Density Functional Theory Study on the Cleavage Mechanism of the Carbonyl Bond in Amides on Flat and Stepped Ru Surfaces: Hydrogen-Induced or Direct C-O Bond Breaking?

We have performed density functional theory (DFT) calculations to investigate the reaction mechanism of the cleavage of the carbonyl bond in amides on both flat and stepped Ru surfaces. The simplest amide molecule, N,N-dimethylacetamide (DMA), was used as the exemplar model molecule. Through the calculations, the most stable transition states (TSs) in all the pathways on both flat and stepped Ru surfaces are identified. Comparing the energy profiles of different reaction pathways, we find that a direct cleavage mechanism is always energetically favored as compared with an alternative hydrogen-induced mechanism on either the flat or stepped Ru surface. It is easier for the dissociation process to occur on the stepped surface than on the flat surface. However, as compared with the terrace, the superiority of step sites boosting the C-O bond dissociation is not as evident as that on CO dissociation.

Origin of the Increase of Activity and Selectivity of Nickel Doped by Au, Ag, and Cu for Acetylene Hydrogenation

Activity and selectivity are both important issues in heterogeneous catalysis and recent experimental results have shown that Ni catalysts doped by gold exhibit high activity for the hydrogenation of acetylene with good selectivity of ethylene formation. To unravel the underlying mechanism for this observation, the general trend of activity and selectivity of Ni surfaces doped by Au, Ag, and Cu has been investigated using density functional theory calculations. Complete energy profiles from C2H2 to C2H4 on Ni(111), Au/Ni(111), Ag/Ni(111) and Cu/Ni(111) are obtained and their turnover frequencies (TOFs) are computed. The results show that acetylene adsorption on Ni catalyst is strong which leads to the low activity while the doping of Au, Ag, and Cu on the Ni catalyst weakens the acetylene adsorption, giving rise to the increase of activity. The selectivity of ethylene formation is also quantified by using the energy difference between the hydrogenation barriers and the absolute value of the adsorption energies of ethylene. It is found that the selectivity of ethylene formation increases by doping Au and Ag, while those of Cu/Ni and Ni are similar.

Non-adherence to therapy in children with cystic fibrosis

Hawthorne N., Hawwa A.F., Shields M.D., Reid A.J., McElnay J.C. (2011) Non-adherence to therapy in children with cystic fibrosis. Pediatric Pulmonology, 46: 408.

Non-adherence in children with cystic fibrosis

Hawthorne N., Hawwa A., McElnay J., Shields M., Reid A. (2011) Non-adherence in children with cystic fibrosis. Journal of Pharmacy and Pharmaceutical Sciences, 14: 209s

Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data

Background: Ineffective risk stratification can delay diagnosis of serious disease in patients with hematuria. We applied a systems biology approach to analyze clinical, demographic and biomarker measurements (n = 29) collected from 157 hematuric patients: 80 urothelial cancer (UC) and 77 controls with confounding pathologies.

Methods: On the basis of biomarkers, we conducted agglomerative hierarchical clustering to identify patient and biomarker clusters. We then explored the relationship between the patient clusters and clinical characteristics using Chi-square analyses. We determined classification errors and areas under the receiver operating curve of Random Forest Classifiers (RFC) for patient subpopulations using the biomarker clusters to reduce the dimensionality of the data.

Results: Agglomerative clustering identified five patient clusters and seven biomarker clusters. Final diagnoses categories were non-randomly distributed across the five patient clusters. In addition, two of the patient clusters were enriched with patients with ‘low cancer-risk’ characteristics. The biomarkers which contributed to the diagnostic classifiers for these two patient clusters were similar. In contrast, three of the patient clusters were significantly enriched with patients harboring ‘high cancer-risk” characteristics including proteinuria, aggressive pathological stage and grade, and malignant cytology. Patients in these three clusters included controls, that is, patients with other serious disease and patients with cancers other than UC. Biomarkers which contributed to the diagnostic classifiers for the largest ‘high cancer- risk’ cluster were different than those contributing to the classifiers for the ‘low cancer-risk’ clusters. Biomarkers which contributed to subpopulations that were split according to smoking status, gender and medication were different.

Conclusions: The systems biology approach applied in this study allowed the hematuric patients to cluster naturally on the basis of the heterogeneity within their biomarker data, into five distinct risk subpopulations. Our findings highlight an approach with the promise to unlock the potential of biomarkers. This will be especially valuable in the field of diagnostic bladder cancer where biomarkers are urgently required. Clinicians could interpret risk classification scores in the context of clinical parameters at the time of triage. This could reduce cystoscopies and enable priority diagnosis of aggressive diseases, leading to improved patient outcomes at reduced costs. © 2013 Emmert-Streib et al; licensee BioMed Central Ltd.

Standardization of diagnostic biomarker concentrations in urine; the hematuria caveat

Sensitive and specific urinary biomarkers can improve patient outcomes in many diseases through informing early diagnosis. Unfortunately, to date, the accuracy and translation of diagnostic urinary biomarkers into clinical practice has been disappointing. We believe this may be due to inappropriate standardization of diagnostic urinary biomarkers. Our objective was therefore to characterize the effects of standardizing urinary levels of IL-6, IL-8, and VEGF using the commonly applied standards namely urinary creatinine, osmolarity and protein. First, we report results based on the biomarker levels measured in 120 hematuric patients, 80 with pathologically confirmed bladder cancer, 27 with confounding pathologies and 13 in whom no underlying cause for their hematuria was identified, designated “no diagnosis”. Protein levels were related to final diagnostic categories (p = 0.022, ANOVA). Osmolarity (mean = 529 mOsm; median = 528 mOsm) was normally distributed, while creatinine (mean = 10163 µmol/l, median = 9350 µmol/l) and protein (0.3297, 0.1155 mg/ml) distributions were not. When we compared AUROCs for IL-6, IL-8 and VEGF levels, we found that protein standardized levels consistently resulted in the lowest AUROCs. The latter suggests that protein standardization attenuates the “true” differences in biomarker levels across controls and bladder cancer samples. Second, in 72 hematuric patients; 48 bladder cancer and 24 controls, in whom urine samples had been collected on recruitment and at follow-up (median = 11 (1 to 20 months)), we demonstrate that protein levels were approximately 24% lower at follow-up (Bland Altman plots). There was an association between differences in individual biomarkers and differences in protein levels over time, particularly in control patients.

Modelling recovery of Celtic Sea demersal fish community size-structure

The Large Fish Indicator (LFI) is a size-based indicator of fish community state. The indicator describes the proportion by biomass of a fish community represented by fish larger than some size threshold. From an observed peak value of 0.49 in 1990, the Celtic Sea LFI declined until about 2000 and then fluctuated around 0.10 throughout the 2000s. This decline in the LFI reflected a period of diminishing ‘large’ fish biomass, probably related to high levels of size selective fishing. During the study period, fishing mortality was maintained at consistently high values. Average biomass of ‘small’ fish fluctuated across the whole time series, showing a weak positive trend in recent years. Inter-annual variation in the LFI was increasingly driven by fluctuation in small fish biomass as large fish biomass declined. Simulations using a size-based ecosystem model suggested that recovery in Celtic Sea fish community size-structure (LFI) could demand at least 20% reductions in fishing pressure and occur on decadal timescales.

Balancing Inflammatory, Lipid, and Xenobiotic Signaling Pathways by VSL#3, a Biotherapeutic Agent, in the Treatment of Inflammatory Bowel Disease

Background: The interleukin 10 knockout mouse (IL10-KO) is a model of human inflammatory bowel disease (IBD) used to Study host microbial interactions and the action of potential therapeutics. Using Affymetrix data analysis, important signaling pathways and transcription factors relevant to gut inflammation and antiinflammatory probiotics were identified.

Methods: Affymetrix microarray analysis on both wildtype (WT) and IL10-KO mice orally administered with and without the probiotic VSL#3 was performed and the results validated by real-time polymerase chain reaction (PCR), immunocytochemistry, proteomics, and histopathology. Changes in metabolically active bacteria were assessed with denaturing gradient gel electrophoresis (DGGE).

Results: Inflammation in IL10-KO mice was characterized by differential regulation of inflammatory, nuclear receptor, lipid, and xenobiotic signaling pathways. Probiotic intervention resulted in downregulation of CXCL9 (fold change [FC] = -3.98, false discovery rate [FDR] = 0.019), CXCL10 (FC = -4.83, FDR = 0.0008), CCL5 (FC -3.47 FDR = 0.017), T-cell activation (Itgal [FC = -4.72, FDR = 0.00009], Itgae [FC = -2.54 FDR = 0.0044]) and the autophagy gene IRGM (FC = -1.94, FDR = 0.01), a recently identified susceptibility gene in human IBD. Consistent with a marked reduction in integrins, probiotic treatment decreased the number of CCL5+ CD3+ double-positive T Cells and upregulated galectin2, which triggers apoptosis of activated T cells. Importantly, genes associated with lipid and PPAR signaling (PPAR alpha [FC = 2.36, FDR = 0.043], PPARGC1 alpha [FC 2.58, FDR = 0.016], Nrld2 [FC = 3.11, FDR = 0.0067]) were also upregulated. Altered microbial diversity was noted in probiotic-treated mice.

Conclusions: Bioinformatics analysis revealed important immune response. phagocytic and inflammatory pathways dominated by elevation of T-helper cell 1 type (TH1) transcription factors in IL10-KO mice. Probiotic intervention resulted in a site-specific reduction of these pathways but importantly upregulated PPAR, xenobiotic, and lipid signaling genes. potential antagonists of NF-kappa B inflammatory pathways.

The experiences of palliative care health service provision for people with non-malignant respiratory disease and their caregivers: an all-Ireland study

Aim: To explore the perception of palliative care provision for people with non-malignant respiratory disease from the perspective of bereaved caregivers.

Background: It is recognized that the majority of patients diagnosed with a malignant disease will have access to palliative care provision. However, it is less clear if the same standards of palliative care are available to those with non-malignant respiratory disease in Northern Ireland and the Republic of Ireland.

Design: A qualitative study based on broad interpretivism.

Methods: This research is a PhD study funded by the Department of Education and Learning in Northern Ireland (awarded February 2011). Data collection will consist of two stages; interviews with 20 bereaved caregivers of people who have died 3–18 months previously with a diagnosis of non-malignant respiratory disease and four focus groups with healthcare professionals involved in the care of this client group. This study will be carried out at four healthcare sites across the Island of Ireland. The data will be analysed using thematic content analysis. Research Ethics committee approval was obtained (March 2012).

Discussion: This research will explore the experiences of patients with Chronic Obstructive Pulmonary Disease, Interstitial Lung Disease and Bronchiectasis and their caregivers from the perspective of the bereaved caregiver. The outcomes of this study will provide a critical first step in the development of more responsive palliative care for this client group and have important implications for future practice and policy in the palliative care provided to this client group.

Healthcare professionals’ response to cachexia in advanced cancer: A qualitative study

Purpose/Objectives: To explore healthcare professionals' experience, understanding, and perception of the needs of patients with cachexia in advanced cancer.

Research Approach: A qualitative approach based on symbolic interactionism.

Setting: A regional cancer center in a large teaching hospital in the United Kingdom.

Participants: 34 healthcare professionals who had experience providing care to patients with cachexia in advanced cancer.

Methodologic Approach: Data collection consisted of two phases: focus group and semistructured interviews. Interviews were digitally recorded and transcribed verbatim for analysis. This article reports on findings from the second phase of data collection.

Findings: Analysis revealed that professional approaches to cachexia were influenced by three overarching and interthinking themes: knowledge, culture, and resources. Healthcare professionals commonly recognized the impact of the syndrome; however, for nonpalliative healthcare professionals, a culture of avoidance and an overreliance on the biomedical model of care had considerable influence on the management of cachexia in patients with advanced cancer.

Conclusions: Cachexia management in patients with advanced cancer can be difficult and is directed by a variable combination of the influence of knowledge, culture of the clinical area, and available resources. Distinct differences exist in the management of cachexia among palliative and nonpalliative care professionals.

Interpretation: This study presented a multiprofessional perspective on the management of cachexia in patients with advanced cancer and revealed that cachexia is a complex and challenging syndrome that needs to be addressed from a holistic model of care.

Knowledge Translation: Cachexia management in patients with advanced cancer is complex and challenging and is directed by a combination of variables. An overreliance on the biomedical model of health and illness occurs in the management of cachexia in patients with advanced cancer. Cachexia needs to be addressed from a holistic model of care to reflect the multidimensional needs of patients and their families.

Electric currents and lens regeneration in the rat

We studied the process of lens regeneration in the rat following an extracapsular lens extraction preserving the anterior lens capsule and anterior lens epithelium. We assessed clinically the clarity of the newly regenerated lens, evaluated changes in the lens electrical currents following surgery and during the regeneration process and correlated these changes with findings on light microscopy. Protein analysis of the regenerated lens was also undertaken. Experiments were performed in 41 Sprague-Dawley rats, sacrificed at 0, 2, 4 and 8 weeks postoperatively. Our results showed that complete lens regeneration occurred 8 weeks postoperatively only if the anterior epithelium was preserved and the lens capsule was closed surgically. Lens electrical currents, altered following surgery, recovered in parallel with the process of regeneration of the lens. The newly regenerated lens was optically clear and biochemical analysis revealed a pattern of protein expression resembling that observed during lens development. In conclusion, complete lens regeneration occurs in the rat and it is possible that lens electrical signals, together with other cues, may play an important role in this process. © 2009 Elsevier Ltd.