The rack space

The main result of this paper is a new classification theorem for links (smooth embeddings in codimension 2). The classifying space is the rack space and the classifying bundle is the first James bundle.

We investigate the algebraic topology of this classifying space and report on calculations given elsewhere. Apart from defining many new knot and link invariants (including generalised James-Hopf invariants), the classification theorem has some unexpected applications. We give a combinatorial interpretation for of a complex which can be used for calculations and some new interpretations of the higher homotopy groups of the 3-sphere. We also give a cobordism classification of virtual links.

     

Raman spectroscopy utilizing Fisher‐based feature selection combined with Support Vector Machines for the characterization of breast cell lines

Raman spectroscopy has the potential to significantly aid in the research and diagnosis of cancer. The information dense, complex spectra generate massive datasets in which subtle correlations may provide critical clues for biological analysis and pathological classification. Therefore, implementing advanced data mining techniques is imperative for complete, rapid and accurate spectral processing. Numerous recent studies have employed various data methods to Raman spectra for classification and biochemical analysis. Although, as Raman datasets from biological specimens are often characterized by high dimensionality and low sample numbers, many of these classification models are subject to overfitting. Furthermore, attempts to reduce dimensionality result in transformed feature spaces making the biological evaluation of significant and discriminative spectral features problematic. We have developed a novel data mining framework optimized for Raman datasets, called Fisher‐based Feature Selection Support Vector Machines (FFS‐SVM). This framework provides simultaneous supervised classification and user‐defined Fisher criterion‐based feature selection, reducing overfitting and directly yielding significant wavenumbers from the original feature space. Herein, we investigate five cancerous and non‐cancerous breast cell lines using Raman microspectroscopy and our unique FFS‐SVM framework. Our framework classification performance is then compared to several other frequently employed classification methods on four classification tasks. The four tasks were constructed by an unsupervised clustering method yielding the four different categories of cell line groupings (e.g. cancer vs non‐cancer) studied. FFS‐SVM achieves both high classification accuracies and the extraction of biologically significant features. The top ten most discriminative features are discussed in terms of cell‐type specific biological relevance. Our framework provides comprehensive cellular level characterization and could potentially lead to the discovery of cancer biomarker‐type information, which we have informally termed ‘Raman‐based spectral biomarkers’. The FFS‐SVM framework along with Raman spectroscopy will be used in future studies to investigate in‐situ dynamic biological phenomena. Copyright © 2013 John Wiley & Sons, Ltd.     

An ion-storage time-of-flight mass spectrometer for analysis of electrospray ions.

A preliminary design and implementation of a novel approach to electrospray-mass spectrometry are described. Based on a time-of-flight mass analysis, the instrument provides several important advantages for on-line mass analysis: 1, simplicity, ease of use and low manufacturing cost; 2, rapid scan speed, yielding quasi-instantaneous full mass scans at repetition rates up to several kHz; 3, soft ionization and accurate mass determination of extremely large analyte molecules; 4, high sensitivity.     

Performance of slotted pores in particle manufacture using rotating membrane emulsification

This paper addresses the use of different slotted pores in rotating membrane emulsification technology.Pores of square and rectangular shapes were studied to understand the effect of aspect ratio (1-3.5) and their orientation on oil droplet formation.Increasing the membrane rotation speed decreased the droplet size,and the oil droplets produced were more uniform using slotted pores as compared to circular geometry.At a given rotation speed,the droplet size was mainly determined by the pore size and the fluid velocity of oil through the pore (pore fluid velocity).The ratio of droplet diameter to the equivalent diameter of the slotted pore increased with the pore fluid velocity.At a given pore fluid velocity and rotation speed,pore orientation significantly influences the droplet formation rate: horizontally disposed pores (with their longer side perpendicular to the membrane axis) generate droplets at double the rate of vertically disposed pores.This work indicates practical benefits in the use of slotted membranes over conventional methods.     

3-Deoxygalactosone, a new glucose degradation product in peritoneal dialysis fluids: Identification, quantification by HPLC/DAD/MSMS and its pathway of formation

Heat sterilization of peritoneal dialysis (PD) fluids leads to the formation of glucose degradation products (GDPs), which considerably impair long-term application of PD. Knowledge of the exact composition of GDPs present in a PD fluid is important to improve the biocompatibility of dialysis solutions. The present study conducted a targeted screening for novel GDPs with α-dicarbonyl structure in PD fluids. Thus, 3-deoxygalactosone (3-DGal) was identified for the first time in PD fluids. Quantification of 3-DGal was achieved by high-performance liquid chromatography (HPLC)/DAD/MSMS after derivatization with o-phenylendiamine to yield the quinoxaline derivative. Baseline separation of all α-dicarbonyl GDPs, particularly of the diastereomers 3-deoxyglucosone (3-DG) and 3-DGal, required the application of a polar, phenyl-based RP column for HPLC and additional pH-gradient elution. Concentrations of 3-DGal ranged between 55.8 and 136.9 μM in single-chamber PD fluids, and between 2.5 and 12.4 μM in double-chamber PD fluids. In solutions containing glucose, 3-DGal is formed from 3-DG via the intermediate 3,4-dideoxyglucosone-3-ene (3,4-DGE). Further studies are now required to determine the (patho-)physiological properties of 3-DGal.     

A simple method for analyzing 51V solid-state NMR spectra of complex systems

Five vanadium complexes as models for biological systems were investigated using ⁵¹V-MAS–NMR spectroscopy. All spectra show an uncommon line shape, which can be attributed to a shorter relaxation time of the satellite transition in contrast to the central one. A method for the reliable analysis of such kind of spectra is presented for the first time and the most important NMR parameters of the investigated complexes (quadrupolar coupling constant C_Q, asymmetry of the EFG tensor η_Q, isotropic chemical shift δ_iso, chemical shift anisotropy δ_σ and asymmetry of the CSA tensor η_σ) are presented. These results are of particular importance with respect to the analysis of the ⁵¹V-MAS–NMR spectra of vanadium moieties in biological matrices such as vanadium chloroperoxidase, which show hitherto unexplained low intensity of the satellite sideband pattern.     

Solution of the Thomas-Fermi problem for continuous,spherical, positive charge distribution

A method to make anab initio calculation of the free energy of small drops of liquid metal is presented. The model chosen involves the replacing of the positive ion cores by an equivalent continuous spherical distribution of charge. The Thomas-Fermi potential is calculated as a starting point for a Hartree-Fock self-consistent field calculation. The results of the Thomas-Fermi calculation are reported as an example of the preliminary calculations.Research supported under NSF Grant #20884.     

A Reversibly Porous Supramolecular Peptide Framework**

The ability to use bio-inspired building blocks in the assembly of novel supramolecular frameworks is at the forefront of an exciting research field. Herein, we present the first polyproline helix to self-assemble into a reversibly porous, crystalline, supramolecular peptide framework (SPF). This framework is assembled from a short oligoproline, adopting the polyproline II conformation, driven by hydrogen-bonding and dispersion interactions. Thermal activation, guest-induced dynamic porosity and enantioselective guest inclusion have been demonstrated for this novel system. The principles of the self-assembly associated with this SPF will be used as a blueprint allowing for the further development of helical peptide linkers in the rational design of SPFs and metal-peptide frameworks.     

Structural resolution of carbohydrate positional and structural isomers based on gas-phase ion mobility-mass spectrometry

This report describes the rapid characterization of positional and structural carbohydrate isomers based on structural separations provided by ion mobility-mass spectrometry (IM-MS). Many of the diseases associated with glycoprotein variation can be more effectively treated with earlier detection substantiating the need for high-throughput methodologies for glycan characterization. This remains particularly difficult due to heterogeneity, branching, and large size of carbohydrate moieties which creates the potential for numerous isobaric positional and structural isomers that are difficult to characterize using conventional MS methods. IM-MS provides rapid (μs to ms) structural separations by IM and subsequent identification by MS which presents a means for characterization of positional and structural carbohydrate isomers. To chart the structural variation observed in IM-MS, the ion-neutral collision cross sections for over 300 carbohydrates are reported. This diversity can also be varied through the utility of using different alkali metals to tune separation selectivity via alkali metal-carbohydrate coordination. Furthermore, the advantages of combining either pre- and/or post-IM fragmentation prior to MS analysis is demonstrated for enhanced confidence in carbohydrate identification.