of β-cell function in patients with new-onset T1D (duration <100 days).

RESEARCH DESIGN AND METHODS

A three-arm, randomized, double-masked, placebo-controlled trial was performed by the Type 1 Diabetes TrialNet Study Group in 89 subjects: 29 subjects randomized to ATG (2.5 mg/kg intravenously) followed by pegylated GCSF (6 mg subcutaneously every 2 weeks for 6 doses), 29 to ATG alone (2.5 mg/kg), and 31 to placebo. The primary end point was mean area under the curve (AUC) C-peptide during a 2-h mixed-meal tolerance test 1 year after initiation of therapy. Significance was defined as one-sided P value < 0.025.

RESULTS

The 1-year mean AUC C-peptide was significantly higher in subjects treated with ATG (0.646 nmol/L) versus placebo (0.406 nmol/L) (P = 0.0003) but not in those treated with ATG/GCSF (0.528 nmol/L) versus placebo (P = 0.031). HbA_1c was significantly reduced at 1 year in subjects treated with ATG and ATG/GCSF, P = 0.002 and 0.011, respectively.

CONCLUSIONS

Low-dose ATG slowed decline of C-peptide and reduced HbA_1c in new-onset T1D. Addition of GCSF did not enhance C-peptide preservation afforded by low-dose ATG. Future studies should be considered to determine whether low-dose ATG alone or in combination with other agents may prevent or delay the onset of the disease.

A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk

OBJECTIVE

We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals.

RESEARCH DESIGN AND METHODS

We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables.

RESULTS

Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002).

CONCLUSIONS

The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.

Kent experience of radical chemoradiotherapy for muscle invasive bladder cancer

373

Background: The BC2001 trial in 2012 showed concurrent chemoradiotherapy to be the new standard of care for bladder preserving treatment of muscle invasive bladder cancer. Addition of concurrent MMC and infusional 5FU showed a relative risk reduction of 33% in locoregional recurrence (James ND, Hussain S, Hall E et al. Radiotherapy with or without chemotherapy in muscle-invasive bladder cancer. N Engl J Med. 2012;366(16):1477–88.). This audit evaluates the experience across Kent in six hospitals adopting this protocol. Methods: 116 patients treated with radical radiotherapy for bladder cancer between January 2013 and December 2015 were retrospectively reviewed. 64 patients received radiotherapy alone due to contraindications to chemotherapy, performance status and patient choice. 52 patients received concurrent chemotherapy, the majority with 5FU/MMC and a subset with oral Capecitabine in place of infusional 5FU. Kaplan Meier and Log-Rank analysis of overall survival, local recurrence free survival and metastasis free survival were performed using SPSS. Results: Local recurrence free survival in the chemoradiotherapy group was 73% (95% CI 59-87%) compared to the radiotherapy group 61% (45-77) (p=0.27). There was a trend for greater metastasis free survival at 2 years, 63% (47-79) in the chemoradiotherapy group compared to 52% (38-66) in the radiotherapy group (p=0.21). Similarly, overall 2 year survival was 74% (60-88) and 59% (43-75) respectively (p=0.21). Conclusions: Our results showed a trend towards improved local control, distant control and increased overall survival in patients treated with concurrent chemoradiotherapy compared to radiotherapy alone. The differences did not meet statistical significance; however this was a small retrospective series with a relatively short median followup of 17.5 months. Treatment was well tolerated in our patient group. Overall, our data is in keeping with the results of the BC2001 trial (James ND, Hussain S, Hall E et al. Radiotherapy with or without chemotherapy in muscle-invasive bladder cancer. N Engl J Med. 2012;366(16):1477–88.)

Differential Cell Composition and Cytokine Expression Within Lymph Node Granulomas from BCG-Vaccinated and Non-vaccinated Cattle Experimentally Infected with Mycobacterium bovis

Cattle vaccination against bovine tuberculosis (bTB) has been proposed as a supplementary method to help control the incidences of this disease. Bacillus Calmette-Guérin (BCG) is currently the only viable candidate vaccine for immunization of cattle against bTB, caused by Mycobacterium bovis (M. bovis). In an attempt to characterize the differences in the immune response following M. bovis infection between BCG-vaccinated and non-vaccinated animals, a combination of gross pathology, histopathology and immunohistochemical (IHC) analyses was used. BCG vaccination was found to significantly reduce the number of gross and microscopic lesions present within the lungs and lymph nodes. Additionally, the microscopically visible bacterial load of stages III and IV granulomas was reduced. IHC using cell surface markers revealed the number of CD68+ (macrophages), CD3+ (T lymphocytes) and WC1+ cells (γδ T cells) to be significantly reduced in lymph node granulomas of BCG-vaccinated animals, when compared to non-vaccinated animals. B lymphocytes (CD79a+) were significantly increased in BCG-vaccinated cattle for granulomas at stages II, III and IV. IHC staining for iNOS showed a higher expression in granulomas from BCG-vaccinated animals compared to non-vaccinated animals for all stages, being statistically significant in stages I and IV. TGFβ expression decreased alongside the granuloma development in non-vaccinated animals, whereas BCG-vaccinated animals showed a slight increase alongside lesion progression. IHC analysis of the cytokines IFN-γ and TNF-α demonstrated significantly increased expression within the lymph node granulomas of BCG-vaccinated cattle. This is suggestive of a protective role for IFN-γ and TNF-α in response to M. bovis infection. Findings shown in this study suggest that the use of BCG vaccine can reduce the number and severity of lesions, induce a different phenotypic response and increase the local expression of key cytokines related to protection.

Pathology and Virus Distribution in the Lung and Lymphoid Tissues of Pigs Experimentally Inoculated with Three Distinct Type 1 PRRS Virus Isolates of Varying Pathogenicity

Porcine reproductive and respiratory syndrome (PRRS) continues to be the most economically important disease of swine worldwide. The appearance of highly pathogenic PRRS virus (PRRSV) strains in Europe and Asia has raised concerns about this disease and initiated increased efforts to understand the pathogenesis. In this study, we have compared the pathology and the virus distribution in tissues of pigs experimentally inoculated with three different genotype 1 PRRSV isolates. Sixty 5-week-old pigs were inoculated intranasally with a) the Lelystad virus (LV), b) a field strain from the UK causing respiratory clinical signs (UK) or c) a highly pathogenic strain from Belarus (BE). Sixteen animals were mock-infected and used as controls. The animals were euthanized at 3, 7 and 35 days post-infection (dpi), and lung and lymphoid tissues collected for histopathological examination and PRRSV detection by immunohistochemistry (IHC). Histopathological lesions consisted of interstitial pneumonia with mononuclear cell infiltrates in the lungs, lymphoid depletion, apoptosis and follicular hyperplasia in the spleen, lymph nodes and tonsil and lymphoid depletion in the thymus. Porcine reproductive and respiratory syndrome virus was detected mainly in monocytes-macrophages. BE-infected animals showed the highest pathological scores and the highest presence of virus at 3 and 7 dpi, followed by the UK field strain and then LV. Moderate lesions were observed at 35 dpi with lesser detection of PRRSV by IHC in each infected group. The highly pathogenic BE strain induced more severe pathology in both lungs and lymphoid organs of pigs compared with the classic field isolate and the prototype LV. The increased severity of pathology was in correlation with the presence of a higher number of PRRSV-infected cells in the tissues.

Experimental vaccination of sheep and cattle against tick infestation using recombinant 5'-nucleotidase

Limited prior evidence suggests that 5′-nucleotidase, an ectoenzyme principally located in the Malpighian tubules of the tick Rhipicephalus (Boophilus) microplus, could be an effective antigen in an anti-tick vaccine. To assess this, recombinant 5′-nucleotidase was expressed in Escherichia coli and used in vaccination trials with both sheep and cattle. Vaccinated sheep were challenged with freshly moulted adult ticks. Those with high titres of anti-nucleotidase antibodies showed significant protection against tick infestation, although protection was less than that found with the previously characterized antigen, Bm86. Cattle were vaccinated, in separate groups, with 5′-nucleotidase, Bm86 and both antigens combined. Cattle, as the natural host, were challenged with larval ticks. Although Bm86 showed typical efficacy, no significant protection was seen in cattle vaccinated with 5′-nucleotidase. Cattle receiving a dual antigen formulation were no better protected than those receiving Bm86 alone. One possible reason for the difference between host species, namely antibody titre, was examined and shown to be an unlikely explanation. This demonstrates a limitation of using a model host like sheep in vaccine studies.

Pelioid hepatocellular carcinoma in an adult Eurasian badger (Meles meles)

A mass was identified within the left lateral lobe of the liver of a 10-year-old Eurasian badger (Meles meles). The mass was friable and multilobulated, with blood-filled spaces between the lobules. Microscopically, the lesion consisted of sheets and trabeculae of neoplastic hepatocytes often forming cystic spaces containing erythrocytes, fibrin and necrotic debris. The histological appearance was consistent with hepatocellular carcinoma (HCC). Immunohistochemically, the neoplastic cells expressed cytokeratin 18 but not von Willebrand factor. Multiple intranuclear (amphophilic or acidophilic) inclusion bodies were observed in hepatocytes at the junction between the tumour and normal hepatic tissue. HCCs have also been reported in other domestic and wild animals. As hepadnavirus infection has been associated with HCC in woodchucks, further histochemical and transmission electron microscopical studies were performed; however, these demonstrated that the inclusions consisted of lipid droplets and not viral particles. To our knowledge, this is the first report of a naturally occurring HCC in a Eurasian badger.

Expression of intracellular calcium signalling genes in cattle skin during tick infestation

It is widely acknowledged that changes in intracellular calcium ion (Ca(2+)) concentration provide dynamic signals that control a plethora of cellular processes, including triggering and mediating host defence mechanisms. In this study, quantitative real-time PCR was used to analyse gene expression of 14 Ca(2+) signalling proteins in skin obtained from high tick-resistant (HR) and low tick-resistant (LR) cattle following artificial challenge with cattle tick (Rhipicephalus (Boophilus) microplus). Up-regulation of numerous genes was observed in both HR and LR skin following tick challenge, however substantially higher transcription activation was found in HR tissue. The elevated expression in HR skin of specific Ca(2+) signalling genes such as AHNAK, CASQ, IL2, NFAT2CIP and PLCG1 may be related to host resistance. Our data suggest that Ca(2+) and its associated proteins might play an important role in host response to ticks and that further investigation is warranted.

Seven genomic subtypes of chronic fatigue syndrome/myalgic encephalomyelitis: a detailed analysis of gene networks and clinical phenotypes

AIM

Chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) is a multisystem disease, the pathogenesis of which remains undetermined. The authors have recently reported a study of gene expression that identified differential expression of 88 human genes in patients with CFS/ME. Clustering of quantitative PCR (qPCR) data from patients with CFS/ME revealed seven distinct subtypes with distinct differences in Medical Outcomes Survey Short Form-36 scores, clinical phenotypes and severity.

METHODS

In this study, for each CFS/ME subtype, those genes whose expression differed significantly from that of normal blood donors were identified, and then gene interactions, disease associations and molecular and cellular functions of those gene sets were determined. Genomic analysis was then related to clinical data for each CFS/ME subtype.

RESULTS

Genomic analysis revealed some common (neurological, haematological, cancer) and some distinct (metabolic, endocrine, cardiovascular, immunological, inflammatory) disease associations among the subtypes. Subtypes 1, 2 and 7 were the most severe, and subtype 3 was the mildest. Clinical features of each subtype were as follows: subtype 1 (cognitive, musculoskeletal, sleep, anxiety/depression); subtype 2 (musculoskeletal, pain, anxiety/depression); subtype 3 (mild); subtype 4 (cognitive); subtype 5 (musculoskeletal, gastrointestinal); subtype 6 (postexertional); subtype 7 (pain, infectious, musculoskeletal, sleep, neurological, gastrointestinal, neurocognitive, anxiety/depression).

CONCLUSION

It was particularly interesting that in the seven genomically derived subtypes there were distinct clinical syndromes, and that those which were most severe were also those with anxiety/depression, as would be expected in a disease with a biological basis.

Pathology of naturally occurring bovine tuberculosis in England and Wales

The aim of this study was to obtain a contemporary data set of pathology in tuberculin reactor and in-contact cattle in England and Wales. Four hundred animals (200 reactors and 200 in-contacts) from 242 farms located in 14 counties in Western England and Wales were examined. The mean number of lymph nodes (LNs) with tuberculosis (TB)-like lesions per TB-confirmed animal was 1.7 in reactors and 1.5 in in-contact animals. Tuberculous lesions in both reactor and in-contact animals were most commonly observed in the LNs of the thorax, followed by the head and abdomen, particularly the mediastinal, retropharyngeal and tracheobronchial LNs. Twenty-five reactors had macroscopic lesions in the palatine tonsils. Among TB-confirmed cattle, 27% of reactors and 9% of in-contact animals had gross TB-like lesions in the lungs, particularly in the caudal lobes. Gross lesions that were not TB-confirmed were parasitic granulomas (45%), bacterial or mycotic club-forming pyogranulomas (27%) and bacterial abscesses (23%). Diagnostic sensitivity was maximised when bacteriology and histopathology were used concurrently. Stage IV granulomas, alone or in combination with other stages, constituted 63% of lesions, while 16% of lesions were stage I/II granulomas. Caseous necrosis and calcification were common features of the granulomas encountered in natural Mycobacterium bovis infections, even with pathology limited to a small number of sites. Granulomas often covered large areas of histological sections and typically contained only small numbers of acid fast bacilli.

Distribution and activation of T-lymphocyte subsets in tuberculous bovine lymph-node granulomas

The immune response against mycobacterial infections is dependant upon a complex interaction between T lymphocytes and macrophages in the context of the granuloma. For this study, we performed the analysis of 18 stage I or II, and 13 stage III or IV granulomas found in lymph nodes from 8 experimentally and 2 naturally infected cattle. T-cell subpopulations (CD3(+), CD4(+), CD8(+), WC1(+), CD25(+)) were investigated by immunohistochemistry. In the majority of stage I/II lesions, CD8(+) and CD25(+) cells were predominantly found in the lymphocytic outer region of the granuloma, suggesting a possible role for activated CD8(+) cells in the initial attempt to restrain the granuloma growth. CD4(+) T cells appeared equally distributed in the lymphocytic mantle and in the internal areas of the granulomas. WC1(+) cells appeared interspersed among the macrophages. We speculated that this could indicate a role for these 2 subsets in the maintenance and the maturation of the granuloma. In stage III/IV lesions, all of the T-cell subsets investigated appeared interspersed among the mononuclear component of the granulomas. In general terms, there was a higher density of CD8(+) cells compared with CD4(+) cells. However, there was no sense of rimming effect for any of the investigated cell populations.

Evaluation of zinc salt based fixatives for preserving antigenic determinants for immunohistochemical demonstration of murine immune system cell markers

Conventional aldehyde based fixatives produce good morphological preservation. However, owing to their cross-linking mechanism of action, epitope loss may occur during fixation compromising the tissue for subsequent immunohistochemical (IHC) analysis. IHC is an important tool for characterizing antigen, cytokine and cytomorphological markers. The increasing use of mouse models for study of pathogenesis has highlighted the need to investigate alternative fixatives. In the study reported here, tissue samples from RIII mice with immune mediated lesions, Mycobacterium bovis infected mice, and uninfected control mice were fixed in either zinc salt fixative or buffered formalin, then tested for IHC using a panel of antibodies (CD3, CD4, CD8, CD45, CD54, F4/80, Interferon-gamma and MIP2). Zinc salt fixation preserved processing-sensitive murine cell markers (CD4, CD8 and CD54) and improved the intensity of immunolabeling for CD45, F4/80 and CD3. Buffered formalin failed to preserve any of the processing-sensitive murine epitopes for demonstration by subsequent IHC.

A phase II trial of pemetrexed plus gemcitabine in locally advanced and/or metastatic transitional cell carcinoma of the urothelium

BACKGROUND

Both pemetrexed and gemcitabine have single-agent activity in bladder cancer, but the combination of these two drugs has not been previously evaluated for safety and efficacy in this disease. Thus, the objectives in the current study were to determine overall response rate (ORR), progression-free survival, overall survival and safety and toxicity in chemonaive patients with locally advanced and/or metastatic transitional cell carcinoma of the urothelium.

PATIENTS AND METHODS

Gemcitabine 1250 mg/m2 was administered over 30 min i.v. on days 1 and 8, and pemetrexed 500 mg/m2 over 10 min i.v. on day 8 after gemcitabine, every 21 days.

RESULTS

Sixty-four patients were enrolled, 11 female and 53 male, median age 65 years (range 38-81), median WHO performance status of 1. Visceral metastases were present in 55% of patients. ORR among 47 patients evaluable for response was 28% (95% CI 16% to 43%) and ORR for the intention-to-treat population was 20% (95% CI 11% to 32%) with three CR and 10 PR. Median response duration was 11.2 months and median overall survival 10.3 months (95% CI 8.1-14.6 months). CTC grade 3/4 hematologic toxicities included anemia (19%), thrombocytopenia (9%), neutropenia (38%), febrile neutropenia (17%) and neutropenic sepsis (3%). Grade 3/4 non-hematologic toxicities included elevated transaminases (12%), dyspnea (8%), fatigue (8%) and stomatitis (5%). There was one toxic death due to neutropenic sepsis.

CONCLUSIONS

The combination of pemetrexed and gemcitabine had a manageable safety profile. However, efficacy was apparently not superior to that of single-agent gemcitabine.

Ten-year Brisbane experience in petrol burns: a preventable health burden

Petrol is one of the most widely used and freely available fuels in use in developed countries today. This study examines the clinical details and demographics of adults with petrol burns over a 10-year period with a view to identifying any trends. The majority of petrol burns were due to human error and thus theoretically preventable. This study determined that the young male (aged 16-25) is most at risk, mainly through the misuse of petrol. The best method of prevention of these burns might be education targeting this group of population. This study provides a basis upon which effective intervention programmes can be designed.

Impact of antibiotic administrative restrictions on trends in antibiotic resistance

CONTEXT

In March 2001, in response to concerns about increasing resistance to fluoroquinolone (FQ) antibiotics, the Ontario Drug Benefit (ODB) program limited reimbursement of FQs to ODB beneficiaries defined as high risk or in whom other therapies are not tolerated.

OBJECTIVE

To analyze the impact of the limited use (LU) policy changes on antibiotic resistance rates in Ontario, focussing on community-acquired pathogens.

DESIGN

Ontario data submitted to the Canadian Bacterial Surveillance Network (CBSN) between January 1, 1998 and June 30, 2002 were analyzed for rates of resistance in various pathogen-antibiotic combinations. The effect of the LU policy on the level and rate of change of antibiotic resistance was estimated using time series models.

RESULTS

Resistance rates for S. pneumoniae were 10-12% for penicillin, erythromycin and trimethoprim sulfamethoxazole (TMP/SMX) and less than 3% for amoxicillin and all three FQs tested. There was a statistically significant increasing trend in resistance rates of S. pneumoniae to amoxicillin and levofloxacin throughout the study period. Antibiotic resistance of S. pneumoniae to ciprofloxacin indicated a statistically significant decreasing trend over the study period with a statistically significant increase in the level of antibiotic resistance at the time of the LU policy implementation. No other indication of any statistically significant decrease in resistance rates associated with the LU policy was found.

CONCLUSIONS

Although no direct cause and effect can be proven with these observational data, there is no evidence that the limited use policy to restrict fluoroquinolones decreased antibiotic resistance in any of the pathogen-antibiotic combinations tested.

Impact of antibiotic administrative restrictions on trends in antibiotic resistance

CONTEXT

In March 2001, in response to concerns about increasing resistance to fluoroquinolone (FQ) antibiotics, the Ontario Drug Benefit (ODB) program limited reimbursement of FQs to ODB beneficiaries defined as high risk or in whom other therapies are not tolerated.

OBJECTIVE

To analyze the impact of the limited use (LU) policy changes on antibiotic resistance rates in Ontario, focussing on community-acquired pathogens.

DESIGN

Ontario data submitted to the Canadian Bacterial Surveillance Network (CBSN) between January 1, 1998 and June 30, 2002 were analyzed for rates of resistance in various pathogen-antibiotic combinations. The effect of the LU policy on the level and rate of change of antibiotic resistance was estimated using time series models.

RESULTS

Resistance rates for S. pneumoniae were 10-12% for penicillin, erythromycin and trimethoprim sulfamethoxazole (TMP/SMX) and less than 3% for amoxicillin and all three FQs tested. There was a statistically significant increasing trend in resistance rates of S. pneumoniae to amoxicillin and levofloxacin throughout the study period. Antibiotic resistance of S. pneumoniae to ciprofloxacin indicated a statistically significant decreasing trend over the study period with a statistically significant increase in the level of antibiotic resistance at the time of the LU policy implementation. No other indication of any statistically significant decrease in resistance rates associated with the LU policy was found.

CONCLUSIONS

Although no direct cause and effect can be proven with these observational data, there is no evidence that the limited use policy to restrict fluoroquinolones decreased antibiotic resistance in any of the pathogen-antibiotic combinations tested.

Advanced Granulomatous Lesions in Mycobacterium bovis-infected Cattle are Associated with Increased Expression of Type I Procollagen, γδ (WC1+) T Cells and CD 68+ Cells

The pathognomonic characteristic of tuberculosis (TB) is the formation of a tuberculous granuloma. The objective of this study was to classify lymph node granulomas from experimentally infected calves into different histopathological stages and characterize them further by studying cell types and markers of fibrosis associated with each of the stages. Four stages of granuloma were identified and mRNA and protein expression for cell markers, cytokines and pro-fibrotic markers were studied by immunohistochemistry (IHC) and in-situ hybridization (ISH). In advanced stage granulomas, there was an increase in the expression of TGF-beta, and of type I procollagen as demonstrated by IHC and ISH. As the granulomas advanced, there were fewer CD3+T cells and they tended to be more prominent towards the periphery of the lesions, with a steady increase in the number of CD68+ cells and gammadelta (WC1+) T cells. Granuloma classification and application of cell cytokine markers will assist in improving understanding of the pathogenesis of bovine TB and may help to identify the immunopathology of active disease versus contained or inactive disease. Such disease correlates may help to inform the development of improved diagnostic methods and support vaccine development programmes.

The transcriptional landscape of the mammalian genome

This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

Correlation between neoral 2 hours post-dose levels and histologic findings on surveillance biopsies

Use of 2-hour postdose (C2) monitoring has been a major step in optimizing immunosuppression following kidney transplantation, and extensive data has confirmed the superiority of C2 monitoring over the conventional trough monitoring (C0) in reducing the occurrence of acute rejection early after transplantation. In this retrospective study, we explored the relationship between Neoral pharmacokinetic parameters and the presence of subclinical rejections (ScRj). In the absence of acute rejection, lower C2 level was associated with more frequent episodes of ScRj. C0 monitoring was not predictive of AR, ScRj or any combinations thereof. Fast elimination in a subgroup of patients is not detected by the C0 and may lead to unnecessary increase of the drug dosage and increased risk of rejection.

Changing practice in residential aged care using participatory methods

BACKGROUND

Residential aged care staff play a significant role in the day-to-day lives of residents yet are faced with many barriers to providing care that promotes resident wellbeing.

APPROACH

Action research is a useful approach for clarifying issues, identifying education and training needs, and identifying, and in some cases overcoming, organizational barriers to change. The Well for Life project aimed to enhance the social and physical health and well being of residents of aged care settings by empowering the staff of facilities to make change. The project had a particular focus on nutrition and physical activity. This paper reports on the action research group process undertaken during Phase I of the Well for Life project. Five residential aged care settings participated in the action research process facilitated by project staff independent of the facilities. The action plan and outcomes from one of these settings is used to illustrate the process and outcomes.

FINDINGS

The main findings of the project indicate that using a process that encourages staff involvement in identification of issues and actions can facilitate change in the practice of resident care. The action research groups identified specific gaps in knowledge and skill leading to targeted education that addressed areas of need. The importance of presenting information and learning opportunities for staff in a variety of formats was also recognized, as was the importance of organizational context, management support and empowerment of staff to make change.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

An insight into domain combinations

Domains are the building blocks of all globular proteins, and are units of compact three-dimensional structure as well as evolutionary units. There is a limited repertoire of domain families, so that these domain families are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products. The processes that produce new genes are duplication and recombination as well as gene fusion and fission. We attempt to gain an overview of these processes by studying the structural domains in the proteins of seven genomes from the three kingdoms of life: Eubacteria, Archaea and Eukaryota. We use here the domain and superfamily definitions in Structural Classification of Proteins Database (SCOP) in order to map pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 624 out of the 764 superfamilies in SCOP in these genomes, and the 624 families occur in 585 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour. This type of pattern can be described by a scale-free network. Finally, we study domain repeats and we compare the set of the domain combinations in the genomes to those in PDB, and discuss the implications for structural genomics.

Small-molecule metabolism: an enzyme mosaic

Escherichia coli has been a popular organism for studying metabolic pathways. In an attempt to find out more about how these pathways are constructed, the enzymes were analysed by defining their protein domains. Structural assignments and sequence comparisons were used to show that 213 domain families constitute approximately 90% of the enzymes in the small-molecule metabolic pathways. Catalytic or cofactor-binding properties between family members are often conserved, while recognition of the main substrate with change in catalytic mechanism is only observed in a few cases of consecutive enzymes in a pathway. Recruitment of domains across pathways is very common, but there is little regularity in the pattern of domains in metabolic pathways. This is analogous to a mosaic in which a stone of a certain colour is selected to fill a position in the picture.

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

Of the sequence comparison methods, profile-based methods perform with greater selectively than those that use pairwise comparisons. Of the profile methods, hidden Markov models (HMMs) are apparently the best. The first part of this paper describes calculations that (i) improve the performance of HMMs and (ii) determine a good procedure for creating HMMs for sequences of proteins of known structure. For a family of related proteins, more homologues are detected using multiple models built from diverse single seed sequences than from one model built from a good alignment of those sequences. A new procedure is described for detecting and correcting those errors that arise at the model-building stage of the procedure. These two improvements greatly increase selectivity and coverage. The second part of the paper describes the construction of a library of HMMs, called SUPERFAMILY, that represent essentially all proteins of known structure. The sequences of the domains in proteins of known structure, that have identities less than 95 %, are used as seeds to build the models. Using the current data, this gives a library with 4894 models. The third part of the paper describes the use of the SUPERFAMILY model library to annotate the sequences of over 50 genomes. The models match twice as many target sequences as are matched by pairwise sequence comparison methods. For each genome, close to half of the sequences are matched in all or in part and, overall, the matches cover 35 % of eukaryotic genomes and 45 % of bacterial genomes. On average roughly 15% of genome sequences are labelled as being hypothetical yet homologous to proteins of known structure. The annotations derived from these matches are available from a public web server at: http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY. This server also enables users to match their own sequences against the SUPERFAMILY model library.

The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli

The 106 small molecule metabolic (SMM) pathways in Escherichia coli are formed by the protein products of 581 genes. We can define 722 domains, nearly all of which are homologous to proteins of known structure, that form all or part of 510 of these proteins. This information allows us to answer general questions on the structural anatomy of the SMM pathway proteins and to trace family relationships and recruitment events within and across pathways. Half the gene products contain a single domain and half are formed by combinations of between two and six domains. The 722 domains belong to one of 213 families that have between one and 51 members. Family members usually conserve their catalytic or cofactor binding properties; substrate recognition is rarely conserved. Of the 213 families, members of only a quarter occur in isolation, i.e. they form single-domain proteins. Most members of the other families combine with domains from just one or two other families and a few more versatile families can combine with several different partners. Excluding isoenzymes, more than twice as many homologues are distributed across pathways as within pathways. However, serial recruitment, with two consecutive enzymes both being recruited to another pathway, is rare and recruitment of three consecutive enzymes is not observed. Only eight of the 106 pathways have a high number of homologues. Homology between consecutive pairs of enzymes with conservation of the main substrate-binding site but change in catalytic mechanism (which would support a simple model of retrograde pathway evolution) occurs only six times in the whole set of enzymes. Most of the domains that form SMM pathways have homologues in non-SMM pathways. Taken together, these results imply a pervasive "mosaic" model for the formation of protein repertoires and pathways.

Neointimal and tubulointerstitial infiltration by recipient mesenchymal cells in chronic renal-allograft rejection

BACKGROUND

Tissue remodeling depends on mesenchymal cells (fibroblasts and myofibroblasts) and is a prominent feature of chronic renal-transplant rejection. It is not known whether the mesenchymal cells that participate in remodeling originate locally or from circulating precursor cells.

METHODS

We obtained biopsy specimens of renal allografts from six male recipients of an allograft from a female donor, four female recipients of an allograft from a male donor, two male recipients of an allograft from a male donor, and two female recipients of an allograft from a female donor. All the allografts were undergoing chronic rejection. All but two specimens were obtained within six months after transplantation. We used immunohistochemical methods to identify mesenchymal cells with smooth-muscle alpha-actin and in situ hybridization to identify mesenchymal cells with Y-chromosome DNA.

RESULTS

No Y-chromosome bodies were identified in the case of the two renal-allograft specimens in which both the donor and the recipient were female. In the case of the two renal-allograft specimens in which both the donor and the recipient were male, approximately 40 percent of mesenchymal cells contained a Y-chromosome body. In the case of the six specimens in which the donor was female and the recipient was male, a mean (+/-SD) of 34+/-16 percent of mesenchymal cells in the neointima, 38+/-12 percent of such cells in the adventitia, and 30+/-7 percent of such cells in the interstitium contained the Y-chromosomal marker, indicating that they originated from the recipient rather than the donor. In the case of the four renal-allograft specimens in which the donor was male and the recipient was female, the respective values were 24+/-15 percent, 33+/-9 percent, and 23+/-8 percent, indicating a persistent population of donor mesenchymal cells.

CONCLUSIONS

The presence of mesenchymal cells of host origin in the vascular and interstitial compartments of renal allografts undergoing chronic rejection provides evidence that a circulating mesenchymal precursor cell has the potential to migrate to areas of inflammation.

Domain combinations in archaeal, eubacterial and eukaryotic proteomes

There is a limited repertoire of domain families that are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products, and at the level of genes, duplication, recombination, fusion and fission are the processes that produce new genes. We attempt to gain an overview of these processes by studying the evolutionary units in proteins, domains, in the protein sequences of 40 genomes. The domain and superfamily definitions in the Structural Classification of Proteins Database are used, so that we can view all pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 783 out of the 859 superfamilies in SCOP in these genomes, and the 783 families occur in 1307 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour; 209 families do not make combinations with other families. This type of pattern can be described as a scale-free network. We also study the N to C-terminal orientation of domain pairs and domain repeats. The phylogenetic distribution of domain combinations is surveyed, to establish the extent of common and kingdom-specific combinations. Of the kingdom-specific combinations, significantly more combinations consist of families present in all three kingdoms than of families present in one or two kingdoms. Hence, we are led to conclude that recombination between common families, as compared to the invention of new families and recombination among these, has also been a major contribution to the evolution of kingdom-specific and species-specific functions in organisms in all three kingdoms. Finally, we compare the set of the domain combinations in the genomes to those in the RCSB Protein Data Bank, and discuss the implications for structural genomics.

Peritubular capillary basement membrane reduplication in allografts and native kidney disease: a clinicopathologic study of 278 consecutive renal specimens

BACKGROUND

An association has been found between transplant glomerulopathy (TG) and reduplication of peritubular capillary basement membranes (PTCR). Although such an association is of practical and theoretical importance, only one prospective study has tried to confirm it.

METHODS

We examined 278 consecutive renal specimens (from 135 transplants and 143 native kidneys) for ultrastructural evidence of PTCR. In addition to renal allografts with TG, we also examined grafts with acute rejection, recurrent glomerulonephritis, chronic allograft nephropathy and stable grafts ("protocol biopsies"). Native kidney specimens included a wide range of glomerulopathies as well as cases of thrombotic microangiopathy, malignant hypertension, acute interstitial nephritis, and acute tubular necrosis.

RESULTS

We found PTCR in 14 of 15 cases of TG, in 7 transplant biopsy specimens without TG, and in 13 of 143 native kidney biopsy specimens. These 13 included cases of malignant hypertension, thrombotic microangiopathy, lupus nephritis, Henoch-Schonlein nephritis, crescentic glomerulonephritis, and cocaine-related acute renal failure. Mild PTCR in allografts without TG did not predict renal failure or significant proteinuria after follow-up periods of between 3 months and 1 year.

CONCLUSIONS

We conclude that in transplants, there is a strong association between well-developed PTCR and TG, while the significance of mild PTCR and its predictive value in the absence of TG is unclear. PTCR also occurs in certain native kidney diseases, though the association is not as strong as that for TG. We suggest that repeated endothelial injury, including immunologic injury, may be the cause of this lesion both in allografts and native kidneys.