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Search Results: 1 - 10 of 191973 matches for " Micah D Halpern "
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Comparative Analysis of the Full-Length Genome Sequence of a Clinical Isolate of Human Parainfluenza Virus 4B
John A. Lednicky,Thomas B. Waltzek,Micah D. Halpern,Sara B. Hamilton
Scientifica , 2012, DOI: 10.6064/2012/871201
Comparative Analysis of the Full-Length Genome Sequence of a Clinical Isolate of Human Parainfluenza Virus 4B
John A. Lednicky,Thomas B. Waltzek,Micah D. Halpern,Sara B. Hamilton
Scientifica , 2012, DOI: 10.6064/2012/871201
Abstract: We are engaged in airborne transmission and epidemiology studies of respiratory pathogens, with particular interest in human parainfluenza virus type 4 (hPIV-4) and other lesser studied viruses. In this paper, hPIV-4 was detected in primary rhesus monkey kidney (PRMK) cells that had been inoculated with nasopharyngeal swab material obtained from a child with a mild upper respiratory tract illness. Attempts to isolate the virus in pure culture were hampered by the presence of a fast-growing simian spumavirus that was a contaminant of the PRMK cells. Total RNA was extracted from the PRMK cell culture, and PCR followed by sequencing of a subgenomic section of the fusion protein gene suggested the hPIV-4 was subtype 4B. At the time of this work, two complete but dissimilar hPIV-4B genomes had been deposited by others in GenBank. To gain better insights on hPIV-4B, and to test methods that we are developing for viral forensics, the entire genomic sequence of our virus was determined from archived RNA. The hPIV-4B genomic sequence that we determined conforms to the paramyxovirus “rule of six.” Here, we compare and contrast the genetic features of the three completely sequenced hPIV-4B genomes currently present in GenBank. Human parainfluenza viruses (hPIVs) are single-stranded, negative sense RNA viruses of the genus Rubulavirus, family Paramyxoviridae, which cause acute respiratory tract infections in children and adults. Four hPIV serotypes (hPIV 1–4) have been identified; serotype 4 is further subdivided into two antigenic subtypes: 4A and 4B [1, 2]. The epidemiology and clinical manifestations of hPIV 1–3 are well known, whereas comparatively little is known about hPIV4s, as they are difficult to isolate in cell culture and are absent from routine respiratory virus detection tests in most clinical virology laboratories [3–5]. Whereas hPIV4s were formerly mostly associated with mild respiratory illnesses in young people, recent studies indicate the viruses can cause more severe infections such as pneumonia in young and older patients (mentioned in [3–5]). The genomic cRNAs of hPIV-4 subtypes 4A and B are a little >17.0?kbp in length. Their viral genomes encode for nucleocapsid (NP), phospho (P), nonstructural (V), matrix (M), fusion (F), haemagglutinin-neuraminidase (HN), and large (L) proteins. Prior to this work, there were two complete hPIV-4B sequences in GenBank: those of strains 68–333 [6] and SKPIV-4 [7]. Primary monkey kidney (PMK) cells are inoculated with appropriate specimens for the detection of human parainfluenza viruses in many American
Gas-permeable ethylene bags for the small scale cultivation of highly pathogenic avian influenza H5N1 and other viruses in embryonated chicken eggs
Sara B Hamilton, Deirdre E Daniels, William A Sosna, Eric R Jeppesen, Julie M Owells, Micah D Halpern, Kimberly S McCurdy, Jonathan O Rayner, John A Lednicky
Virology Journal , 2010, DOI: 10.1186/1743-422x-7-23
Abstract: Virus yields acceptable for many applications were attained when influenza-, alpha-, flavi-, canine distemper-, and mousepox viruses were propagated in ECE sealed within ethylene breather bags.For many small-scale applications, ethylene breather bags can be used to encase ECE inoculated with various viruses.Embryonated (embryonating) chicken eggs (ECE) have long been used for isolating or propagating influenza and other viruses and certain bacteria such as Rickettsia [1-5]. Alpha-, corona-, flavi-, paramyxo-, and poxviruses are among the non-influenza viruses sometimes grown in ECE. For small-scale work with pathogens that must be worked with in BSL3 facilities, inoculated ECE are sometimes housed in small egg incubators kept within a BSC [such a practice is not practical for medium-to-large diagnostic operations, wherein ECE are placed in incubators within a bioBubble (Ft. Collins, CO) or similar barrier and containment enclosure]. Since ECE are fragile, accidental egg breakage is possible. Furthermore, diagnostic specimens inoculated into ECE may contain contaminating flora that form enough gas to break the egg shell. We sought a simple method to contain spillage from a broken ECE inoculated with dangerous pathogens, and explored the feasibility of using ethylene breather bags for that purpose. Ethylene breather bags are permeable to oxygen and carbon dioxide but retain water, and are used in the aquarium industry to transport live fish. Chicken embryo survival was examined and the yield of various influenza and other viruses in bagged eggs was determined.No differences were detected in the survival of chicken embryos in bagged vs non-bagged 7 - 12 day old ECE after five days of incubation without rotation as performed for virus-inoculated ECE. Noteworthy, especially during summer months, up to 20% attrition (death of non-inoculated ECE) occurred with some batches, regardless of whether the ECE were bagged or not bagged. Since the ECE are checked and culled if dea
Switchgrass (Panicum virgatum) Fermentation by Clostridium thermocellum and Clostridium beijerinckii Sequential Culture: Effect of Feedstock Particle Size on Gas Production  [PDF]
Michael D. Flythe, Noelia M. Elía, Micah B. Schmal, Sue E. Nokes
Advances in Microbiology (AiM) , 2015, DOI: 10.4236/aim.2015.55031
Abstract: Fermentation of cellulosic biomass can be done in a single step with cellulolytic, solventogenic bacteria, such as Clostridium thermocellum. However, the suite of products is limited in consolidated bioprocessing. Fortunately, the thermophilic nature of C. thermocellum can be exploited in sequential culture. Experiments were conducted to determine the effect of feedstock particle size on fermentation by sequential cultures and to demonstrate this effect could be shown by gas production. Dual-temperature sequential cultures were conducted by first culturing with C. thermocellum (63°C, 48 h) before culturing with C. beijerinckii (35°C, 24 h). Switchgrass (2, 5 or 15 mm particle size) was the feedstock in submerged substrate (10% w/v) fermentation. The extent of fermentation was evaluated by gas production and compared by analysis of variance with Tukey’s test post hoc. C. thermocellum alone produced 78 kPa cumulative pressure (approx. 680 mL gas) when the particle size was 2 or 5 mm. The C. thermocellum cultures with 15 mm feedstock particles had a mean cumulative pressure of 15 kPa after 48 h, which was less than the 2 and 5 mm treatments (P < 0.05). When the culture vessels were cooled (to 35°C) and inoculated with C. beijerinckii, and the cumulative pressures were reset to ambient, cumulative pressure values as great as 70 kPa (equivalent to an additional 670 mL gas) were produced in 24 h. Again, the longer (15 mm) particle size produced less gas (P < 0.05). When the substrates were inoculated with C. beijerinckii without previous fermentation by C. thermocellum, the mean cumulative pressures were approximately 10 kPa. These results indicate that biological pretreatment with C. thermocellum increased the availability of switchgrass carbohydrates to C. beijerinckii, and that gas production is suitable method to show the effectiveness of a pretreatment.
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Micah Hamady, M D Betterton, Rob Knight
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-476
Abstract: First, we introduce a new class of methods for detecting HGT based on the changes in nucleotide substitution rates that occur when a gene is transferred to a new organism. Our new methods discriminate simulated HGT events with an error rate up to 10 times lower than does GC content. Use of models that are not time-reversible is crucial for detecting HGT. Second, we show that using combinations of multiple predictors of HGT offers substantial improvements over using any single predictor, yielding as much as a factor of 18 improvement in performance (a maximum reduction in error rate from 38% to about 3%). Multiple predictors were combined by using the random forests machine learning algorithm to identify optimal classifiers that separate HGT from non-HGT trees.The new class of HGT-detection methods introduced here combines advantages of phylogenetic and compositional HGT-detection techniques. These new techniques offer order-of-magnitude improvements over compositional methods because they are better able to discriminate HGT from non-HGT trees under a wide range of simulated conditions. We also found that combining multiple measures of HGT is essential for detecting a wide range of HGT events. These novel indicators of horizontal transfer will be widely useful in detecting HGT events linked to the evolution of important bacterial traits, such as antibiotic resistance and pathogenicity.Horizontal gene transfer (HGT) has distributed genes that are required for pathogenicity among many bacterial lineages [1-4]. HGT, also known as lateral gene transfer, occurs when genes move between different genomes. Transfers can occur both between closely and distantly related species or strains, and are thought to be frequent events. For example, marine bacteriophages alone have been estimated to cause 2 × 1016 horizontal transfer events per second [5]. Most of these horizontally transferred genes are lost from the population through drift or selection. However, under extreme select
The Complex Structure of Receptive Fields in the Middle Temporal Area
Micah Richert,Thomas D. Albright,Bart Krekelberg
Frontiers in Systems Neuroscience , 2013, DOI: 10.3389/fnsys.2013.00002
Abstract: Neurons in the middle temporal area (MT) are often viewed as motion detectors that prefer a single direction of motion in a single region of space. This assumption plays an important role in our understanding of visual processing, and models of motion processing in particular. We used extracellular recordings in area MT of awake, behaving monkeys (M. mulatta) to test this assumption with a novel reverse correlation approach. Nearly half of the MT neurons in our sample deviated significantly from the classical view. First, in many cells, direction preference changed with the location of the stimulus within the receptive field. Second, the spatial response profile often had multiple peaks with apparent gaps in between. This shows that visual motion analysis in MT has access to motion detectors that are more complex than commonly thought. This complexity could be a mere byproduct of imperfect development, but can also be understood as the natural consequence of the non-linear, recurrent interactions among laterally connected MT neurons. An important direction for future research is to investigate whether these in homogeneities are advantageous, how they can be incorporated into models of motion detection, and whether they can provide quantitative insight into the underlying effective connectivity.
Scaling state of dry two-dimensional froths: universal angle deviations and structure
Andrew D. Rutenberg,Micah B. McCurdy
Physics , 2005, DOI: 10.1103/PhysRevE.73.011403
Abstract: We characterize the late-time scaling state of dry, coarsening, two-dimensional froths using a detailed, force-based vertex model. We find that the slow evolution of bubbles leads to systematic deviations from 120degree angles at three-fold vertices in the froth, with an amplitude proportional to the vertex speed, v ~ sqrt(t), but with a side-number dependence that is independent of time. We also find that a significant number of T1 side-switching processes occur for macroscopic bubbles in the scaling state, though most bubble annihilations involve four-sided bubbles at microscopic scales.
Diversions: Obstacles for Undergraduate Students when Applying for Internship Positions Online  [PDF]
Clarisse Halpern, Bruno Halpern
Open Journal of Business and Management (OJBM) , 2018, DOI: 10.4236/ojbm.2018.61011
The objective of this research was to investigate how the decision of Brazilian university students to enroll (or not) in internships’ selection processes would be affected by the form and content of the ads published in social media. Thus, a qualitative research was carried out through a multiple-case study. Data were collected in semi-structured interviews via Skype, as well as direct observations of eight individuals. The category?Diversions presented the most relevant results shedding light as to how the interviewees’ focus was shifted while searching for internship positions during their interviews. The title refers to how distractions make students stray from their intended search for internship positions. Instead, social media exerts a sort of magnetism that is more powerful than recruiting posts and ads, attracting their attention away from internship openings search, making them secondary. In conclusion, diversions were found to become obstacles for undergraduate students when applying for internship positions online.
Trade Liberalization and Tax Revenue Performance in Uganda  [PDF]
Micah Samuel Gaalya
Modern Economy (ME) , 2015, DOI: 10.4236/me.2015.62021
Abstract: The study uses fixed and random effects models to establish the determinants of tax revenue performance. The data cover the period 1994 to 2012, with the results suggesting that exchange rates, trade openness and share of industry to GDP positively influence tax revenue performance while the agriculture share to GDP and foreign aid negatively influence tax revenue performance. Importantly the coefficient for trade openness that is used as a proxy for trade liberalization indicates a positive influence on tax revenue performance.
Trade Liberalization and Disaggregated Import Demand in Uganda  [PDF]
Gaalya Micah Samuel
Modern Economy (ME) , 2015, DOI: 10.4236/me.2015.63030
Abstract: Studies investigating determinants of import demand for Uganda present aggregate findings yet there is a need to disaggregate the findings for specific sectors. This creates a research gap on disaggregated findings of import demand. This research attempts to fill this research gap by establishing determinants of import demand using disaggregated sector level data for consumer, intermediate and capital goods. The study estimates the long-run and short-run import demand elasticities for consumer, intermediate and capital goods over the period (1994 to 2012). The results show that there exists a cointegrating relationship between the disaggregated import demand and the following set of variables; relative import price, GDP per capita, real effective exchange rate, foreign exchange rate reserves and trade openness. The long run elasticity appears more responsive to import demand compared to the short-run elasticity. Importantly the effect of a change in trade openness on the volume of imports is positive, suggesting trade liberalization increases import demand.
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