Digital wearable insole-based identification of knee arthropathies and gait signatures using machine learning

Gait is impaired in musculoskeletal conditions, such as knee arthropathy. Gait analysis is used in clinical practice to inform diagnosis and to monitor disease progression or intervention response. However, clinical gait analysis relies on subjective visual observation of walking, as objective gait analysis has not been possible within clinical settings due to the expensive equipment, large-scale facilities, and highly trained staff required. Relatively low-cost wearable digital insoles may offer a solution to these challenges. In this work, we demonstrate how a digital insole measuring osteoarthritis-specific gait signatures yields similar results to the clinical gait-lab standard. To achieve this, we constructed a machine learning model, trained on force plate data collected in participants with knee arthropathy and controls. This model was highly predictive of force plate data from a validation set (area under the receiver operating characteristics curve [auROC] = 0.86; area under the precision-recall curve [auPR] = 0.90) and of a separate, independent digital insole dataset containing control and knee osteoarthritis subjects (auROC = 0.83; auPR = 0.86). After showing that digital insole derived gait characteristics are comparable to traditional gait measurements, we next showed that a single stride of raw sensor time series data could be accurately assigned to each subject, highlighting that individuals using digital insoles can be identified by their gait characteristics. This work provides a framework for a promising alternative to traditional clinical gait analysis methods, adds to the growing body of knowledge regarding wearable technology analytical pipelines, and supports clinical development of at-home gait assessments, with the potential to improve the ease, frequency, and depth of patient monitoring.

Differential modulation of allergic rhinitis nasal transcriptome by dupilumab and allergy immunotherapy

BACKGROUND

Nasal epithelial cells are important regulators of barrier function and immune signaling; however, in allergic rhinitis (AR) these functions can be disrupted by inflammatory mediators. We aimed to better discern AR disease mechanisms using transcriptome data from nasal brushing samples from individuals with and without AR.

METHODS

Data were drawn from a feasibility study of individuals with and without AR to Timothy grass and from a clinical trial evaluating 16 weeks of treatment with the following: dupilumab, a monoclonal antibody that binds interleukin (IL)-4Rα and inhibits type 2 inflammation by blocking signaling of both IL-4/IL-13; subcutaneous immunotherapy with Timothy grass (SCIT), which inhibits allergic responses through pleiotropic effects; SCIT + dupilumab; or placebo. Using nasal brushing samples from these studies, we defined distinct gene signatures in nasal tissue of AR disease and after nasal allergen challenge (NAC) and assessed how these signatures were modulated by study drug(s).

RESULTS

Treatment with dupilumab (normalized enrichment score [NES] = -1.73, p = .002) or SCIT + dupilumab (NES = -2.55, p < .001), but not SCIT alone (NES = +1.16, p = .107), significantly repressed the AR disease signature. Dupilumab (NES = -2.55, p < .001), SCIT (NES = -2.99, p < .001), and SCIT + dupilumab (NES = -3.15, p < .001) all repressed the NAC gene signature.

CONCLUSION

These results demonstrate type 2 inflammation is an important contributor to the pathophysiology of AR disease and that inhibition of the type 2 pathway with dupilumab may normalize nasal tissue gene expression.

TRAPnSeq allows high-throughput profiling of antigen-specific antibody-secreting cells

Following activation by cognate antigen, B cells undergo fine-tuning of their antigen receptors and may ultimately differentiate into antibody-secreting cells (ASCs). While antigen-specific B cells that express surface receptors (B cell receptors [BCRs]) can be readily cloned and sequenced following flow sorting, antigen-specific ASCs that lack surface BCRs cannot be easily profiled. Here, we report an approach, TRAPnSeq (antigen specificity mapping through immunoglobulin [Ig] secretion TRAP and Sequencing), that allows capture of secreted antibodies on the surface of ASCs, which in turn enables high-throughput screening of single ASCs against large antigen panels. This approach incorporates flow cytometry, standard microfluidic platforms, and DNA-barcoding technologies to characterize antigen-specific ASCs through single-cell V(D)J, RNA, and antigen barcode sequencing. We show the utility of TRAPnSeq by profiling antigen-specific IgG and IgE ASCs from both mice and humans and highlight its capacity to accelerate therapeutic antibody discovery from ASCs.

Spontaneous tumor regression mediated by human T cells in a humanized immune system mouse model

Immunodeficient mice reconstituted with a human immune system (HIS mice) give rise to human T cells, which make them an attractive system to study human immune responses to tumors. However, such HIS mice typically exhibit sub-optimal responses to immune challenges as well as fail to develop antigen-specific B or T cell memory. Here we report HIS mice mediate spontaneous regression of human B cell lymphoma Raji. Tumor regression was dependent on CD4+ and CD8+ T cell responses and resulted in T cell memory. The T cell memory elicited was mainly Raji-specific, however some level of cross-protection was also elicited to a related B cell lymphoma cell line Ramos. Single-cell RNAseq analysis indicated activation of CD8+ T cells in regressing Raji tumors as well as clonal expansion of specific T cell receptors (TCRs). Cloning of TCRs from Raji-infiltrating T cells into a Jurkat reporter cell line showed reactivity specific for Raji tumor cells. Overall, we report a platform for studying in vivo human T cell tumor immunity by highlighting spontaneous Raji tumor regression, clonal TCR expansion, and T cell memory in HIS mice.

Autoantibodies are associated with disease progression of idiopathic pulmonary fibrosis

Several reports have highlighted a potential role of auto-reactive B cells and autoantibodies that correlates with increased disease severity in patients with IPF. Here we show that patients with IPF have an altered B cell phenotype and that those subjects that have autoantibodies against the intermediate filament protein periplakin (PPL) have a significantly worse outcome in terms of progression free survival. Using a mouse model of lung fibrosis, we demonstrate that the instillation of antibodies targeting the endogenous protein PPL, mimicking naturally occurring autoantibodies seen in patients, directly to the lung increased lung injury, inflammation, collagen and fibronectin expression, through direct activation of follicular dendritic cells which in turn activates and drive proliferation of fibroblasts. This fibrocyte population was also observed in fibrotic foci of patients with IPF and increased in peripheral blood of IPF patients compared to aged matched control. This study re-iterates complex and heterogeneous nature of IPF, identifying new pathways that may prove suitable for therapeutic intervention.

IL-4 and IL-13, not eosinophils, drive type 2 airway inflammation, remodeling and lung function decline

RATIONALE

Type 2 (T2) asthma is characterized by airflow limitations and elevated levels of blood and sputum eosinophils, fractional exhaled nitric oxide, IgE, and periostin. While eosinophils are associated with exacerbations, the contribution of eosinophils to lung inflammation, remodeling and function remains largely hypothetical.

OBJECTIVES

To determine the effect of T2 cytokines IL-4, IL-13 and IL-5 on eosinophil biology and compare the impact of depleting just eosinophils versus inhibiting all aspects of T2 inflammation on airway inflammation.

METHODS

Human eosinophils or endothelial cells stimulated with IL-4, IL-13 or IL-5 were assessed for gene changes or chemokine release.Mice exposed to house dust mite extract received anti-IL-4Rα (dupilumab), anti-IL-5 or control antibodies and were assessed for changes in lung histological and inflammatory endpoints.

MEASUREMENTS AND MAIN RESULTS

IL-4 or IL-13 stimulation of human eosinophils and endothelial cells induced gene expression changes related to granulocyte migration; whereas, IL-5 induced changes reflecting granulocyte differentiation.In a mouse model, blocking IL-4Rα improved lung function by impacting multiple effectors of inflammation and remodeling, except peripheral eosinophil counts, thereby disconnecting blood eosinophils from airway inflammation, remodeling and function. Blocking IL-5 globally reduced eosinophil counts but did not impact inflammatory or functional measures of lung pathology. Whole lung transcriptome analysis revealed that IL-5 or IL-4Rα blockade impacted eosinophil associated genes, whereas IL-4Rα blockade also impacted genes associated with multiple cells, cytokines and chemokines, mucus production, cell:cell adhesion and vascular permeability.

CONCLUSIONS

Eosinophils are not the sole contributor to asthma pathophysiology or lung function decline and emphasizes the need to block additional mediators to modify lung inflammation and impact lung function.

Blocking common γ chain cytokine signaling ameliorates T cell-mediated pathogenesis in disease models

The common γ chain (γc; IL-2RG) is a subunit of the interleukin (IL) receptors for the γc cytokines IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21. The lack of appropriate neutralizing antibodies recognizing IL-2RG has made it difficult to thoroughly interrogate the role of γc cytokines in inflammatory and autoimmune disease settings. Here, we generated a γc cytokine receptor antibody, REGN7257, to determine whether γc cytokines might be targeted for T cell-mediated disease prevention and treatment. Biochemical, structural, and in vitro analysis showed that REGN7257 binds with high affinity to IL-2RG and potently blocks signaling of all γc cytokines. In nonhuman primates, REGN7257 efficiently suppressed T cells without affecting granulocytes, platelets, or red blood cells. Using REGN7257, we showed that γc cytokines drive T cell-mediated disease in mouse models of graft-versus-host disease (GVHD) and multiple sclerosis by affecting multiple aspects of the pathogenic response. We found that our xenogeneic GVHD mouse model recapitulates hallmarks of acute and chronic GVHD, with T cell expansion/infiltration into tissues and liver fibrosis, as well as hallmarks of immune aplastic anemia, with bone marrow aplasia and peripheral cytopenia. Our findings indicate that γc cytokines contribute to GVHD and aplastic anemia pathology by promoting these characteristic features. By demonstrating that broad inhibition of γc cytokine signaling with REGN7257 protects from immune-mediated disorders, our data provide evidence of γc cytokines as key drivers of pathogenic T cell responses, offering a potential strategy for the management of T cell-mediated diseases.

Dupilumab in Adults and Adolescents with Eosinophilic Esophagitis

BACKGROUND

Dupilumab, a fully human monoclonal antibody, blocks interleukin-4 and interleukin-13 signaling, which have key roles in eosinophilic esophagitis.

METHODS

We conducted a three-part, phase 3 trial in which patients 12 years of age or older underwent randomization in a 1:1 ratio to receive subcutaneous dupilumab at a weekly dose of 300 mg or placebo (Part A) or in a 1:1:1 ratio to receive 300 mg of dupilumab either weekly or every 2 weeks or weekly placebo (Part B) up to week 24. Eligible patients who completed Part A or Part B continued the trial in Part C, in which those who completed Part A received dupilumab at a weekly dose of 300 mg up to week 52 (the Part A-C group); Part C that included the eligible patients from Part B is ongoing. The two primary end points at week 24 were histologic remission (≤6 eosinophils per high-power field) and the change from baseline in the Dysphagia Symptom Questionnaire (DSQ) score (range, 0 to 84, with higher values indicating more frequent or more severe dysphagia).

RESULTS

In Part A, histologic remission occurred in 25 of 42 patients (60%) who received weekly dupilumab and in 2 of 39 patients (5%) who received placebo (difference, 55 percentage points; 95% confidence interval [CI], 40 to 71; P<0.001). In Part B, histologic remission occurred in 47 of 80 patients (59%) with weekly dupilumab, in 49 of 81 patients (60%) with dupilumab every 2 weeks, and in 5 of 79 patients (6%) with placebo (difference between weekly dupilumab and placebo, 54 percentage points; 95% CI, 41 to 66 [P<0.001]; difference between dupilumab every 2 weeks and placebo, 56 percentage points; 95% CI, 43 to 69 [not significant per hierarchical testing]). The mean (±SD) DSQ scores at baseline were 33.6±12.41 in Part A and 36.7±11.22 in Part B; the scores improved with weekly dupilumab as compared with placebo, with differences of -12.32 (95% CI, -19.11 to -5.54) in Part A and -9.92 (95% CI, -14.81 to -5.02) in Part B (both P<0.001) but not with dupilumab every 2 weeks (difference in Part B, -0.51; 95% CI, -5.42 to 4.41). Serious adverse events occurred in 9 patients during the Part A or B treatment period (in 7 who received weekly dupilumab, 1 who received dupilumab every 2 weeks, and 1 who received placebo) and in 1 patient in the Part A-C group during the Part C treatment period who received placebo in Part A and weekly dupilumab in Part C.

CONCLUSIONS

Among patients with eosinophilic esophagitis, subcutaneous dupilumab administered weekly improved histologic outcomes and alleviated symptoms of the disease. (Funded by Sanofi and Regeneron Pharmaceuticals; ClinicalTrials.gov number, NCT03633617.).

Butyrophilin-like 2 regulates site-specific adaptations of intestinal γδ intraepithelial lymphocytes

Tissue-resident γδ intraepithelial lymphocytes (IELs) orchestrate innate and adaptive immune responses to maintain intestinal epithelial barrier integrity. Epithelia-specific butyrophilin-like (Btnl) molecules induce perinatal development of distinct Vγ TCR⁺ IELs, however, the mechanisms that control γδ IEL maintenance within discrete intestinal segments are unclear. Here, we show that Btnl2 suppressed homeostatic proliferation of γδ IELs preferentially in the ileum. High throughput transcriptomic characterization of site-specific Btnl2-KO γδ IELs reveals that Btnl2 regulated the antimicrobial response module of ileal γδ IELs. Btnl2 deficiency shapes the TCR specificities and TCRγ/δ repertoire diversity of ileal γδ IELs. During DSS-induced colitis, Btnl2-KO mice exhibit increased inflammation and delayed mucosal repair in the colon. Collectively, these data suggest that Btnl2 fine-tunes γδ IEL frequencies and TCR specificities in response to site-specific homeostatic and inflammatory cues. Hence, Btnl-mediated targeting of γδ IEL development and maintenance may help dissect their immunological functions in intestinal diseases with segment-specific manifestations.

Panea et al showed that epithelia-specific butyrophilinlike 2 (Btnl2) suppressed homeostatic proliferation of γδ intraepithelial lymphocytes (IELs) preferentially in the ileum and used high throughput transcriptomic characterization of Btnl2-deficient γδ IELs to demonstrate that Btnl2 impacts γδ TCR specificities and repertoire diversity of ileal γδ IELs. In addition, they showed that Btnl2-deficient mice exhibited increased inflammation and delayed mucosal repair in the colon, suggesting that it plays a key immunological function in intestinal diseases.

Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing

With the rapid advancement of single-cell RNA-sequencing (scRNA-seq) technology, many data-preprocessing methods have been proposed to address numerous systematic errors and technical variabilities inherent in this technology. While these methods have been demonstrated to be effective in recovering individual gene expression, the suitability to the inference of gene-gene associations and subsequent gene network reconstruction have not been systemically investigated. In this study, we benchmarked five representative scRNA-seq normalization/imputation methods on Human Cell Atlas bone marrow data with respect to their impacts on inferred gene-gene associations. Our results suggested that a considerable amount of spurious correlations was introduced during the data-preprocessing steps due to oversmoothing of the raw data. We proposed a model-agnostic noise-regularization method that can effectively eliminate the correlation artifacts. The noise-regularized gene-gene correlations were further used to reconstruct a gene co-expression network and successfully revealed several known immune cell modules.

Enhanced IL-36R signaling promotes barrier impairment and inflammation in skin and intestine

Deficiency in interleukin-36R (IL-36R) antagonist caused by loss-of-function mutations in IL-36RN leads to DITRA (deficiency of IL-36 receptor antagonist), a rare inflammatory human disease that belongs to a subgroup of generalized pustular psoriasis (GPP). We report a functional genetic mouse model of DITRA with enhanced IL-36R signaling analogous to that observed in patients with DITRA, which provides new insight into our understanding of the IL-36 family of molecules in regulating barrier integrity across multiple tissues. Humanized DITRA-like mice displayed increased skin inflammation in a preclinical model of psoriasis, and in vivo blockade of IL-36R pathway using anti-human IL-36R antibody ameliorated imiquimod-induced skin pathology as both prophylactic and therapeutic treatments. Deeper characterization of the humanized DITRA-like mice revealed that deregulated IL-36R signaling promoted tissue pathology during intestinal injury and led to impairment in mucosal restoration in the repair phase of chronic dextran sulfate sodium (DSS)-induced colitis. Blockade of IL-36R pathway significantly ameliorated DSS-induced intestinal inflammation and rescued the inability of DITRA-like mice to recover from mucosal damage in vivo. Our results indicate a central role for IL-36 in regulating proinflammatory responses in the skin and epithelial barrier function in the intestine, suggesting a new therapeutic potential for targeting the IL-36R axis in psoriasis and at the later stages of intestinal pathology in inflammatory bowel disease.

Activin A does not drive post-traumatic heterotopic ossification

Heterotopic ossification (HO), the formation of ectopic bone in soft tissues, has been extensively studied in its two primary forms: post-traumatic HO (tHO) typically found in patients who have experienced musculoskeletal or neurogenic injury and in fibrodysplasia ossificans progressiva (FOP), where it is genetically driven. Given that in both diseases HO arises via endochondral ossification, the molecular mechanisms behind both diseases have been postulated to be manifestations of similar pathways including those activated by BMP/TGFβ superfamily ligands. A significant step towards understanding the molecular mechanism by which HO arises in FOP was the discovery that FOP causing ACVR1 variants trigger HO in response to activin A, a ligand that does not activate signaling from wild type ACVR1, and that is not inherently osteogenic in wild type settings. The physiological significance of this finding was demonstrated by showing that activin A neutralizing antibodies stop HO in two different genetically accurate mouse models of FOP. In order to explore the role of activin A in tHO, we performed single cell RNA sequencing and compared the expression of activin A as well as other BMP pathway genes in tHO and FOP HO. We show that activin A is expressed in response to injury in both settings, but by different types of cells. Given that wild type ACVR1 does not transduce signal when engaged by activin A, we hypothesized that inhibition of activin A will not block tHO. Nonetheless, as activin A was expressed in tHO lesions, we tested its inhibition and compared it with inhibition of BMPs. We show here that anti-activin A does not block tHO, whereas agents such as antibodies that neutralize ACVR1 or ALK3-Fc (which blocks osteogenic BMPs) are beneficial, though not completely curative. These results demonstrate that inhibition of activin A should not be considered as a therapeutic strategy for ameliorating tHO.

Dual blockade of IL-4 and IL-13 with dupilumab, an IL-4Rα antibody, is required to broadly inhibit type 2 inflammation

BACKGROUND

Dupilumab, a fully human monoclonal antibody that binds IL-4Rα and inhibits signaling of both IL-4 and IL-13, has shown efficacy across multiple diseases with underlying type 2 signatures and is approved for treatment of asthma, atopic dermatitis, and chronic sinusitis with nasal polyposis. We sought to provide a comprehensive analysis of the redundant and distinct roles of IL-4 and IL-13 in type 2 inflammation and report dupilumab mechanisms of action.

METHODS

Using primary cell assays and a mouse model of house dust mite-induced asthma, we compared IL-4 vs IL-13 vs IL-4Rα blockers.

RESULTS

Intranasal administration of either IL-4 or IL-13 confers an asthma-like phenotype in mice by inducing immune cell lung infiltration, including eosinophils, increasing cytokine/chemokine expression and mucus production, thus demonstrating redundant functions of these cytokines. We further teased out their respective contributions using human in vitro culture systems. Then, in a mouse asthma model by comparing in head-to-head studies, either IL-4 or IL-13 inhibition to dual IL-4/IL-13 inhibition, we demonstrate that blockade of both IL-4 and IL-13 is required to broadly block type 2 inflammation, which translates to protection from allergen-induced lung function impairment. Notably, only dual IL-4/IL-13 blockade prevented eosinophil infiltration into lung tissue without affecting circulating eosinophils, demonstrating that tissue, but not circulating eosinophils, contributes to disease pathology.

CONCLUSIONS

Overall, these data support IL-4 and IL-13 as key drivers of type 2 inflammation and help provide insight into the therapeutic mechanism of dupilumab, a dual IL-4/IL-13 blocker, in multiple type 2 diseases.

IL-33 blockade affects mediators of persistence and exacerbation in a model of chronic airway inflammation

BACKGROUND

Severe inflammatory airway diseases are associated with inflammation that does not resolve, leading to structural changes and an overall environment primed for exacerbations.

OBJECTIVE

We sought to identify and inhibit pathways that perpetuate this heightened inflammatory state because this could lead to therapies that allow for a more quiescent lung that is less predisposed to symptoms and exacerbations.

METHODS

Using prolonged exposure to house dust mite in mice, we developed a mouse model of persistent and exacerbating airway disease characterized by a mixed inflammatory phenotype.

RESULTS

We show that lung IL-33 drives inflammation and remodeling beyond the type 2 response classically associated with IL-33 signaling. IL-33 blockade with an IL-33 neutralizing antibody normalized established inflammation and improved remodeling of both the lung epithelium and lung parenchyma. Specifically, IL-33 blockade normalized persisting and exacerbating inflammatory end points, including eosinophilic, neutrophilic, and ST2⁺CD4⁺ T-cell infiltration. Importantly, we identified a key role for IL-33 in driving lung remodeling because anti-IL-33 also re-established the presence of ciliated cells over mucus-producing cells and decreased myofibroblast numbers, even in the context of continuous allergen exposure, resulting in improved lung function.

CONCLUSION

Overall, this study shows that increased IL-33 levels drive a self-perpetuating amplification loop that maintains the lung in a state of lasting inflammation and remodeled tissue primed for exacerbations. Thus IL-33 blockade might ameliorate symptoms and prevent exacerbations by quelling persistent inflammation and airway remodeling.

Do health assets have a protective effect for hospitalized frail older adults?

BACKGROUND

Although increasing frailty is predictive of increased mortality and length of stay for hospitalized older adults, this approach ignores health assets that individuals can utilize to recover following hospital admission.

AIM

To examine whether health assets mitigate the effect of frailty on outcomes for older adults admitted to hospital.

DESIGN

Patients of 1418 aged ≥ 70 years admitted to 11 hospitals in Australia were evaluated at admission using the interRAI assessment system for Acute Care, which surveys a large number of domains, including cognition, communication, mood and behaviour, activities of daily living, continence, nutrition, skin condition, falls and medical diagnosis.

METHODS

The data set was interrogated for potential health assets and a multiple logistic regression adjusted for frailty index, age and gender as covariates was performed for the outcomes mortality, length of stay, re-admission and new need for residential care.

RESULTS

Inpatient mortality was 3% and 4.5% of patients died within 28 days of discharge. Median length of stay was 7 days (IQR 4-11). In multivariate analysis that includes frailty, being able to walk further [OR 0.08 (0.01-0.63)], ability to leave the house [OR 0.35 (0.17-0.74)] and living alone [OR 0.28 (0.10-0.79)] were protective against mortality. The presence of a support person was associated with a decreased length of stay [OR 0.14 (0.08-0.25)].

CONCLUSION

The inclusion of health assets in predictive models can improve prognostication and highlights potential interventions to improve outcomes for hospitalized older adults.

Medication adherence 1 month after hospital discharge in medical inpatients

BACKGROUND

The rate of medication non-adherence has been consistently reported to be between 20 and 50%. The majority of available data comes from international studies, and we hypothesised that a similar rate of adherence may be observed in Australian patients.

AIMS

To determine the rate of adherence to medications after discharge from acute general hospital admission and identify factors that may be associated with non-adherence.

METHODS

A prospective cohort study of 68 patients, comparing admission and discharge medication regimens to self-reported regimens 30-40 days after discharge from hospital. Patients were followed up via telephone call and univariate and multivariate binary logistic regression used to determine patient factors associated with non-adherence.

RESULTS

In all, 27 of 68 patients (39.7%) were non-adherent to one or more regular medications at follow up. Intentional and unintentional non-adherence contributed equally to non-adherence. Using multivariate analysis, presence of a carer responsible for medications was associated with significantly lower non-adherence (odds ratio (OR) 0.20 (0.05-0.83), P = 0.027) when adjusted for age, co-morbidities, chemist blister pack and total number of discharge medications.

CONCLUSIONS

Non-adherence to prescription medications is suboptimal and consistent with previous overseas studies. Having a carer responsible for medications is associated with significantly lower rates of non-adherence. Understanding patients' preferences and involving them in their healthcare may reduce intentional non-adherence.

Arrythmogenic Right Ventricular Dysplasia

A 10-year-old well and asymptomatic female was referred for screening of acute right ventricular dilatation (ARVD) as she had an elder brother diagnosed with ARVD whom died of sudden cardiac death. Electrocardiography (ECG), transthoracic echocardiography (TTE) and cardiac magnetic resonance imaging (CMR) were performed. Results of these investigations were suggestive of ARVD. Despite being a rare cardiac disease and largely unrecognised in children and young adult population, ARVD is an important cause of ventricular arrhythmias in this group of patients and is one of the causes of sudden cardiac death (SCD) in this population.

Stenting of vertical vein in an infant with obstructed supracardiac total anomalous pulmonary venous drainage

A 1.7 kg infant with obstructed supracardiac total anomalous pulmonary venous drainage (TAPVD) presented with severe pulmonary hypertension secondary to vertical vein obstruction. The child, in addition, had a large omphalocele that was being managed conservatively. The combination of low weight, unoperated omphalocele, and severe pulmonary hypertension made corrective cardiac surgery very high-risk. Therefore, transcatheter stenting of the stenotic vertical vein, as a bridge to corrective surgery was carried out. The procedure was carried out through the right internal jugular vein (RIJ). The stenotic segment of the vertical vein was stented using a coronary stent. After procedure, the child was discharged well to the referred hospital for weight gain and spontaneous epithelialization of the omphalocele. Stenting of the vertical vein through the internal jugular vein can be considered in very small neonates as a bridge to repair obstructed supracardiac total anomalous venous drainage.

JAK-STAT and G-protein-coupled receptor signaling pathways are frequently altered in epitheliotropic intestinal T-cell lymphoma

Epitheliotropic intestinal T-cell lymphoma (EITL, also known as type II enteropathy-associated T-cell lymphoma) is an aggressive intestinal disease with poor prognosis and its molecular alterations have not been comprehensively characterized. We aimed to identify actionable easy-to-screen alterations that would allow better diagnostics and/or treatment of this deadly disease. By performing whole-exome sequencing of four EITL tumor-normal pairs, followed by amplicon deep sequencing of 42 tumor samples, frequent alterations of the JAK-STAT and G-protein-coupled receptor (GPCR) signaling pathways were discovered in a large portion of samples. Specifically, STAT5B was mutated in a remarkable 63% of cases, JAK3 in 35% and GNAI2 in 24%, with the majority occurring at known activating hotspots in key functional domains. Moreover, STAT5B locus carried copy-neutral loss of heterozygosity resulting in the duplication of the mutant copy, suggesting the importance of mutant STAT5B dosage for the development of EITL. Dysregulation of the JAK-STAT and GPCR pathways was also supported by gene expression profiling and further verified in patient tumor samples. In vitro overexpression of GNAI2 mutants led to the upregulation of pERK1/2, a member of MEK-ERK pathway. Notably, inhibitors of both JAK-STAT and MEK-ERK pathways effectively reduced viability of patient-derived primary EITL cells, indicating potential therapeutic strategies for this neoplasm with no effective treatment currently available.

Effects of hospital-acquired conditions on length of stay for patients with diabetes

BACKGROUND

Inpatients with diabetes have longer length of stays (LOS). Understanding patterns of in-hospital complications between patients with diabetes and others may reveal measures to improve patient welfare and minimise LOS.

AIM

This study evaluates the rates and types of hospital-acquired conditions among patients with and without diabetes and assesses any effects on LOS.

METHODS

A total of 47 615 admission episodes from The Northern Hospital over 12 months was reviewed. Episodes were divided into four groups: (i) patients without diabetes; (ii) patients with diabetes without end-organ sequelae (EOS); (iii) patients with diabetes with EOS; and (iv) a subset of non-diabetic patients with a Charlson Co-morbidity score ≥1 (comparison group). The Classification of Hospital Acquired Diagnoses (CHADx) was applied to the groups to compare rates and types of inpatient complications. Linear regression was used to analyse the impact of the number of CHADx on LOS.

RESULTS

Almost 30% of admissions of patients with diabetes and EOS had at least one CHADx, compared with 13% for non-diabetes patients and 17% for the comparison group. The types of CHADx experienced by diabetes patients with EOS were similar to the comparison group. However, rates were 10 times higher. Linear regression demonstrated diabetes patients with EOS have increased LOS and each CHADx per episode has a larger effect on LOS.

CONCLUSION

We demonstrate that diabetes patients have consistently higher rates of CHADx and longer LOS than similar patients with complex and chronic conditions. This provides a foundation for future studies to investigate preventative practices for this high-risk patient population.

The Goals of Patient Care project: implementing a proactive approach to patient-centred decision-making

BACKGROUND

Patients in the later stages of their lives risk being harmed by futile or unwanted interventions if realistic care goals and patient values are not recognised. Doctors have difficulty discussing and informing patients' healthcare goals.

AIMS

To review implementation of a Goals of Patient Care (GOPC) summary in medical inpatients and its applicability in emergency medical response (EMR) situations.

METHODS

Single-centre cross-sectional study of adult medical inpatients and adult inpatients requiring EMR at a Victorian general hospital.

MEASURES

presence and content of GOPC summary, secondary review of decision-making and discussion documentation, patient characteristics; EMR precipitants and outcomes.

RESULTS

GOPC were documented for 82 of 101 patients. One had an existing advance directive, and six had records of a patient-appointed substitute decision-maker. For patients with GOPC, 80 had life-prolonging treatment aims, with a varying degree of treatment limitation in 48. Discussion with patient or substitute decision-maker was evident in 43 cases. GOPC were documented prior to nine of 23 EMR. The EMR triggered a GOPC modification in three instances.

CONCLUSIONS

Introduction of a routine GOPC summary encourages consideration of goals of care for most medical inpatients. Few have pre-existing records of their wishes, and there are opportunities for improvement in this regard. Doctors may still have difficulty determining goals of care, and discussion of GOPC with patients and families may not be clearly documented. Most patients requiring EMR do not have prior GOPC review, and the role of the summary in these situations remains unclear.

A longitudinal cohort study evaluating the impact of a geriatrician-led residential care outreach service on acute healthcare utilisation

BACKGROUND

over the last decade, high demand for acute healthcare services by long-term residents of residential care facilities (RCFs) has stimulated interest in exploring alternative models of care. The Residential Care Intervention Program in the Elderly (RECIPE) service provides expert outreach services to RCFs residents, interventions include comprehensive care planning, management of inter-current illness and rapid access to acute care substitution services.

OBJECTIVE

to evaluate whether the RECIPE service decreased acute healthcare utilisation.

DESIGN

a retrospective cohort study using interrupted time series analysis to analyse change in acute healthcare utilisation before and after enrolment.

SETTING

a 300-bed metropolitan teaching hospital in Australia and 73 RCFs within its catchment.

SUBJECTS

there were 1,327 patients enrolled in the service with a median age of 84 years; 61% were female.

METHODS

data were collected prospectively on all enrolled patients from 2004 to 2011 and linked to the acute health service administrative data set. Primary outcomes change in admission rates, length of stay and bed days per quarter.

RESULTS

in the 2 years prior to enrolment, the mean number of acute care admissions per patient per year was 3.03 (SD 2.9) versus post 2.4 (SD 3.3), the service reducing admissions by 0.13 admissions per patient per quarter (P = 0.046). Prior to enrolment, the mean length of stay was 8.6 (SD 11.0) versus post 3.5 (SD 5.0), a reduction of 1.5 days per patient per quarter (P = 0.003).

CONCLUSIONS

this study suggests that an outreach service comprising a geriatrician-led multidisciplinary team can reduce acute hospital utilisation rates.

Emergency stenting of vertical vein in a neonate with obstructed supracardiac total anomalous pulmonary venous drainage

A late preterm newborn baby presented with respiratory distress and increasing cyanosis within 2 hours of birth. Bedside transthroracic echocardiography showed a critically obstructed vertical vein in a supracardiac total anomalous pulmonary venous drainage (TAPVd). Emergency stenting of the vertical vein was successfully performed at 24 hours of life.

Assembling cell context-specific gene sets: a case in cardiomyopathy

An increasing amount of evidence suggests that canonical pathways and standard molecular signature databases are incomplete and inadequate to model the complex behavior of cell physiology and pathology. Yet, many Gene Set Analysis (GSA) studies still rely on these databases to identify disease biomarkers and molecular mechanisms within a specific cell context. While tremendous effort has been invested in developing GSA tools, there is limited number of studies focusing on de novo assembly of context-specific gene sets as opposed to simply applying GSA using the standard gene set database.

In this paper, we propose a pipeline to derive the entire collection of Cell context-Specific Gene Sets (CSGS) from a molecular interaction network, based on the hypothesis that molecular events linked to a specific phenotypic response should cluster within a subnet of interacting genes. Gene sets are assigned using both physical properties of the network and functional annotations of the neighboring nodes. The identified gene sets could provide a precise starting point such that the downstream GSA will cover all functional pathways in this particular cell context and, at the same time, avoid the noise and excessive multiple-hypothesis testing due to inclusion of irrelevant gene sets from the standard database. We applied the pipeline in the context of cardiomyopathy and demonstrated its superiority over MSigDB gene set collection in terms of: (i) reproducibility and robustness in GSA, (ii) effectiveness in uncovering molecular mechanisms associated with cardiomyopathy, and (iii) the performance in distinguishing diseased vs. normal states.

Performance of new signal-to-noise ratio estimation for SEM images based on single image noise cross-correlation

A new technique for estimation of signal-to-noise ratio in scanning electron microscope images is reported. The method is based on the image noise cross-correlation estimation model recently developed. We derive the basic performance limits on a single image signal-to-noise ratio estimation using the Cramer-Rao inequality. The results are compared with those from existing estimation methods including the nearest neighbourhood (the simple method), the first order linear interpolator, and the autoregressive based estimator. The comparisons were made using several tests involving different images within the performance bounds. From the results obtained, the efficiency and accuracy of image noise cross-correlation estimation technique is considerably better than the other three methods.

Impact of troponin 1 on long-term mortality after emergency orthopaedic surgery in older patients

OBJECTIVES

To determine the association between post-operative troponin rises and longer term (2-year) mortality after emergency orthopaedic surgery in patients over 60 years of age.

METHODS

One hundred and two patients were recruited in 2006 and had inpatient troponin 1 measurements. These patients were followed up by a telephone call annually for complications.

RESULTS

At 2 years, 29.4% (30/102) of patients had died. Twenty-five patients (25/54 or 49.3%) with a troponin rise were dead at 2 years compared with five patients without a troponin rise (5/48 or 10.4%), which was significantly different P < 0.0001. Patients with a higher troponin level (>0.1 µg/L) were more likely to be dead at 2 years compared with those with a lower level of troponin. However, when adjusted for other comorbidities the association between troponin elevation and death at 2 years did not persist. Using Cox regression multivariate analysis, only one factor, sustaining an in-hospital cardiac event odds ratio 4.3 (95% confidence interval 1.8-10.3, P = 0.001), was associated with 2 years all-cause mortality . Furthermore, patients who sustained a symptomatic troponin rise (P < 0.0001) or asymptomatic troponin rise (P = 0.004) were more likely to have died at 2 years compared with those with no troponin rise. Three factors were significantly associated with a cardiac event during the second year: (i) post-operative troponin rise (P = 0.05); (ii) pre-morbid atrial fibrillation (P = 0.04); and (iii) post-operative renal failure (P < 0.001).

CONCLUSION

Elevated post-operative troponin levels are predictive of 1-year but not 2-year mortality in older patients undergoing emergency orthopaedic surgery.

T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses

T-cell acute lymphoblastic leukemia (T-ALL) and lymphoma (T-LBL) share common morphological and immunophenotypic features and are treated with similar therapeutic approaches. Nonetheless, they show distinct clinical presentations, suggesting that they may represent two different biological entities. To investigate the genetic characteristics of T-LBL and T-ALL, we used genomic and transcriptional profiling approaches. Genome-wide gene expression profiling, performed on 20 T-LBL and 10 T-ALL diagnostic specimens, revealed that the two malignancies shared a large fraction of their transcriptional profile while a subset of genes appeared to be differentially expressed in T-LBL versus T-ALL. This signature included genes involved in chemotactic responses and angiogenesis, which may play a role in tumor cell localization. Genome-wide copy number alteration analysis was performed on a subset of the samples analyzed by gene expression profiling and detected 41 recurrently altered genetic loci. Although most aberrations were found in both entities, several were selectively identified in T-LBL or T-ALL. In addition, NOTCH1 mutational status was found to correlate with a subset of genetic aberrations. Taken together, these results suggest that T-LBL and T-ALL are indeed two distinct diseases with unique transcriptional and genetic characteristics.

Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation

Technological development led to an increased interest in systems biological approaches to characterize disease mechanisms and candidate genes relevant to specific diseases. We suggested that the human peripheral blood mononuclear cells (PBMC) network can be delineated by cellular reconstruction to guide identification of candidate genes. Based on 285 microarrays (7370 genes) from 98 heart transplant patients enrolled in the Cardiac Allograft Rejection Gene Expression Observational study, we used an information-theoretic, reverse-engineering algorithm called ARACNe (algorithm for the reconstruction of accurate cellular networks) and chromatin immunoprecipitation assay to reconstruct and validate a putative gene PBMC interaction network. We focused our analysis on transcription factor (TF) genes and developed a priority score to incorporate aspects of network dynamics and information from published literature to supervise gene discovery. ARACNe generated a cellular network and predicted interactions for each TF during rejection and quiescence. Genes ranked highest by priority score included those related to apoptosis, humoural and cellular immune response such as GA binding protein transcription factor (GABP), nuclear factor of κ light polypeptide gene enhancer in B-cells (NFκB), Fas (TNFRSF6)-associated via death domain (FADD) and c-AMP response element binding protein. We used the TF CREB to validate our network. ARACNe predicted 29 putative first-neighbour genes of CREB. Eleven of these (37%) were previously reported. Out of the 18 unknown predicted interactions, 14 primers were identified and 11 could be immunoprecipitated (78.6%). Overall, 75% (n= 22) inferred CREB targets were validated, a significantly higher fraction than randomly expected (P < 0.001, Fisher’s exact test). Our results confirm the accuracy of ARACNe to reconstruct the PBMC transcriptional network and show the utility of systems biological approaches to identify possible molecular targets and biomarkers.

Reducing scanning electron microscope charging by using exponential contrast stretching technique on post-processing images

An exponential contrast stretching (ECS) technique is developed to reduce the charging effects on scanning electron microscope images. Compared to some of the conventional histogram equalization methods, such as bi-histogram equalization and recursive mean-separate histogram equalization, the proposed ECS method yields better image compensation. Diode sample chips with insulating and conductive surfaces are used as test samples to evaluate the efficiency of the developed algorithm. The algorithm is implemented in software with a frame grabber card, forming the front-end video capture element.

The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain

Self-renewal and proliferation of neural stem cells and the decision to initiate neurogenesis are crucial events directing brain development. Here we show that the ubiquitin ligase Huwe1 operates upstream of the N-Myc-DLL3-Notch pathway to control neural stem cell activity and promote neurogenesis. Conditional inactivation of the Huwe1 gene in the mouse brain caused neonatal lethality associated with disorganization of the laminar patterning of the cortex. These defects stemmed from severe impairment of neurogenesis associated with uncontrolled expansion of the neural stem cell compartment. Loss- and gain-of-function experiments in the mouse cortex demonstrated that Huwe1 restrains proliferation and enables neuronal differentiation by suppressing the N-Myc-DLL3 cascade. Notably, human high-grade gliomas carry focal hemizygous deletions of the X-linked Huwe1 gene in association with amplification of the N-myc locus. Our results indicate that Huwe1 balances proliferation and neurogenesis in the developing brain and that this pathway is subverted in malignant brain tumors.

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

The ability of a transcription factor (TF) to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms, resulting in highly context-dependent regulatory networks. However, high-throughput methods for the identification of proteins that affect TF activity are still largely unavailable. Here we introduce an algorithm, modulator inference by network dynamics (MINDy), for the genome-wide identification of post-translational modulators of TF activity within a specific cellular context. When used to dissect the regulation of MYC activity in human B lymphocytes, the approach inferred novel modulators of MYC function, which act by distinct mechanisms, including protein turnover, transcription complex formation and selective enzyme recruitment. MINDy is generally applicable to study the post-translational modulation of mammalian TFs in any cellular context. As such it can be used to dissect context-specific signaling pathways and combinatorial transcriptional regulation.

Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL), the most common form of lymphoma in adulthood, comprises multiple biologically and clinically distinct subtypes including germinal centre B-cell-like (GCB) and activated B-cell-like (ABC) DLBCL. Gene expression profile studies have shown that its most aggressive subtype, ABC-DLBCL, is associated with constitutive activation of the NF-kappaB transcription complex. However, except for a small fraction of cases, it remains unclear whether NF-kappaB activation in these tumours represents an intrinsic program of the tumour cell of origin or a pathogenetic event. Here we show that >50% of ABC-DLBCL and a smaller fraction of GCB-DLBCL carry somatic mutations in multiple genes, including negative (TNFAIP3, also called A20) and positive (CARD11, TRAF2, TRAF5, MAP3K7 (TAK1) and TNFRSF11A (RANK)) regulators of NF-kappaB. Of these, the A20 gene, which encodes a ubiquitin-modifying enzyme involved in termination of NF-kappaB responses, is most commonly affected, with approximately 30% of patients displaying biallelic inactivation by mutations and/or deletions. When reintroduced in cell lines carrying biallelic inactivation of the gene, A20 induced apoptosis and cell growth arrest, indicating a tumour suppressor role. Less frequently, missense mutations of TRAF2 and CARD11 produce molecules with significantly enhanced ability to activate NF-kappaB. Thus, our results demonstrate that NF-kappaB activation in DLBCL is caused by genetic lesions affecting multiple genes, the loss or activation of which may promote lymphomagenesis by leading to abnormally prolonged NF-kappaB responses.

Master regulators used as breast cancer metastasis classifier

Computational identification of prognostic biomarkers capable of withstanding follow-up validation efforts is still an open challenge in cancer research. For instance, several gene expression profiles analysis methods have been developed to identify gene signatures that can classify cancer sub-phenotypes associated with poor prognosis. However, signatures originating from independent studies show only minimal overlap and perform poorly when classifying datasets other than the ones they were generated from. In this paper, we propose a computational systems biology approach that can infer robust prognostic markers by identifying upstream Master Regulators, causally related to the presentation of the phenotype of interest. Such a strategy effectively extends and complements other existing methods and may help further elucidate the molecular mechanisms of the observed pathophysiological phenotype. Results show that inferred regulators substantially outperform canonical gene signatures both on the original dataset and across distinct datasets.

Image signal-to-noise ratio estimation using Shape-Preserving Piecewise Cubic Hermite Autoregressive Moving Average model

We propose to cascade the Shape-Preserving Piecewise Cubic Hermite model with the Autoregressive Moving Average (ARMA) interpolator; we call this technique the Shape-Preserving Piecewise Cubic Hermite Autoregressive Moving Average (SP2CHARMA) model. In a few test cases involving different images, this model is found to deliver an optimum solution for signal to noise ratio (SNR) estimation problems under different noise environments. The performance of the proposed estimator is compared with two existing methods: the autoregressive-based and autoregressive moving average estimators. Being more robust with noise, the SP2CHARMA estimator has efficiency that is significantly greater than those of the two methods.

Gene expression profiling suggests primary central nervous system lymphomas to be derived from a late germinal center B cell

To characterize the molecular origin of primary lymphomas of the central nervous system (PCNSL), 21 PCNSLs of immunocompetent patients were investigated by microarray-based gene expression profiling. Comparison of the transcriptional profile of PCNSL with various normal and neoplastic B-cell subsets demonstrated PCNSL (i) to display gene expression patterns most closely related to late germinal center B cells, (ii) to display a gene expression profile similar to systemic diffuse large B-cell lymphomas (DLBCLs) and (iii) to be in part assigned to the activated B-cell-like (ABC) or the germinal center B-cell-like (GCB) subtype of DLBCL.

Reverse engineering cellular networks

We describe a computational protocol for the ARACNE algorithm, an information-theoretic method for identifying transcriptional interactions between gene products using microarray expression profile data. Similar to other algorithms, ARACNE predicts potential functional associations among genes, or novel functions for uncharacterized genes, by identifying statistical dependencies between gene products. However, based on biochemical validation, literature searches and DNA binding site enrichment analysis, ARACNE has also proven effective in identifying bona fide transcriptional targets, even in complex mammalian networks. Thus we envision that predictions made by ARACNE, especially when supplemented with prior knowledge or additional data sources, can provide appropriate hypotheses for the further investigation of cellular networks. While the examples in this protocol use only gene expression profile data, the algorithm's theoretical basis readily extends to a variety of other high-throughput measurements, such as pathway-specific or genome-wide proteomics, microRNA and metabolomics data. As these data become readily available, we expect that ARACNE might prove increasingly useful in elucidating the underlying interaction models. For a microarray data set containing approximately 10,000 probes, reconstructing the network around a single probe completes in several minutes using a desktop computer with a Pentium 4 processor. Reconstructing a genome-wide network generally requires a computational cluster, especially if the recommended bootstrapping procedure is used.

Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks

MOTIVATION

An increasingly common application of gene expression profile data is the reverse engineering of cellular networks. However, common procedures to normalize expression profiles generated using the Affymetrix GeneChips technology were originally developed for a rather different purpose, namely the accurate measure of differential gene expression between two or more phenotypes. As a result, current evaluation strategies lack comprehensive metrics to assess the suitability of available normalization procedures for reverse engineering and, in general, for measuring correlation between the expression profiles of a gene pair.

RESULTS

We benchmark four commonly used normalization procedures (MAS5, RMA, GCRMA and Li-Wong) in the context of established algorithms for the reverse engineering of protein-protein and protein-DNA interactions. Replicate sample, randomized and human B-cell data sets are used as an input. Surprisingly, our study suggests that MAS5 provides the most faithful cellular network reconstruction. Furthermore, we identify a crucial step in GCRMA responsible for introducing severe artifacts in the data leading to a systematic overestimate of pairwise correlation. This has key implications not only for reverse engineering but also for other methods, such as hierarchical clustering, relying on accurate measurements of pairwise expression profile correlation. We propose an alternative implementation to eliminate such side effect.

Real-time image quality assessment with mixed Lagrange time delay estimation autoregressive (MLTDEAR) model

A proposal to assess the quality of scanning electron microscope images using mixed Lagrange time delay estimation technique is presented. With optimal scanning electron microscope scan rate information, online images can be quantified and improved. The online quality assessment technique is embedded onto a scanning electron microscope frame grabber card for real-time image processing. Different images are captured using scanning electron microscope and a database is built to optimally choose filter parameters. An optimum choice of filter parameters is obtained. With the optimum choice of scan rate, noise can be removed from real-time scanning electron microscope images without causing any sample contamination or increasing scanning time.

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth

The NOTCH1 signaling pathway directly links extracellular signals with transcriptional responses in the cell nucleus and plays a critical role during T cell development and in the pathogenesis over 50% of human T cell lymphoblastic leukemia (T-ALL) cases. However, little is known about the transcriptional programs activated by NOTCH1. Using an integrative systems biology approach we show that NOTCH1 controls a feed-forward-loop transcriptional network that promotes cell growth. Inhibition of NOTCH1 signaling in T-ALL cells led to a reduction in cell size and elicited a gene expression signature dominated by down-regulated biosynthetic pathway genes. By integrating gene expression array and ChIP-on-chip data, we show that NOTCH1 directly activates multiple biosynthetic routes and induces c-MYC gene expression. Reverse engineering of regulatory networks from expression profiles showed that NOTCH1 and c-MYC govern two directly interconnected transcriptional programs containing common target genes that together regulate the growth of primary T-ALL cells. These results identify c-MYC as an essential mediator of NOTCH1 signaling and integrate NOTCH1 activation with oncogenic signaling pathways upstream of c-MYC.

Autocorrelation-based technique for automated segmentation of endocardial border in 3D echocardiograms

Left-ventricular (LV) segmentation is essential in the early detection of heart disease, where left-ventricular wall motion is being tracked in order to detect ischemia. In this paper, a new method for automated segmentation of the left-ventricular chamber is described. An autocorrelation-based technique isolates the LV cavity from the myocardial wall on 2-D slices of 3D short-axis echocardiograms. A morphological closing function and median filtering are used to generate a uniform border. The proposed segmentation technique is designed to be used in identifying the endocardial border and estimating the motion of the endocardial wall over a cardiac cycle. To this purpose, the proposed technique is particularly successful in border delineation by tracing around structures like papillary muscles and the mitral valve, which constitute the typical obstacle in LV segmentation techniques. The results using this new technique are compared to the manual detection results in short-axis views obtained at the papillary muscle level from 3D datasets in human and canine experiments in vivo. Qualitatively, the automatically-detected borders are highly comparable to the manually-detected borders enclosing regions in the left-ventricular cavity with a relative error within the range of 4.2%-6%. Thus, the new technique constitutes a robust segmentation method for automated segmentation of endocardial borders and is suitable for wall motion tracking for automated detection of ischemia in vivo.

Implementing evidence-based guidelines: inpatient management of chronic obstructive pulmonary disease

BACKGROUND

Evidence-based guidelines exist to guide inpatient management of chronic obstructive pulmonary disease (COPD) exacerbations, but we do not know how well these recommendations are adhered to.

AIMS

The aims of this study were: (i) to examine concordance with evidence based guidelines for inpatient management of COPD and (ii)to address deficiencies in compliance with guidelines by feedback of audit results and distribution of an education package.

METHODS

Retrospective chart reviews were performed using a data collection tool based on current guidelines. Forty-nine consecutive COPD admissions were audited, and results presented to medical staff. An education package was distributed directly after the presentation. One month later,35 consecutive separations were reviewed. Concordance with recommendations supported by the highest level of evidence was calculated.

RESULTS

Data were complete for 84 cases. Concordance rates ranged from 0 to 100%. Apart from initiation of systemic steroids (80-83%)and avoidance of intravenous aminophylline (100%),concordance rates were less than 60%. The only significant improvement post-intervention was for steroid duration (10 vs 29%,95% confidence interval for difference (-36.2, -1.8)).

CONCLUSION

Recommendations for steroid initiation and avoidance of aminophylline are well adhered to. Concordance rates for other recommendations were generally less than 60%. Concordance with recommendations for steroid duration was significantly improved by our intervention. The findings suggest that to facilitate evidence-based practice, alternative interventions should be evaluated.

Classification of mammographic masses using generalized dynamic fuzzy neural networks

In this article, computer-aided classification of mammographic masses using generalized dynamic fuzzy neural networks (GDFNN) is presented. The texture parameters, derived from first-order gradient distribution and gray-level co-occurrence matrices, were computed from the regions of interest. A total of 343 images containing 180 benign masses and 163 malignant masses from the Digital Database for Screening Mammography were analyzed. A fast approach of automatically generating fuzzy rules from training samples was implemented to classify tumors. This work is novel in that it alleviates the problem of requiring a designer to examine all the input-output relationships of a training database in order to obtain the most appropriate structure for the classifier in a conventional computer-aided diagnosis. In this approach, not only the connection weights can be adjusted, but also the structure can be self-adaptive during the learning process. By virtue of the automatic generation of the classifier by the GDFNN learning algorithm, the area under the receiver-operating characteristic curve, Az, attains 0.868 +/- 0.020, which corresponds to a true-positive fraction of 95.0% at a false positive fraction of 52.8%. The corresponding accuracy is 70.0%, the positive predictive value is 62.0%, and the negative predictive value is 91.4%.

Low-dose intravenous methylprednisolone or conservative treatment in the management of traumatic optic neuropathy

PURPOSE

To compare the efficacy of low-dose intravenous methylprednisolone or conservative treatment in the management of traumatic optic neuropathy.

METHODS

A non-randomized retrospective study of 21 patients (21 eyes) with traumatic optic neuropathy treated between October 95 and November 97 in a tertiary ophthalmology unit. Traumatic optic neuropathy was defined as traumatic visual loss with afferent pupillary defect in the absence of direct injury to the globe or optic nerve. The median follow-up period was one year. Nine patients were treated with 125-250 mg methylprednisolone 6-hourly intravenously for a mean of 3.3 days (range 2-5 days) and 12 patients were treated conservatively. Visual acuity (VA) was measured with a Snellen chart before and after treatment at each follow-up visit. Visual recovery was defined as an improvement of 2 or more Snellen lines one week post-injury or later.

RESULTS

The patients' mean age was 37.1 years (range 12-65 years). There were more males (90.5%) than females (9.5%). Traumatic optic neuropathy was in 12 right eyes and 9 left eyes. The cause of injury included traffic accidents (52.4%), falls (28.6%), assault (14.2%) and others (4.8%). The mean interval between the injury and steroid therapy was 3.6 days (range 1-11 days). Visual recovery was observed in 44.4% of eyes treated with methylprednisolone and in 33.3% treated conservatively (p = 0.673, Fisher's exact test).

CONCLUSIONS

Intravenous methylprednisolone at the dosage and duration used in this retrospective study did not significantly improve the visual recovery of eyes with traumatic optic neuropathy compared to conservative treatment. However, this small sample may not be sensitive enough to detect a small difference in visual recovery rates, and further studies with larger samples may be warranted.

Melioidosis of the head and neck

Melioidosis is a potentially deadly infection that can affect any organ system. Reports of melioidosis of the ENT/head and neck region are relatively uncommon. Four cases are presented: (i) parotid abscess evolving into necrotising fasciitis, (ii) acute sinusitis and parapharyngeal cellulitis resulting in upper airway obstruction, (iii) acute suppurative lymphadenitis (iv) and chronic suppurative otitis media causing meningoencephalitis. Three of the four cases are believed to be unique, as a literature review of melioidosis in ENT/head and neck is also presented. Some practical issues of management are also discussed. Not suspecting melioidosis does not change contemporary empirical broadspectrum antibiotic therapy. The value of suspicion or on confirmation of diagnosis lies in anticipating and planning for rapid change.

Homodimers of mutant tryptophan synthase alpha-subunits in Escherichia coli

Tryptophan synthase alpha-subunit from Escherichia coli functionally exists as a heterotetramer of alpha(2)beta(2) with beta-subunit. While wild-type and mutant (F139W, T24M/F139W, and T24L/F139W) alpha-subunits were expressed as a monomer from recombinant plasmids in Escherichia coli, T24A/F139W, T24S/F139W, and T24K/F139W mutant alpha-subunits were abnormally expressed as soluble homodimers in addition to monomers. Monomers of dimer-forming mutant alpha-subunits retain high affinity to beta-subunit, high activity in stimulating catalytic activities of beta-subunit, and nearly intact content of secondary structure, indicating that the global structures of these monomers are identical to that of F139W alpha-subunit. However, fluorescence spectra of Trp139 and ANS binding indicate that significant perturbations occur in the mutant proteins. Interestingly, these defective properties of monomers caused by residue replacement were partially repaired by the dimer formation. As a result, it is suggested that dimers may be formed by domain or loop swapping, and that residue 24 may play important role in maintaining on-pathway of alpha-subunit folding.