An Efficient Algorithm For Chinese Postman Walk on Bi-directed de Bruijn Graphs

Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double stranded DNA string (SDDNA) containing all the k-long words in the reads seems to be a good heuristic to get close to the original genome. This problem is equivalent to finding a cyclic Chinese Postman (CP) walk on the underlying un-weighted bi-directed de Bruijn graph built from the reads. The Chinese Postman walk Problem (CPP) is solved by reducing it to a general bi-directed flow on this graph which runs in O(|E|2 log2(|V |)) time. In this paper we show that the cyclic CPP on bi-directed graphs can be solved without reducing it to bi-directed flow. We present a ?(p(|V | + |E|) log(|V |) + (dmaxp)3) time algorithm to solve the cyclic CPP on a weighted bi-directed de Bruijn graph, where p = max{|{v|din(v) - dout(v) > 0}|, |{v|din(v) - dout(v) < 0}|} and dmax = max{|din(v) - dout(v)}. Our algorithm performs asymptotically better than the bidirected flow algorithm when the number of imbalanced nodes p is much less than the nodes in the bi-directed graph. From our experimental results on various datasets, we have noticed that the value of p/|V | lies between 0.08% and 0.13% with 95% probability

A Brief Discussion of Radiation Hardening of CMOS Microelectronics

Commercial microchips work well in their intended environments. However, generic microchips will not fimction correctly if exposed to sufficient amounts of ionizing radiation, the kind that satellites encounter in outer space. Modern CMOS circuits must overcome three specific concerns from ionizing radiation: total-dose, single-event, and dose-rate effects. Minority-carrier devices such as bipolar transistors, optical receivers, and solar cells must also deal with recombination-generation centers caused by displacement damage, which are not major concerns for majority-carrier CMOS devices. There are ways to make the chips themselves more resistant to radiation. This extra protection, called radiation hardening, has been called both a science and an art. Radiation hardening requires both changing the designs of the chips and altering the ways that the chips are manufactured

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Transitions between lifetime alcohol use, regular use and remission: Results from the 2004 South African Stress and Health Survey

Background. Hazardous alcohol consumption presents a serious threat to the health and wellbeing of all people and is linked to chronic and acute health problems.Objectives. To: (i) estimate the prevalence of alcohol use disorders and remission from alcohol abuse and dependence in the South African (SA) population; and (ii) determine whether age of onset, education, sex and level of cohort alcohol use are associated with commencement of use, regularity of use, and transitions to and remission from more harmful levels of use.Methods. The study was a nationally representative sample of 4 315  individuals aged ≥18 years. In a multistage, area probability sample of adults, data were collected from 4 311 alcohol users using the World Mental Health Survey Initiative version of the Composite International Diagnostic Interview version 3.0. All analyses were carried out using SAS version 9.4.Results. Of the respondents, 40.6% indicated lifetime use of alcohol,  35.3% reported regular use, and 8.8% met diagnostic criteria for alcohol abuse and 2.7% for alcohol dependence. The prevalence of remission from lifetime abuse without dependence was 55.9%. The median age of onset of alcohol use was 20 years, with transition from use to regular use occurring within ~1 - 3 years. The results suggest that males, students (compared with those who had completed a high level of education) and greater  alcohol use in the respondent’s birth cohort were all associated with increased odds of commencing alcohol use. For transitions from use to regular use, increased odds were associated with males, greater birth cohort alcohol use, low education and later (&gt;21 years) onset of first alcohol use.Conclusions. Our findings suggest that cohort alcohol use is associated with transition to commencement of use and from use to regular use in the general SA population. The study further highlighted the need for  interventions among males and university students, given that hazardous alcohol consumption seems to be the most prevalent public health issue encountered by university students and males

Surface selective membranes for carbon dioxide separation

In this study, hybrid membranes have been developed for the selective separation of CO2 from mixtures containing H2. Beginning with commercially available Pall alumina membrane tubes with nominal pore diameter of 5 nm, hybrids were produced by silation with a variety of functionalities designed to facilitate the selective adsorption of CO2 onto the pore surface. The goal is to produce a membrane which can harness the power of surface diffusion to give the selectivity of polymer membranes with the permeance of inorganic membranes

Influences of atmospheric conditions and air mass on the ratio of ultraviolet to total solar radiation

The technology to detoxify hazardous wastes using ultraviolet (UV) solar radiation is being investigated by the DOE/SERI Solar Thermal Technology Program. One of the elements of the technology evaluation is the assessment and characterization of UV solar radiation resources available for detoxification processes. This report describes the major atmospheric variables that determine the amount of UV solar radiation at the earth&#x27;s surface, and how the ratio of UV-to-total solar radiation varies with atmospheric conditions. These ratios are calculated from broadband and spectral solar radiation measurements acquired at SERI, and obtained from the literature on modeled and measured UV solar radiation. The following sections discuss the atmospheric effects on UV solar radiation and provide UV-to-total solar radiation ratios from published studies, as well as measured values from SERI&#x27;s data. A summary and conclusions are also given

Diagnosis and treatment of pseudoachalasia: how to catch the mimic

Published: 25 June 2020Pseudoachalasia, or secondary achalasia, is an uncommon esophageal dysmotility syndrome with symptoms and manometric findings indistinguishable from primary achalasia, but due to any mechanism other than idiopathic degeneration of the inhibitory neurons of the esophageal submucosal myenteric plexus. Whilst pseudoachalasia is rare, affecting some 1.4–5.4% of all achalasia patients, it is essential this diagnosis is always considered and excluded, as the treatment and outcomes for these patients will be very different from those with true achalasia. Pseudoachalasia can be difficult to differentiate from primary or “idiopathic achalasia”. Several particular clinical features have been described as more common in patients with pseudoachalasia than in achalasia, but because of the low prevalence of this condition, the positive predictive value remains low. The majority of patients with pseudoachalasia have an underlying malignancy, predominantly gastro-esophageal adenocarcinoma, which is usually advanced. Management revolves around treating the underlying cause where possible, as this may lead to reversal of the esophageal dysmotility. In patients presenting with symptoms and manometry findings consistent with achalasia, the diagnosis initially should be one of an achalasia-like syndrome. Idiopathic achalasia can then only be confirmed after other potential causes have been considered and excluded. We describe a case of pseudoachalasia encountered in our clinical practice, followed by a review of current practice regarding diagnosis and management of pseudoachalasia.Dylan R. Barnett, George L. Balalis, Jennifer C. Myers, Peter G. Devit

Carbon Dioxide Separation with Supported Ionic Liquid Membranes

A practical form of CO2 capture at water-gas shift conditions in the IGCC process could serve the dual function of producing a pure CO2 stream for sequestration and forcing the equilibrium-limited shift reaction to completion enriching the stream in H2. The shift temperatures, ranging from the low temperature shift condition of 260°C to the gasification condition of 900°C, limit capture options by diminishing associative interactions which favor removal of CO2 from the gas stream. Certain sorption interactions, such as carbonate formation, remain available but generally involve exceptionally high sorbent regeneration energies that contribute heavily to parasitic power losses. Carbon dioxide selective membranes need only establish an equilibrium between the gas phase and sorption states in order to transport CO2, giving them a potential energetic advantage over other technologies. Supported liquid membranes take advantage of high, liquid phase diffusivities and a solution diffusion mechanism similar to that observed in polymeric membranes to achieve superior permeabilities and selectivites. The primary shortcoming of the supported liquid membranes demonstrated in past research has been the lack of stability caused by volatilization of the transport liquid. Ionic liquids, which possess high CO2 solubility relative to light gases such as H2, are excellent candidates for this type of membrane since they have negligible vapor pressure and are not susceptible to evaporation. A study has been conducted evaluating the use of ionic liquids including 1-hexyl-3-methyl-imidazolium bis(trifuoromethylsulfonyl)imide in supported ionic liquid membranes for the capture of CO2 from streams containing H2. In a joint project, researchers at the University of Notre Dame synthesized and characterized ionic liquids, and researchers at the National Energy Technology Laboratory incorporated candidate ionic liquids into supports and evaluated the resulting materials for membrane performance. Improvements to the ionic liquid and support have allowed testing of these supported ionic liquid membranes at temperatures up to 300°C without loss of support mechanical stability or degradation of the ionic liquid. Substantial improvements in selectivity have also been observed at elevated temperature with the best membrane currently achieving optimum performance at 75°C

Curved, extended classical solutions I. The undulating kink

The energy of extended classical objects, such as vortices, depends on their shape. In particular, we show that the curvature energy of a kink in two spatial dimensions, as a prototype of extended classical solutions, is always negative. We obtain a closed form for the curvature energy, assuming small deviations from the straight line.Comment: 7 pages, LaTe