Gas profiling in quasi-closed pressure regulated anaerobic fermentation systems

Fermentation of organic materials by microorganisms is an essential component in a variety of medical, industrial and agricultural applications. Many of these fermentations take place in quasi-closed pressure regulated anaerobic fermentation systems and involve the production of different gases. These gases are highly indicative as they are identifiable with biological processes and different bacteria species. Profiling gas components in such systems can assist with their microbial activities analysis, diagnosis and monitoring. However, methods for gas profiling in such fermentation systems lack real-time, accurate, simple, portable and cost-effective gas profiling technologies for continuously measuring gases in both anaerobic headspaces and in liquid media. The aim of this PhD research is to enhance the understanding, diagnosis and monitoring of these systems and their associated applications using gas components. This was specifically achieved by resolving the limitations and inadequacies of gas profiling in quasi-closed pressure regulated anaerobic fermentation systems. Firstly, the author of this thesis thoroughly reviewed the methods utilized for accurate profiling of gas components. Specifically, he focused on profiling intestinal gases produced in-vitro during fecal incubation. Secondly, the author investigated the calculation methods for profiling the production of these gases and their kinetics. Finally, the author explored gas profiling in both liquid and gas phases for in-situ monitoring of anaerobic digestion fermentation systems. The first stage involved addressing limitations of profiling intestinal gases produced by incubation of fecal matters in-vitro. The past available technologies for sensing colonic gases in-vitro were either bulky, expensive, offline or included only limited number of gas types. In addition, the gut environment in-vitro is generally simulated with N2 as an inert gas where the supplementation of important fermentation gases, such as CO2 and H2, was not understood. As such, the author developed a low-cost, portable and real-time gas sensing technology for monitoring CO2, CH4, H2, H2S and NOx simultaneously in the anaerobic headspace of fecal fermentation systems in-vitro. The author demonstrated the performance of the new technology on healthy human fecal samples and validated the new technology for both accuracy and reproducibility. The author also explored the impact of the initial headspace environment composition on the fermentation gas profiles. It was found that supplying the reactor with CO2 enhanced CH4 and H2 production and inhibited H2S production. Furthermore, it was shown that fecal incubation together with high fermentable fibre could suppress H2S production. Finally, the author found that healthy human fecal samples did not produce NOx spontaneously. In the second stage, the author investigated the calculation methods for profiling the production of gases and their kinetics in quasi-closed pressure regulated anaerobic fermentation systems. Surprisingly, the author discovered that there was no existing standardized or comprehensive method for such calculations. Therefore, the author developed a rigorous gas fermentation model and a novel mass-flow equation for accurately profiling the produced gases and introduced these into the literature. This new model was designed to match the commonly used commercial fermentation systems, making the new technology readily available for many applications and studies. The author demonstrated the performance of the new model for human fecal sample incubation using the in-vitro technology developed in the first stage and validated its accuracy. Moreover, the author found that the contribution of newly introduced components in the mass-flow equation exceeded 9.1% of the overall gas profile. In the final stage, the author researched the monitoring capability of anaerobic digestion processes using in-situ measurements of gas components in both liquid and gas phases. As an integral part of the microbial activity of anaerobic digestion processes, gas components have the potential of providing the necessary information for monitoring such processes effectively. However, current technologies for gas sensing in liquid-phase have been inadequate. Previously, Real-time profiling of gas components in both phases simultaneously has not been thoroughly studied due to lack of the required technology. This has possibly hindered important insights about the system’s health. In order to conduct this research, the author developed a novel, relatively simple, low-cost technique for measuring gas components in both phases simultaneously. Using this technique, dissolved gases were measured in-situ using membrane protected gas sensors which, in comparison to other approaches, eliminated many complications, delays or sample contamination. The author demonstrated the performances of the new technology on a series of anaerobic digestion batch experiments and confirmed its accuracy, longevity and reproducibly. Utilizing the new technique, the author identified patterns and signatures that were associated with process imbalances but not clearly observed in commonly used indicators such as volatile acids and pH. The author also explored the impact of inoculum age on the process and showed that, relative to freshly collected inoculum, processes using aged inoculum had a higher potential to enter imbalanced states and failure. It is the position of this author that the insights and technological advances achieved in this PhD research have contributed significantly to the advancement of the field of anaerobic fermentation. In particular, this was achieved by creating new, simple, accurate and reliable technologies, while adding significantly to the knowledge of quasi-closed, pressure regulated anaerobic fermentation systems and their applications

Dynamic and Multi-functional Labeling Schemes

We investigate labeling schemes supporting adjacency, ancestry, sibling, and connectivity queries in forests. In the course of more than 20 years, the existence of $\log n + O(\log \log)$ labeling schemes supporting each of these functions was proven, with the most recent being ancestry [Fraigniaud and Korman, STOC '10]. Several multi-functional labeling schemes also enjoy lower or upper bounds of $\log n + \Omega(\log \log n)$ or $\log n + O(\log \log n)$ respectively. Notably an upper bound of $\log n + 5\log \log n$ for adjacency+siblings and a lower bound of $\log n + \log \log n$ for each of the functions siblings, ancestry, and connectivity [Alstrup et al., SODA '03]. We improve the constants hidden in the $O$-notation. In particular we show a $\log n + 2\log \log n$ lower bound for connectivity+ancestry and connectivity+siblings, as well as an upper bound of $\log n + 3\log \log n + O(\log \log \log n)$ for connectivity+adjacency+siblings by altering existing methods. In the context of dynamic labeling schemes it is known that ancestry requires $\Omega(n)$ bits [Cohen, et al. PODS '02]. In contrast, we show upper and lower bounds on the label size for adjacency, siblings, and connectivity of $2\log n$ bits, and $3 \log n$ to support all three functions. There exist efficient adjacency labeling schemes for planar, bounded treewidth, bounded arboricity and interval graphs. In a dynamic setting, we show a lower bound of $\Omega(n)$ for each of those families.Comment: 17 pages, 5 figure

Aseptic Meningitis in Children: Analysis of 506 Cases

BACKGROUND: Non-polio human enteroviruses are the leading cause of aseptic meningitis in children. The role of enterovirus PCR for diagnosis and management of aseptic meningitis has not been fully explored. METHODOLOGY/PRINCIPAL FINDINGS: A retrospective study was conducted to determine the epidemiological, clinical, and laboratory characteristics of aseptic meningitis and to evaluate the role of enterovirus PCR for the diagnosis and management of this clinical entity. The medical records of children who had as discharge diagnosis aseptic or viral meningitis were reviewed. A total of 506 children, median age 5 years, were identified. The annual incidence rate was estimated to be 17/100,000 children less than 14 years of age. Most of the cases occurred during summer (38%) and autumn (24%). The dominant clinical symptoms were fever (98%), headache (94%) and vomiting (67%). Neck stiffness was noted in 60%, and irritation in 46% of the patients. The median number of CSF cell count was 201/mm(3) with polymorphonuclear predominance (>50%) in 58.3% of the cases. Enterovirus RNA was detected in CSF in 47 of 96 (48.9%) children tested. Children with positive enterovirus PCR had shorter hospitalization stay as compared to children who had negative PCR or to children who were not tested (P = 0.01). There were no serious complications or deaths. CONCLUSIONS: Enteroviruses accounted for approximately one half of cases of aseptic meningitis. PCR may reduce the length of hospitalization and plays important role in the diagnosis and management of children with aseptic meningitis

Physisorption-based charge transfer in two-dimensional SnS2 for selective and reversible NO2 gas sensing

Nitrogen dioxide (NO2) is a gas species that plays an important role in certain industrial, farming, and healthcare sectors. However, there are still significant challenges for NO2 sensing at low detection limits, especially in the presence of other interfering gases. The NO2 selectivity of current gas-sensing technologies is significantly traded-off with their sensitivity and reversibility as well as fabrication and operating costs. In this work, we present an important progress for selective and reversible NO2 sensing by demonstrating an economical sensing platform based on the charge transfer between physisorbed NO2 gas molecules and two-dimensional (2D) tin disulfide (SnS2) flakes at low operating temperatures. The device shows high sensitivity and superior selectivity to NO2 at operating temperatures of less than 160 °C, which are well below those of chemisorptive and ion conductive NO2 sensors with much poorer selectivity. At the same time, excellent reversibility of the sensor is demonstrated, which has rarely been observed in other 2D material counterparts. Such impressive features originate from the planar morphology of 2D SnS2 as well as unique physical affinity and favorable electronic band positions of this material that facilitate the NO2 physisorption and charge transfer at parts per billion levels. The 2D SnS2-based sensor provides a real solution for low-cost and selective NO2 gas sensing

An outbreak of aseptic meningitis due to echovirus 30 associated with attending school and swimming in pools

Summary Objectives To identify the risk factors of an outbreak of meningitis associated with echovirus 30-infection that occurred in Rome, Italy, in late 1997 among children from two different schools. Methods A case-control study was carried out. A case was defined as a child from either of the two schools, A or B, who presented meningitis-like (fever, headache and vomiting), diarrhea, or respiratory tract symptoms. All asymptomatic students were included in the analysis as controls. Results Among 446 pupils (80%) who answered the questionnaire, 68 met the case definition. Twenty pupils developed a meningitis-like illness. Echovirus 30 was isolated from cerebrospinal fluid (CSF) in four and from stools in six. Forty-eight pupils reported other symptoms. The attack rate was 10.8% in school A and 0.8% in school B for meningitis-like illness; it was 12% and 10%, respectively, for other enterovirus-like illnesses. The risk of meningitis-like illness was higher among children attending school A (crude OR=14.9; 95% CI=4.3–52.1), among children using any public pool (OR=3.8; 95% CI=1.5–9.9) and those using an outside swimming pool X (OR=13.4; 95% CI=2.7–65.8 versus no swimming pool and OR=8.3; 95% CI=1.1–62.6 versus other pools). The epidemic curve appears to suggest a person-to-person transmission. Conclusions The epidemic occurred by person-to-person transmission in a number of classrooms and at swimming pool X

Inhibition of Enterovirus 71 (EV-71) Infections by a Novel Antiviral Peptide Derived from EV-71 Capsid Protein VP1

Enterovirus 71 (EV-71) is the main causative agent of hand, foot and mouth disease (HFMD). In recent years, EV-71 infections were reported to cause high fatalities and severe neurological complications in Asia. Currently, no effective antiviral or vaccine is available to treat or prevent EV-71 infection. In this study, we have discovered a synthetic peptide which could be developed as a potential antiviral for inhibition of EV-71. Ninety five synthetic peptides (15-mers) overlapping the entire EV-71 capsid protein, VP1, were chemically synthesized and tested for antiviral properties against EV-71 in human Rhabdomyosarcoma (RD) cells. One peptide, SP40, was found to significantly reduce cytopathic effects of all representative EV-71 strains from genotypes A, B and C tested, with IC50 values ranging from 6–9.3 µM in RD cells. The in vitro inhibitory effect of SP40 exhibited a dose dependent concentration corresponding to a decrease in infectious viral particles, total viral RNA and the levels of VP1 protein. The antiviral activity of SP40 peptide was not restricted to a specific cell line as inhibition of EV-71 was observed in RD, HeLa, HT-29 and Vero cells. Besides inhibition of EV-71, it also had antiviral activities against CV-A16 and poliovirus type 1 in cell culture. Mechanism of action studies suggested that the SP40 peptide was not virucidal but was able to block viral attachment to the RD cells. Substitutions of arginine and lysine residues with alanine in the SP40 peptide at positions R3A, R4A, K5A and R13A were found to significantly decrease antiviral activities, implying the importance of positively charged amino acids for the antiviral activities. The data demonstrated the potential and feasibility of SP40 as a broad spectrum antiviral agent against EV-71

Acyclovir for treating varicella in otherwise healthy children and adolescents: a systematic review of randomised controlled trials

BACKGROUND: Acyclovir has the potential to shorten the course of chickenpox which may result in reduced costs and morbidity. We conducted a systematic review of randomised controlled trials that evaluated acyclovir for the treatment of chickenpox in otherwise healthy children. METHODS: MEDLINE, EMBASE, and the Cochrane Library were searched. The reference lists of relevant articles were examined and primary authors and Glaxo Wellcome were contacted to identify additional trials. Two reviewers independently screened studies for inclusion, assessed study quality using the Jadad scale and allocation concealment, and extracted data. Continuous data were converted to a weighted mean difference (WMD). Overall estimates were not calculated due to differences in the age groups studied. RESULTS: Three studies were included. Methodological quality was 3 (n = 2) and 4 (n = 1) on the Jadad scale. Acyclovir was associated with a significant reduction in the number of days with fever, from -1.0 (95% CI -1.5,-0.5) to -1.3 (95% CI -2.0,-0.6). Results were inconsistent with respect to the number of days to no new lesions, the maximum number of lesions and relief of pruritis. There were no clinically important differences between acyclovir and placebo with respect to complications or adverse effects. CONCLUSION: Acyclovir appears to be effective in reducing the number of days with fever among otherwise healthy children with chickenpox. The results were inconsistent with respect to the number of days to no new lesions, the maximum number of lesions and the relief of itchiness. The clinical importance of acyclovir treatment in otherwise healthy children remains controversial

A Retrospective Overview of Enterovirus Infection Diagnosis and Molecular Epidemiology in the Public Hospitals of Marseille, France (1985–2005)

Human enteroviruses (HEV) are frequent human pathogens and, associated in particular with large outbreaks of aseptic meningitis. Here, we have compiled a database of clinical HEV isolates from the Public Hospitals of Marseille, from 1985 to 2005. Amongst 654 isolates that could be characterized by complete sequencing of the VP1 gene, 98% belonged to species HEV-B; the most frequently isolated serotypes were Echovirus E30, E11, E7, E6 and E4. The high incidence of E30 and the recent emergence of E13 are consistent with reports worldwide and peak HEV isolation occurred mostly in the late spring and summer months. The proportion of echoviruses has decreased across the years, while that of coxsackieviruses has increased. Stool (the most frequent sample type) allowed detection of all identified serotypes. MRC5 (Human lung fibroblasts) cell line was the most conducive cell line for HEV isolation (84.9% of 10 most common serotype isolates, 96.3% in association with BGM (Buffalo green monkey kidney cells)). Previous seroneutralization-based serotype identification demonstrated 55.4% accuracy when compared with molecular VP1 analysis. Our analysis of a large number of clinical strains over 20 years reinforced the validity of VP1 serotyping and showed that comparative p-distance scores can be coupled with phylogenetic analysis to provide non-ambiguous serotype identification. Phylogenetic analysis in the VP1, 2C and 3D regions also provided evidence for recombination events amongst clinical isolates. In particular, it identified isolates with dissimilar VP1 but almost identical nonstructural regions

A Diverse Group of Previously Unrecognized Human Rhinoviruses Are Common Causes of Respiratory Illnesses in Infants

Human rhinoviruses (HRVs) are the most prevalent human pathogens, and consist of 101 serotypes that are classified into groups A and B according to sequence variations. HRV infections cause a wide spectrum of clinical outcomes ranging from asymptomatic infection to severe lower respiratory symptoms. Defining the role of specific strains in various HRV illnesses has been difficult because traditional serology, which requires viral culture and neutralization tests using 101 serotype-specific antisera, is insensitive and laborious.To directly type HRVs in nasal secretions of infants with frequent respiratory illnesses, we developed a sensitive molecular typing assay based on phylogenetic comparisons of a 260-bp variable sequence in the 5' noncoding region with homologous sequences of the 101 known serotypes. Nasal samples from 26 infants were first tested with a multiplex PCR assay for respiratory viruses, and HRV was the most common virus found (108 of 181 samples). Typing was completed for 101 samples and 103 HRVs were identified. Surprisingly, 54 (52.4%) HRVs did not match any of the known serotypes and had 12-35% nucleotide divergence from the nearest reference HRVs. Of these novel viruses, 9 strains (17 HRVs) segregated from HRVA, HRVB and human enterovirus into a distinct genetic group ("C"). None of these new strains could be cultured in traditional cell lines.By molecular analysis, over 50% of HRV detected in sick infants were previously unrecognized strains, including 9 strains that may represent a new HRV group. These findings indicate that the number of HRV strains is considerably larger than the 101 serotypes identified with traditional diagnostic techniques, and provide evidence of a new HRV group

Identification of Resource Use and Associated Costs for Viral Meningitis

ABSTRACT Purpose: This study involved identifying resource use and assigning monetary value to the diagnostic work-up and management of viral meningitis. Methodology: Using a previously established decision analytic framework, various resources were identified as part of routine management of viral meningitis. Secondary database analyses were used to quantify resources and assign a monetary value as a part of routine management of viral meningitis requiring use of the resource units identified in the decision analytic framework. Discharge data sources from the states of California, Florida, and Illinois, and Medicaid data sources from the state of Pennsylvania, were used for the purpose of analysis. Principal Findings: Physician visits, emergency room visits, hospital admissions, procedures, and medications were identified as the major resources used. Lumbar punctures, CT scans, and antibiotics were identified as the major procedures and medications utilized. No significant difference was found in the major resources used between the states' discharge data and the Medicaid data sources. The mean total charges for patient admissions with CT scans were significantly higher than for patient admissions without CT scans ($11,531.80 vs.$7,841.30, P<0.05). The mean lengths of stay for patients with CT scan were significantly higher than for patient admissions without CT scans (4.71 days vs. 3.88 days, P<0.05). The patient readmission rate was 10.7 percent, while the readmission rate for episodes with more than one hospitalization was 11.1 percent. The mean charge associated with readmission was $12,200