An open-source approach to automation in organic synthesis: The flow chemical formation of benzamides using an inline liquid-liquid extraction system and a homemade 3-axis autosampling/product-collection device

Several open-source hardware and software technologies (RAMPS, Python, PySerial, OpenCV) were used to control an automated flow chemical synthesis system. The system was used to effect the synthesis of a series of benzamides. An inexpensive Raspberry Pi single board computer provided an electronic interface between the control computer and the RAMPS motor driver boards.     

Configurations in abelian categories. IV. Invariants and changing stability conditions

This is the last in a series on configurations in an abelian category A. Given a finite poset (I,?), an (I,?)-configuration (σ,ι,π) is a finite collection of objects σ(J) and morphisms ι(J,K) or in A satisfying some axioms, where J,K are subsets of I. Configurations describe how an object X in A decomposes into subobjects.The first paper defined configurations and studied moduli spaces of configurations in A, using Artin stacks. It showed well-behaved moduli stacks ObjA,MA(I,?) of objects and configurations in A exist when A is the abelian category coh(P) of coherent sheaves on a projective scheme P, or mod-KQ of representations of a quiver Q. The second studied algebras of constructible functions and stack functions on ObjA.The third introduced stability conditions(τ,T,?) on A, and showed the moduli space of τ-semistable objects in class α is a constructible subset in ObjA, so its characteristic function is a constructible function. It formed algebras , , , of constructible and stack functions on ObjA, and proved many identities in them.In this paper, if (τ,T,?) and are stability conditions on A we write in terms of the , and deduce the algebras are independent of (τ,T,?). We study invariants or Iss(I,?,κ,τ) ‘counting’ τ-semistable objects or configurations in A, which satisfy additive and multiplicative identities. We compute them completely when A=mod-KQ or A=coh(P) for P a smooth curve. We also find invariants with special properties when A=coh(P) for P a smooth surface with nef, or a Calabi-Yau 3-fold.     

The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters

With the increasing number of genomes sequenced and available in the public domain, a large number of orphan gene clusters, for which the encoded natural product is unknown, have been identified. These orphan gene clusters represent a tremendous source of novel and possibly bioactive compounds. Here, we describe a "genomisotopic approach," which employs a combination of genomic sequence analysis and isotope-guided fractionation to identify unknown compounds synthesized from orphan gene clusters containing nonribosomal peptide synthetases. Analysis of the Pseudomonas fluorescens Pf-5 genome led to the identification of an orphan gene cluster predicted to code for the biosynthesis of a lipopeptide natural product. Application of the genomisotopic approach to isolate the product of this gene cluster resulted in the discovery of orfamide A, founder of a group of bioactive cyclic lipopeptides.     

Development and application of immunoaffinity column chromatography for atrazine in complex sample media

A rabbit antibody immunoaffinity (IA) column procedure was evaluated as a cleanup method for the determination of atrazine in soil, sediment, and food. Four IA columns were prepared by immobilizing a polyclonal rabbit anti-atrazine antibody solution to HiTrap Sepharose columns. Atrazine was bound to the IA columns when the loading solvents were either 100% water, 2% acetonitrile in water, or 10% methanol in phosphate buffered saline (PBS). Quantitative removal of atrazine from the IA columns was achieved with elution solvents of either 70% ethanol in water, 70% methanol in water, or 100% methanol. One control column was prepared using nonspecific rabbit IgG antibody. This control column did not retain any applied atrazine indicating atrazine did not bind indiscriminately to protein or the Sepharose support. The four IA columns showed reproducible coupling efficiency for the immobilization of the atrazine antibody and consistent binding and releasing of atrazine. The coupling efficiency (4.25 mg of antibody in 1 mL of resin bed) for the four IA columns ranged from 93 to 97% with an average of 96 ± 2% (2.1%). Recoveries of the 500, 50, and 5 ng mL⁻¹ atrazine standard solutions from the four IA columns were 107 ± 7% (6.5%), 122 ± 14% (12%), and 114 ± 9% (8.0%) respectively, based on enzyme-linked immunosorbent assay (ELISA) data. The maximum loading was approximately 700 ng of atrazine for each IA column (∼0.16 μg of atrazine per mg of antibody). The IA columns could withstand 100% methanol as the elution solvent and could be reused more than 50 times with no change in performance. The IA columns were challenged with soil, sediment, and duplicate-diet food samples and effectively removed interferences from these various matrices for subsequent gas chromatography/mass spectrometry (GC/MS) or ELISA analysis. The log-transformed ELISA and GC/MS data were significantly correlated for soil, sediment and food samples although the ELISA values were slightly higher than those obtained by GC/MS. The IA column cleanup procedure coupled with ELISA analysis could be used as an alternative effective analytical method for the determination of atrazine in complex sample media such as soil, sediment, and food samples.     

Shear wave speed recovery using moving interference patterns obtained in sonoelastography experiments

Two new experiments were created to characterize the elasticity of soft tissue using sonoelastography. In both experiments the spectral variance image displayed on a GE LOGIC 700 ultrasound machine shows a moving interference pattern that travels at a very small fraction of the shear wave speed. The goal of this paper is to devise and test algorithms to calculate the speed of the moving interference pattern using the arrival times of these same patterns. A geometric optics expansion is used to obtain Eikonal equations relating the moving interference pattern arrival times to the moving interference pattern speed and then to the shear wave speed. A cross-correlation procedure is employed to find the arrival times; and an inverse Eikonal solver called the level curve method computes the speed of the interference pattern. The algorithm is tested on data from a phantom experiment performed at the University of Rochester Center for Biomedical Ultrasound.     

Exotic phases of finite temperature gauge theories

We calculate the phase diagrams at high temperature of SU(N) gauge theories with massive fermions by minimizing the one-loop effective potential. Considering fermions in the adjoint (Adj) representation at various N we observe a variety of phases when N_f2 Majorana flavours and periodic boundary conditions are applied to fermions. Also the confined phase is perturbatively accessible. For N=3, we add Fundamental (F) representation fermions with antiperiodic boundary conditions to adjoint QCD to show how the Z(3)-symmetry breaks in the confined phase.