Treatment of chronic hepatitis D patients with pegylated interferon: a real-world experience

Background: Published experience of treating chronic hepatitis D patients with pegylated interferon (PEG-IFN)-alpha is limited. The aim of this study was to determine the efficacy of 48 weeks of treatment with PEG-IFN in naive patients outside the clinical trial setting, in the real world. Methods: Patients with chronic hepatitis D were treated with PEG-IFN. The primary end points were sustained clearance of HDV RNA and normal alanine aminotransferase (ALT) at 24 weeks post-treatment. Results: The total number of patients treated with PEG-IFN was 104; 91 males, mean age ±SD 30.1 ±10.0 years (range 15-55). Cirrhosis was present in 41 patients. With an intention-to-treat analysis, end of treatment virological response (ETR) was achieved in 44 (42.3%), normalization of ALT in 38 (35%) and a combined response in 23 (22.1%) patients. Sustained virological response (SVR) at 24 weeks post-treatment was seen in 24 (23.1%) patients each for the virological and biochemical responses and in 13 (12.5%) as combined response. Both ETR and SVR were associated with a negative HDV RNA at 24 weeks of treatment (P=0.001 and P=0.000, respectively). Detectable HDV RNA at this point had a positive predictive value of 0.95 (range 0.85-0.99) for detectable RNA at 6 months post-treatment. End of treatment biological response, that is, normal ALT at the end of treatment was also a predictor of ETR and SVR (P=0.004 and P=0.041, respectively). Conclusion:: Treatment with PEG-IFN for hepatitis D is of limited efficacy. Detectable HDV RNA at 24 weeks of treatment is a predictor for a failed SVR

Promoting female participation in professional development programmes

A recent publication of the Ministry of Education, Islamabad, shows that the province of Sindh has a population of over 30 million. The overall literacy rate in this province is 46.7 %, while the female literacy rate is 35.4%. However, in the rural areas of Sindh the female literacy rate is 13.11% against the male literacy rate of 52.1%. There are many social, cultural and economic factors that inhibit females from availing opportunities on an equal basis with the other segments of society. The literature also reveals that due to the above-mentioned factors females are confined to play a passive role in general and in the education sector in particular. According to a recent UNDP publication, there is considerable disparity between males and females in terms of professional development. Considering the importance of professional development of females in the education sector in Sindh, the Aga Khan University Institute for Educational Development (AKU-IED), under the Pakistan Non- Government Initiatives (PNI-II), took an initiative to launch a project titled ‘Strengthening the Capacity of NGOs/CBOs’. The project targeted to provide opportunities of professional development to 258 individuals, but the actual number of those who graduated was 388, considerably exceeding the planned target. Out of 388, 68 % (262) were females, which show the enthusiasm and commitment of the participants, collaborating NGOs/CBOs and AKU-IED towards the professional development of females. Through this initiative, females were trained as ‘agents of change’ to motivate their communities towards education of their children, in particular the girl child. This presentation unfolds the learning experiences of the USAID Project-III team in promoting female participation in professional development programmes at AKU-IED

Potential pitfalls in MitoChip detected tumor-specific somatic mutations: a call for caution when interpreting patient data

<p>Abstract</p> <p>Background</p> <p>Several investigators have employed high throughput mitochondrial sequencing array (MitoChip) in clinical studies to search mtDNA for markers linked to cancers. In consequence, a host of somatic mtDNA mutations have been identified as linked to different types of cancers. However, closer examination of these data show that there are a number of potential pitfalls in the detection tumor-specific somatic mutations in clinical case studies, thus urging caution in the interpretation of mtDNA data to the patients. This study examined mitochondrial sequence variants demonstrated in cancer patients, and assessed the reliability of using detected patterns of polymorphisms in the early diagnosis of cancer.</p> <p>Methods</p> <p>Published entire mitochondrial genomes from head and neck, adenoid cystic carcinoma, sessile serrated adenoma, and lung primary tumor from clinical patients were examined in a phylogenetic context and compared with known, naturally occurring mutations which characterize different populations.</p> <p>Results</p> <p>The phylogenetic linkage analysis of whole arrays of mtDNA mutations from patient cancerous and non-cancerous tissue confirmed that artificial recombination events occurred in studies of head and neck, adenoid cystic carcinoma, sessile serrated adenoma, and lung primary tumor. Our phylogenetic analysis of these tumor and control leukocyte mtDNA haplotype sequences shows clear cut evidence of mixed ancestries found in single individuals.</p> <p>Conclusions</p> <p>Our study makes two prescriptions: both in the clinical situation and in research 1. more care should be taken in maintaining sample identity and 2. analysis should always be undertaken with respect to all the data available and within an evolutionary framework to eliminate artifacts and mix-ups.</p

Elevated tau and interleukin-6 concentrations in adults with obstructive sleep apnea

The article of record as published may be found at http://dx.doi.org/10.1016/j.sleep.2017.11.1121Obstructive sleep apnea (OSA) is characterized by apneas and hypopneas that result in hypoxia, cerebral hypoperfusion, endothelial dysfunction, inflammation, and oxidative stress. These pathophysiologic processes likely contribute to neuronal damage. Tau is a protein that stabilizes microtubules and, along with amyloid beta (Ab), is associated with neurodegenerative processes. We sought to determine if tau and other biomarkers of inflammation were related to OSA severity. Concentrations of tau, Ab40, Ab42, c-reactive protein (CRP), TNF-a, interleukin (IL)-6, and IL-10 were measured in blood and compared between participants with moderate-severe OSA (n 1⁄4 28), those with mild OSA (n 1⁄4 22), and healthy controls (n 1⁄4 24). The cohort included relatively young, primarily male active duty military personnel without a history of traumatic brain injury or neurodegenerative disease. Total biomarker concentrations were determined from plasma samples using an ultra-sensitive detection method, SimoaTM, and CRP was assayed by ELISA. Total tau and IL-6 concentrations were elevated in participants with moderate-severe OSA, with a mean apnea-hypopnea index (AHI) of 26.1/h, compared to those with mild OSA (mean AHI 8.6/h) and healthy controls (mean AHI 2.1/h). Tau concentrations were also significantly correlated with the AHI (r 1⁄4 0.342, p 1⁄4 0.004). Our findings show that tau is elevated in the blood of young patients with moderate-severe OSA, suggesting that this degree of sleep-disordered breathing is a contributing factor in the development of neurodegenerative disorders. The finding of increased IL-6 further suggests that inflammatory biomarkers are present early in the course of this chronic disease

Acute myocardial infarction: profile and management at a tertiary care hospital in Karachi

Objective: Acute Myocardial Infarction (AMI) is a rising epidemic in developing countries. While studies in the West have established the characteristics and management of AMI patients, comprehensive data reflecting these issues in the Pakistani subjects is scarce. This study examined the profile and management of AMI in patients hospitalized at a tertiary care hospital in Karachi, Pakistan.Methods: Three hundred forty four patients admitted in 1998 with the diagnosis of AMI met our inclusion criteria. Data on presentation, investigations, monitoring and therapy was obtained. Chi-square and t tests were used to analyze the data.Results: Out of 344 patients with AMI, 71% were males; 58% had a Q wave MI. Majority of the patients who presented within 2 hours of symptom onset (36%), had chest pain. Patients with dyspnea and no chest pain were more likely to present after 12 hours of the onset of symptoms. In-house mortality was found to be 10.8%. Low HDL and diabetes was associated with in-hospital complications. Twenty nine percent of patients were given thrombolytic therapy with a mean door-to-needle time of 1 hour 36 minutes; 33% of patients who were eligible of Streptokinase did not receive it. Cardiac catheterization was performed in 28% patients. Echocardiography and Exercise Tolerance Test, both under utilized, were performed in 67% and 16% of patients, respectively. Two hundred sixteen (70%) patients discharged from hospital were contacted via telephone and the 1-year mortality rate among them was 28%.CONCLUSION: The profile and management of AMI was in coherence with earlier, Western studies. Chest pain units need to be established in the Emergency Room. Patients should be risk stratified prior to discharge. Public awareness regarding primary and secondary prevention and symptoms of AMI needs to be increased

A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny

The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions) or complex (incorporating dependencies among reactions) stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks

ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly

<p>Abstract</p> <p>Background</p> <p>The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt) genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis.</p> <p>Results</p> <p>We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at <url>http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/</url>.</p> <p>Conclusions</p> <p>ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.</p

Network Archaeology: Uncovering Ancient Networks from Present-day Interactions

Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been limited by the unavailability of past versions of networks. To overcome these limitations, we propose several algorithms for reconstructing a network's history of growth given only the network as it exists today and a generative model by which the network is believed to have evolved. Our likelihood-based method finds a probable previous state of the network by reversing the forward growth model. This approach retains node identities so that the history of individual nodes can be tracked. We apply these algorithms to uncover older, non-extant biological and social networks believed to have grown via several models, including duplication-mutation with complementarity, forest fire, and preferential attachment. Through experiments on both synthetic and real-world data, we find that our algorithms can estimate node arrival times, identify anchor nodes from which new nodes copy links, and can reveal significant features of networks that have long since disappeared.Comment: 16 pages, 10 figure

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

Comparative metabolic modelling is emerging as a novel field, supported by the development of reliable and standardized approaches for constructing genome-scale metabolic models in high throughput. New software solutions are needed to allow efficient comparative analysis of multiple models in the context of multiple cellular objectives. Here, we present the user-friendly software framework Multi-Metabolic Evaluator (MultiMetEval), built upon SurreyFBA, which allows the user to compose collections of metabolic models that together can be subjected to flux balance analysis. Additionally, MultiMetEval implements functionalities for multi-objective analysis by calculating the Pareto front between two cellular objectives. Using a previously generated dataset of 38 actinobacterial genome-scale metabolic models, we show how these approaches can lead to exciting novel insights. Firstly, after incorporating several pathways for the biosynthesis of natural products into each of these models, comparative flux balance analysis predicted that species like Streptomyces that harbour the highest diversity of secondary metabolite biosynthetic gene clusters in their genomes do not necessarily have the metabolic network topology most suitable for compound overproduction. Secondly, multi-objective analysis of biomass production and natural product biosynthesis in these actinobacteria shows that the well-studied occurrence of discrete metabolic switches during the change of cellular objectives is inherent to their metabolic network architecture. Comparative and multi-objective modelling can lead to insights that could not be obtained by normal flux balance analyses. MultiMetEval provides a powerful platform that makes these analyses straightforward for biologists. Sources and binaries of MultiMetEval are freely available from https://github.com/PiotrZakrzewski/MetEv​al/downloads