Crystal Structures of Influenza A Virus Matrix Protein M1: Variations on a Theme

Matrix protein 1 (M1) of the influenza A virus plays multiple roles in virion assembly and infection. Interest in the pH dependence of M1\u27s multiple functions led us to study the effect of subtle pH changes on M1 structure, resulting in the elucidation of a unique low-pH crystal structure of the N1-165-domain of A/WSN/33 (H1N1) M1 that has never been reported. Although the 2.2 Å crystal structure of M1 N-terminus shows a dimer with the two monomers interacting in a face-to-face fashion at low pH as observed earlier, a 44° rotation of the second monomer has led to a significantly different dimer interface that possibly affects dimer stability. More importantly, while one of the monomers is fully defined, the N-terminal half of the second monomer shows considerable disorder that appears inherent in the protein and is potentially physiologically relevant. Such disorder has not been observed in any other previously reported structure at either low or high pH conditions, despite similar crystallization pH conditions. By comparing our novel N1-165-domain structure with other low-pH or neutral-pH M1 structures, it appears that M1 can energetically access different monomer and dimer conformations, as well as oligomeric states, with varying degree of similarities. The study reported here provides further insights into M1 oligomerization that may be essential for viral propagation and infectivity

Effect of Lignin Variation on Biomass Conversion: An analysis of pretreatment methods for poplar samples

The conversion of lignocellulosic polysaccharides has been studied as an alternative to petroleum for producing fuels and chemical products, such as those in plastics. However, biomass lignin has been shown to inhibit polysaccharide conversion. Lignin, an organic polymer, surrounds biomass polysaccharides, hemicellulose and cellulose, making the biomass resistant to deconstruction and limiting polysaccharide conversion yields. Increases in polysaccharide conversion yields are seen when using physical or chemical pretreatment methods that increase convertible cellulose, remove lignin, and restructure biomass. A physical pretreatment, liquid hot water (LHW), solubilizes hemicellulose and melts lignin using hot, pressured water. A chemical treatment, sodium-chlorite acetic acid (SCAA), uses a strong oxidizing agent coupled with acid to chemically remove the lignin. This study analyzed LHW and SCAA pretreatments, each at two levels of severity, for aiding in deconstruction of wild type poplar biomass and poplar genetically modified for increased lignin digestibility. Following pretreatments, biomass composition was analyzed via a standard method using a combination of acid hydrolysis deconstruction and biomass fractionation. We report that increasing length of SCAA treatments shows sequential reduction in total lignin (11.8%, 8.0%) when compared to untreated biomass (23.1%) and provides an average 27.3% increase in the portion of total lignin that is acid digestible. LHW pretreatments increase the proportion of available glucan for conversion while minimally changing biomass structure in contrast to the SCAA treatment which largely alters biomass composition. Reported biomass composition changes suggest that pretreatments used with previously studied biomass conversion methods increase polysaccharide conversion yields to value added chemicals

Why Are People's Decisions Sometimes Worse with Computer Support?

In many applications of computerised decision support, a recognised source of undesired outcomes is operators' apparent over-reliance on automation. For instance, an operator may fail to react to a potentially dangerous situation because a computer fails to generate an alarm. However, the very use of terms like "over-reliance" betrays possible misunderstandings of these phenomena and their causes, which may lead to ineffective corrective action (e.g. training or procedures that do not counteract all the causes of the apparently "over-reliant" behaviour). We review relevant literature in the area of "automation bias" and describe the diverse mechanisms that may be involved in human errors when using computer support. We discuss these mechanisms, with reference to errors of omission when using "alerting systems", with the help of examples of novel counterintuitive findings we obtained from a case study in a health care application, as well as other examples from the literature

Pollution Abatement from Cattle Feedlots in Northeastern Colorado and Nebraska

Climatic factors, feedlot runoff, and organic material in the runoff were evaluated in experimental and commercial feedlots. The effects of slope, stocking rates, terraces, basins, and holding ponds were evaluated to obtain the best controls for containing runoff. In eastern Nebraska, 70 cm annual precipitation produces 23 cm of runoff; whereas, in northeastern Colorado, 37 cm annual precipitation gives only 5.5 cm of runoff. Large applications of runoff liquid, up to 91 cmon grass-Ladino and 76 cm on corn, in Nebraska did not decrease yields; however, in northeastern Colorado, the concentrated high-salt runoff required dilution before direct application to crops. The organic manure-soil interface severely restricts the movement of water, nitrates, organic substances, and air into the soil beneath feedlots. The amounts of N03-N in soil cores taken from Nebraska feedlots and croplands ranked as follows: abandoned feedlots\u3e feedlot cropland\u3e upland feedlots\u3e river valley feedlots\u3e manure mounds\u3e alfalfa\u3e grassland. Feedlots contribute NH3, amines, carbonyl sulfide, H2S, and other unidentified substances to the atmosphere. Ammonia and amine can be scavenged from the air by green plants and water bodies. Anaerobic conditions in feedlots are conducive to the production of carbonyl sulfide, H2S, and amines. Management practices, such as good drainage, that enhance aeration will decrease the evolution of these compounds

Machine-Part cell formation through visual decipherable clustering of Self Organizing Map

Machine-part cell formation is used in cellular manufacturing in order to process a large variety, quality, lower work in process levels, reducing manufacturing lead-time and customer response time while retaining flexibility for new products. This paper presents a new and novel approach for obtaining machine cells and part families. In the cellular manufacturing the fundamental problem is the formation of part families and machine cells. The present paper deals with the Self Organising Map (SOM) method an unsupervised learning algorithm in Artificial Intelligence, and has been used as a visually decipherable clustering tool of machine-part cell formation. The objective of the paper is to cluster the binary machine-part matrix through visually decipherable cluster of SOM color-coding and labelling via the SOM map nodes in such a way that the part families are processed in that machine cells. The Umatrix, component plane, principal component projection, scatter plot and histogram of SOM have been reported in the present work for the successful visualization of the machine-part cell formation. Computational result with the proposed algorithm on a set of group technology problems available in the literature is also presented. The proposed SOM approach produced solutions with a grouping efficacy that is at least as good as any results earlier reported in the literature and improved the grouping efficacy for 70% of the problems and found immensely useful to both industry practitioners and researchers.Comment: 18 pages,3 table, 4 figure

A Study of Brain Networks Associated with Swallowing Using Graph-Theoretical Approaches

Functional connectivity between brain regions during swallowing tasks is still not well understood. Understanding these complex interactions is of great interest from both a scientific and a clinical perspective. In this study, functional magnetic resonance imaging (fMRI) was utilized to study brain functional networks during voluntary saliva swallowing in twenty-two adult healthy subjects (all females, 23.1±1.52 years of age). To construct these functional connections, we computed mean partial correlation matrices over ninety brain regions for each participant. Two regions were determined to be functionally connected if their correlation was above a certain threshold. These correlation matrices were then analyzed using graph-theoretical approaches. In particular, we considered several network measures for the whole brain and for swallowing-related brain regions. The results have shown that significant pairwise functional connections were, mostly, either local and intra-hemispheric or symmetrically inter-hemispheric. Furthermore, we showed that all human brain functional network, although varying in some degree, had typical small-world properties as compared to regular networks and random networks. These properties allow information transfer within the network at a relatively high efficiency. Swallowing-related brain regions also had higher values for some of the network measures in comparison to when these measures were calculated for the whole brain. The current results warrant further investigation of graph-theoretical approaches as a potential tool for understanding the neural basis of dysphagia. © 2013 Luan et al

Lactic acid production from lime-treated wheat straw by Bacillus coagulans: neutralization of acid by fed-batch addition of alkaline substrate

Conventional processes for lignocellulose-to-organic acid conversion requires pretreatment, enzymatic hydrolysis, and microbial fermentation. In this study, lime-treated wheat straw was hydrolyzed and fermented simultaneously to lactic acid by an enzyme preparation and Bacillus coagulans DSM 2314. Decrease in pH because of lactic acid formation was partially adjusted by automatic addition of the alkaline substrate. After 55 h of incubation, the polymeric glucan, xylan, and arabinan present in the lime-treated straw were hydrolyzed for 55%, 75%, and 80%, respectively. Lactic acid (40.7 g/l) indicated a fermentation efficiency of 81% and a chiral l(+)-lactic acid purity of 97.2%. In total, 711 g lactic acid was produced out of 2,706 g lime-treated straw, representing 43% of the overall theoretical maximum yield. Approximately half of the lactic acid produced was neutralized by fed-batch feeding of lime-treated straw, whereas the remaining half was neutralized during the batch phase with a Ca(OH)2 suspension. Of the lime added during the pretreatment of straw, 61% was used for the neutralization of lactic acid. This is the first demonstration of a process having a combined alkaline pretreatment of lignocellulosic biomass and pH control in fermentation resulting in a significant saving of lime consumption and avoiding the necessity to recycle lime

HIV-1 Entry, Inhibitors, and Resistance

Entry inhibitors represent a new class of antiretroviral agents for the treatment of infection with HIV-1. While resistance to other HIV drug classes has been well described, resistance to this new class is still ill defined despite considerable clinical use. Several potential mechanisms have been proposed: tropism switching (utilization of CXCR4 instead of CCR5 for entry), increased affinity for the coreceptor, increased rate of virus entry into host cells, and utilization of inhibitor-bound receptor for entry. In this review we will address the development of attachment, fusion, and coreceptor entry inhibitors and explore recent studies describing potential mechanisms of resistance

Technologies, Policies, and Measures for Mitigating Climate Change

This Technical Paper provides an overview and analysis of technologies and measures to limit and reduce greenhouse gas (GHG) emissions and to enhance GHG sinks under the United Nations Framework Convention on Climate Change (FCCC). The paper focuses on technologies and measures for the countries listed in Annex I of the FCCC, while noting information as appropriate for use by non- Annex I countries. Technologies and measures are examined over three time periods -- with a focus on the short term (present to 2010) and the medium term (2010-2020), but also including discussion of longer-term (e.g., 2050) possibilities and opportunities. For this analysis, the authors draw on materials used to prepare the IPCC Second Assessment Report (SAR) and previous IPCC assessments and reports. The Technical Paper includes discussions of technologies and measures that can be adopted in three energy end-use sectors (commercial/residential/institutional buildings, transportation, and industry), as well as in the energy supply sector and the agriculture, forestry, and waste management sectors. Broader measures affecting national economies are discussed in a final section on economic instruments. A range of potential measures are analyzed, including market-based programs; voluntary agreements; regulatory measures; research, development, and demonstration (RD&D); taxes on GHG emissions; and emissions permits/quotas. It should be noted that the choice of instruments could have economic impacts on other countries. The paper identifies and evaluates different options on the basis of three criteria. Because of the difficulty of estimating the economic and market potential (see Box 1) of different technologies and the effectiveness of different measures in achieving emission reduction objectives, and because of the danger of double-counting the results achieved by measures that tap the same technical potentials, the paper does not estimate total global emissions reductions. Nor does the paper recommend adoption of any particular approaches