The TM System for Repairing Non-Theorems

We describe a flexible approach to automated reasoning, where non-theorems can be automatically altered to produce proved results which are related to the original. This is achieved in the TM system through an interaction of the HR machine learning program, the Otter theorem prover and the Mace model generator. Given a non-theorem, Mace is used to generate examples which support the non-theorem, and examples which falsify it. HR then invents concepts which categorise these examples and TM uses these concepts to modify the original non-theorem into specialised theorems which Otter can prove. The methods employed by TM are inspired by the piecemeal exclusion, strategic withdrawal and counterexample barring methods described in Lakatos's philosophy of mathematics. In addition, TM can also determine which modified theorems are likely to be interesting and which are not. We demonstrate the effectiveness of this approach by modifying non-theorems taken from the TPTP library of first order theorems. We show that, for 98 non-theorems, TM produced meaningful modifications for 81 of them. This work forms part of two larger projects. Firstly, we are working towards a full implementation both of the reasoning and the social interaction notions described by Lakatos. Secondly, we are aiming to show that the combination of reasoning systems such as those used in TM will lead to a new generation of more powerful AI systems.     

Quantitative analysis of particle sizes: estimation of the most efficient sampling scheme

Analysis of variance based on a hierarchical experimental design was used to establish a method finding the most economical replication schemes in quantitative television microscopy of particulates. Two products of greatly different average particle diameters and width of distributions were investigated. Error contributions were determined for each of three major steps in the procedure and smoothed curves were plotted of error v. particle size. Then cost and overall error were plotted for a variety of possible replication schemes, and a locus of best combinations drawn in. The optimal replication curve depends somewhat on the nature of the sample; thus, it is beneficial to carry out a variance analysis whenever microscopic particle size analysis is planned for a large number of samples of a new product.     

Length Distribution of Single‐Walled Carbon Nanotubes in Aqueous Suspension Measured by Electrospray Differential Mobility Analysis

The first characterization of the length distribution of single‐walled carbon nanotubes (SWCNT) dispersed in a liquid by electrospray differential mobility analysis (ES‐DMA) is presented. Although an understanding of geometric properties of SWCNTs, including length, diameter, aspect ratio, and chirality, is essential for commercial applications, rapid characterization of nanotube length distributions remains challenging. Here the use of ES‐DMA to obtain length distributions of DNA‐wrapped SWCNTs dispersed in aqueous solutions is demonstrated. Lengths measured by ES‐DMA compare favorably with those obtained from multiangle light scattering, dynamic light scattering, field flow fractionation with UV/vis detection, and atomic force microscopy, validating ES‐DMA as a technique to measure SWCNTs of <250 nm in length. The nanotubes are previously purified and dispersed by wrapping with oligomeric DNA in aqueous solution and centrifuging to remove bundles and amorphous carbon. These dispersions are particularly attractive due to their amenability to bulk processing, ease of storage, high concentration, compatibility with biological and high‐throughput manufacturing environments, and for their potential applications ranging from electronics and hydrogen‐storage vessels to anticancer agents.     

Scalable control of developmental timetables by epigenetic switching networks

During development, progenitor cells follow timetables for differentiation that span many cell generations. These developmental timetables are robustly encoded by the embryo, yet scalably adjustable by evolution, facilitating variation in organism size and form. Epigenetic switches, involving rate-limiting activation steps at regulatory gene loci, control gene activation timing in diverse contexts, and could profoundly impact the dynamics of gene regulatory networks controlling developmental lineage specification. Here, we develop a mathematical framework to model regulatory networks with genes controlled by epigenetic switches. Using this framework, we show that such epigenetic switching networks uphold developmental timetables that robustly span many cell generations, and enable the generation of differentiated cells in precisely defined numbers and fractions. Changes to epigenetic switching networks can readily alter the timing of developmental events within a timetable, or alter the overall speed at which timetables unfold, enabling scalable control over differentiated population sizes. With their robust, yet flexibly adjustable nature, epigenetic switching networks could represent central targets on which evolution acts to manufacture diversity in organism size and form.     

Phosphorus export from artificially drained fields across the Eastern Corn Belt

Field observations that quantify agricultural phosphorus (P) losses are critical for the development of P reduction strategies across the Eastern Corn Belt region of North America. Within this region, surface water bodies including Lake Erie are sensitive to non-point P loadings. It is therefore imperative to quantify the impact of agricultural crop production on surface and subsurface water quality. This study characterized discharge, P concentrations, and P loads in surface runoff and subsurface drainage from 38 edge-of-field research sites in Ohio. Over the four-year study period, 31 ± 16% (mean ± one standard deviation) of annual precipitation became subsurface discharge while 7 ± 8% became surface discharge. Subsurface discharge accounted for 81 ± 23% of annual discharge, 71 ± 26% of annual dissolved reactive phosphorus (DRP) load, and 69 ± 27% of annual total phosphorus (TP) load. A P balance was also developed using management and loading data from the study sites. Under prevailing management practices, P removal (i.e., surface losses, subsurface losses, crop uptake) was greater than P input (i.e., atmospheric deposition, fertilizer application) on 60% of fields. Even so, further reduction of edge-of-field P losses will likely be necessary to meet watershed-scale P load recommendations. Findings suggest that balancing P inputs with crop uptake may not be sufficient to reduce edge-of-field losses due to a combination of legacy P and high-intensity rainfall events. Implementation of management practices targeting P-source will be needed in conjunction with practices at the edge-of-field targeting P-transport in order to meet recommended P loading targets in the Eastern Corn Belt region.     

A monoclonal antibody to a multiphosphorylated, conformational epitope at the carboxy-terminus of p53

Mutations of the gene encoding the tumor suppressor protein p53 are the most common molecular alterations of cancer cells found in about half of all human tumors. Mutations which cluster in well-defined hot spots change the structure of the protein thus affecting its ability to bind to DNA. Post-translational modifications, primarily phosphorylation, might also influence how p53 binds to DNA or folds to its active tetrameric form. However, the lack of appropriate biochemical markers to characterize the status of phosphorylation in different cell types and in cells at different stages of tumor progression has prohibited such investigations. To generate a sensitive and phosphorylation-specific monoclonal antibody (mAb), we chemically synthesized the C-terminal 23 amino acid stretch of human p53 in a double-phosphorylated form. The peptide 371-393, carrying phosphate groups on Ser378 and Ser392, was co-synthesized with a turn-inducing spacer and peptide 31D, an immunodominant T-helper cell epitope in mice of the H-2k haplotype. After immunization and fusion of splenocytes with myeloma cells, a number of mAbs were obtained, from which mAb p53-18 emerged as a highly sensitive reagent. By enzyme-linked immunosorbent assay, p53-18, a mAb of the IgM isotype, recognized phosphorylated p53, expressed in insect cells infected with a recombinant baculovirus but not p53 expressed in Escherichia coli. Moreover, murine p53 from insect cells could be immune purified with mAb p53-18. Mass spectrometry following tryptic digestion of the purified protein and liquid chromatography of the fragments verified the presence of phosphate groups at both Ser375 and Ser389. From the corresponding human protein fragments, mAb p53-18 bound to the immunizing peptide phosphorylated on Ser378 and on Ser392, but failed to cross-react with the unphosphorylated peptide, or peptides phosphorylated individually on either Ser378 or Ser392. The binding to the unphosphorylated peptide could be restored, however, if the peptide conformation was stabilized to that of an alpha-helix. The immunogenic nature of the multiphosphorylated C-terminus of p53 is indicated by the finding that human sera, mostly from cancer patients, preferentially recognized the double-phosphorylated peptide over the monophosphorylated or unphosphorylated analogs. Antibody p53-18 appears to be a highly useful biochemical marker to detect low levels of p53 protein in different tissues, and to be a key tool to characterize the phosphorylation status of the C-terminus of p53 protein originated from various sources.     

Are babies with gastroschisis small for gestational age?

A case is reported in which two separate adenocarcinomas were detected in the bypassed distal stomach 13 years after gastric stapling with loop gastro-enterostomy was performed for the treatment of morbid obesity. Retrograde endoscopy via the afferent loop was used to establish the diagnosis. Although gastritis and metaplasia have been described in the bypassed stomach, only one case of carcinoma in this area has previously been reported.     

A region of conformational variability outside the peptide-binding site of a class I MHC molecule

Peptide binding is known to influence the conformation of the surface of class I molecules as detected with mAbs and TCR. A new conformationally sensitive epitope on the mouse class I molecule Kb is defined by mAb AF6-88.5. The recognized structure is affected by amino acid substitutions in any of the three external domains of the class I heavy chain and, in addition, is influenced by the substitution of human for mouse beta2-microglobulin. Interestingly, the epitope for this Ab is not affected by mutations within the peptide-binding cleft or by the nature of the peptide bound. These findings indicate that the effect of a change in one domain of class I can radiate to other parts of the molecule. Furthermore, the existence of conformationally sensitive structures outside of the peptide-binding site suggests the possibility that class I molecules may change their structure in response to binding by receptors and ligands such as the TCR and the coligand CD8. Such structural changes may represent signals that can influence cellular activation events.     

Retroviral-mediated expression of an MHC class I-restricted T cell receptor in the CD8 T cell compartment of bone marrow-reconstituted mice

The introduction of cloned T cell receptor (TCR) genes into bone marrow cells could provide a way to increase the frequency of tumor- or pathogen-specific cytotoxic T lymphocyte (CTL) precursors. We demonstrate here the ability of a retroviral vector to direct expression of a Valpha15/Vbeta13 MHC class I-restricted TCR in lethally irradiated mice reconstituted with transduced bone marrow cells. We have detected retroviral-mediated TCR expression by flow cytometry 6-19 weeks after transplantation in C57L (Vbeta13(-/-)) and Rag1(-/-) bone marrow-reconstituted mice, and in C57BL/6 hosts reconstituted with transduced C57BL/6-Rag1(-/-) bone marrow. Southern analysis confirmed the presence of integrated provirus and revealed that the frequency of transduction is greater than the frequency of cell surface TCR expression. Although TCR expression on Vbeta13+ transduced cells is lower than endogenous TCR levels, it is largely confined to CD4+CD8+ (thymus) and CD8+ (thymus and spleen) T cells. In Rag1(-/-) mice, which display a developmental arrest of thymocytes at the immature CD4-CD8- stage, retrovirus-mediated TCR expression selectively rescues CD4+CD8+ and CD8+ populations. These results indicate that the ectopically expressed TCR is functional during T cell development. Furthermore, we have observed Vbeta13+ TCR expression by up to 13% of peripheral CD8+ T cells in C57L and C57BL/6 hosts. This represents a substantial increase relative to total Vbeta13 frequency in normal C57BL/6 mice (3-5%), and an even greater increase over the estimated frequency of CTL precursors of a defined specificity (10(-5)-10(-4)). Our findings indicate that TCR gene transfer can be used to develop new approaches to immunotherapy, and provide the basis for further studies examining the contribution of retrovirus-mediated TCR expression to an antigen-specific CTL response.