A knowledge based software engineering environment testbed

The Carnegie Group Incorporated and Boeing Computer Services Company are developing a testbed which will provide a framework for integrating conventional software engineering tools with Artifical Intelligence (AI) tools to promote automation and productivity. The emphasis is on the transfer of AI technology to the software development process. Experiments relate to AI issues such as scaling up, inference, and knowledge representation. In its first year, the project has created a model of software development by representing software activities; developed a module representation formalism to specify the behavior and structure of software objects; integrated the model with the formalism to identify shared representation and inheritance mechanisms; demonstrated object programming by writing procedures and applying them to software objects; used data-directed and goal-directed reasoning to, respectively, infer the cause of bugs and evaluate the appropriateness of a configuration; and demonstrated knowledge-based graphics. Future plans include introduction of knowledge-based systems for rapid prototyping or rescheduling; natural language interfaces; blackboard architecture; and distributed processin

Precursor ion scanning for detection and structural characterization of heterogeneous glycopeptide mixtures

AbstractThe structure of N-linked glycans is determined by a complex, anabolic, intracellular pathway but the exact role of individual glycans is not always clear. Characterization of carbohydrates attached to glycoproteins is essential to aid understanding of this complex area of biology. Specific mass spectral detection of glycopeptides from protein digests may be achieved by on-line HPLC-MS, with selected ion monitoring (SIM) for diagnostic product ions generated by cone voltage fragmentation, or by precursor ion scanning for terminal saccharide product ions, which can yield the same information more rapidly. When glycosylation is heterogeneous, however, these approaches can result in spectra that are complex and poorly resolved. We have developed methodology, based around precursor ion scanning for ions of high m/z, that allows site specific detection and structural characterization of glycans at high sensitivity and resolution. These methods have been developed using the standard glycoprotein, fetuin, and subsequently applied to the analysis of the N-linked glycans attached to the scrapie-associated prion protein, PrPSc. These glycans are highly heterogeneous and over 30 structures have been identified and characterized site specifically. Product ion spectra have been obtained on many glycopeptides confirming structure assignments. The glycans are highly fucosylated and carry Lewis X or sialyl Lewis X epitopes and the structures are in-line with previous results. [Abbreviations: Hex–Hexose, C6H12O6 carbohydrates, including mannnose and galactose; HexNAc—N-acetylhexosamine, C8H15NO6 carbohydrates, including N-acetylglucosamine and N-acetylgalactosamine; GlcNAc—N-acetylglucosamine; GalNAc—N-acetylgalactosamine; Fuc–Fucose; NeuAC—N-acetylneuraminic acid or sialic acid; TSE—Transmissible Spongiform Encephalopathy.

A geometric proof of the Kochen-Specker no-go theorem

We give a short geometric proof of the Kochen-Specker no-go theorem for non-contextual hidden variables models. Note added to this version: I understand from Jan-Aake Larsson that the construction we give here actually contains the original Kochen-Specker construction as well as many others (Bell, Conway and Kochen, Schuette, perhaps also Peres).Comment: This paper appeared some years ago, before the author was aware of quant-ph. It is relevant to recent developments concerning Kochen-Specker theorem

Systematic review of SGLT2 receptor inhibitors in dual or triple therapy in type 2 diabetes

Background Despite the number of medications for type 2 diabetes, many people with the condition do not achieve good glycaemic control. Some existing glucose-lowering agents have adverse effects such as weight gain or hypoglycaemia. Type 2 diabetes tends to be a progressive disease, and most patients require treatment with combinations of glucose-lowering agents. The sodium glucose co-transporter 2 (SGLT2) receptor inhibitors are a new class of glucose-lowering agents. Objective To assess the clinical effectiveness and safety of the SGLT2 receptor inhibitors in dual or triple therapy in type 2 diabetes. Data sources MEDLINE, Embase, Cochrane Library (all sections); Science Citation Index; trial registries; conference abstracts; drug regulatory authorities; bibliographies of retrieved papers. Inclusion criteria Randomised controlled trials of SGLT2 receptor inhibitors compared with placebo or active comparator in type 2 diabetes in dual or combination therapy. Methods Systematic review. Quality assessment used the Cochrane risk of bias score. Results Seven trials, published in full, assessed dapagliflozin and one assessed canagliflozin. Trial quality appeared good. Dapagliflozin 10 mg reduced HbA1c by −0.54% (weighted mean differences (WMD), 95% CI −0.67 to −0.40) compared to placebo, but there was no difference compared to glipizide. Canagliflozin reduced HbA1c slightly more than sitagliptin (up to −0.21% vs sitagliptin). Both dapagliflozin and canagliflozin led to weight loss (dapagliflozin WMD −1.81 kg (95% CI −2.04 to −1.57), canagliflozin up to −2.3 kg compared to placebo). Limitations Long-term trial extensions suggested that effects were maintained over time. Data on canagliflozin are currently available from only one paper. Costs of the drugs are not known so cost-effectiveness cannot be assessed. More data on safety are needed, with the Food and Drug Administration having concerns about breast and bladder cancers. Conclusions Dapagliflozin appears effective in reducing HbA1c and weight in type 2 diabetes, although more safety data are needed

The cognitive demands of second order manual control: Applications of the event related brain potential

Three experiments are described in which tracking difficulty is varied in the presence of a covert tone discrimination task. Event related brain potentials (ERPs) elicited by the tones are employed as an index of the resource demands of tracking. The ERP measure reflected the control order variation, and this variable was thereby assumed to compete for perceptual/central processing resources. A fine-grained analysis of the results suggested that the primary demands of second order tracking involve the central processing operations of maintaining a more complex internal model of the dynamic system, rather than the perceptual demands of higher derivative perception. Experiment 3 varied tracking bandwidth in random input tracking, and the ERP was unaffected. Bandwidth was then inferred to compete for response-related processing resources that are independent of the ERP

Calcium binding activity of the epidermal growth factor-like domains of the apicomplexan microneme protein EtMIC4

Microneme proteins are secreted from apicomplexan parasites during invasion of host cells and they play crucial roles in parasite-host cell adhesion. EtMIC4 is a 240 kDa transmembrane protein from Eimeria tenella that contains 31 tandemly arranged epidermal growth factor (EGF), like repeats within its extracellular domain. The majority of these repeats have calcium binding (cb) consensus sequences. Little is known about cbEGFs in apicomplexan parasites but their presence in microneme proteins suggests that they may contribute to parasite-host interactions. To investigate the potential role of cbEGFs we have expressed and correctly refolded a cbEGF triplet from EtMIC4 (cbEGF7-9) and demonstrated that this triplet binds calcium. Circular dichroism spectroscopic analysis of cbEGF7-9 demonstrates that the molecule undergoes a gradual change in conformation with increasing levels of calcium. In the presence of calcium, the triplet becomes resistant to proteolytic degradation by a variety of proteases, a characteristic feature of cbEGF repeats from higher eukaryotic proteins, such as fibrillin, suggesting that calcium binding induces the formation of a rigid conformation. Moreover, mass spectrometric mapping of the cleavage sites that are protected by calcium shows that these sites are located both close to and distant from the calcium binding sites, indicating that protection is not due to steric hindrance by calcium ions, but rather due to the overall conformation adopted by the triplet in the presence of calcium. Thus, the tandemly-arranged cbEGF repeats within EtMIC4 provide a mechanism whereby, in the calcium-rich extracellular environment, the molecule could adopt a protease-resistant, rigid structure that could favour its interaction with host cell ligands

Significant differences in incubation times in sheep infected with bovine spongiform encephalopathy result from variation at codon 141 in the PRNP gene

The susceptibility of sheep to prion infection is linked to variation in the PRNP gene, which encodes the prion protein. Common polymorphisms occur at codons 136, 154 and 171. Sheep which are homozygous for the A<sub>136</sub>R<sub>154</sub>Q<sub>171</sub> allele are the most susceptible to bovine spongiform encephalopathy (BSE). The effect of other polymorphisms on BSE susceptibility is unknown. We orally infected ARQ/ARQ Cheviot sheep with equal amounts of BSE brain homogenate and a range of incubation periods was observed. When we segregated sheep according to the amino acid (L or F) encoded at codon 141 of the PRNP gene, the shortest incubation period was observed in LL141 sheep, whilst incubation periods in FF<sub>141</sub> and LF<sub>141</sub> sheep were significantly longer. No statistically significant differences existed in the expression of total prion protein or the disease-associated isoform in BSE-infected sheep within each genotype subgroup. This suggested that the amino acid encoded at codon 141 probably affects incubation times through direct effects on protein misfolding rates

Float zone experiments in space

The molten zone/freezing crystal interface system and all the mechanisms were examined. If Marangoni convection produces oscillatory flows in the float zone of semiconductor materials, such as silicon, then it is unlikely that superior quality crystals can be grown in space using this process. The major goals were: (1) to determine the conditions for the onset of Marangoni flows in molten tin, a model system for low Prandtl number molten semiconductor materials; (2) to determine whether the flows can be suppressed by a thin oxide layer; and (3) based on experimental and mathematical analysis, to predict whether oscillatory flows will occur in the float zone silicon geometry in space, and if so, could it be suppressed by thin oxide or nitride films. Techniques were developed to analyze molten tin surfaces in a UHV system in a disk float zone geometry to minimize buoyancy flows. The critical Marangoni number for onset of oscillatory flows was determined to be greater than 4300 on atomically clean molten tin surfaces

Is the transition redshift a new cosmological number?

Observations from Supernovae Type Ia (SNe Ia) provided strong evidence for an expanding accelerating Universe at intermediate redshifts. This means that the Universe underwent a transition from deceleration to acceleration phases at a transition redshift $z_t$ of the order unity whose value in principle depends on the cosmology as well as on the assumed gravitational theory. Since cosmological accelerating models endowed with a transition redshift are extremely degenerated, in principle, it is interesting to know whether the value of $z_t$ itself can be observationally used as a new cosmic discriminator. After a brief discussion of the potential dynamic role played by the transition redshift, it is argued that future observations combining SNe Ia, the line-of-sight (or "radial") baryon acoustic oscillations, the differential age of galaxies, as well as the redshift drift of the spectral lines may tightly constrain $z_t$, thereby helping to narrow the parameter space for the most realistic models describing the accelerating Universe.Comment: 12 pages, 5 figures. Some discussions about how to estimate the transition redshift have been added. New data by Planck and H(z) data have been mentioned. New references have been adde