Comparison of Multivariate Matching Methods: Structures,Distances, and Algorithms

Abstract

A comparison and evaluation is made of recent proposals for multivariate matched sampling in observational studies, where the following three questions are answered: (1) Algorithms: In current statistical practice, matched samples are formed using “nearest available” matching, a greedy algorithm. Greedy matching does not minimize the total distance within matched pairs, though good algorithms exist for optimal matching that do minimize the total distance. How much better is optimal matching than greedy matching? We find that optimal matching is sometimes noticeably better than greedy matching in the sense of producing closely matched pairs, sometimes only marginally better, but it is no better than greedy matching in the sense of producing balanced matched samples. (2) Structures: In common practice, treated units are matched to one control, called pair matching or 1–1 matching, or treated units are matched to two controls, called 1–2 matching, and so on. It is known, however, that the optimal structure is a full matching in which a treated unit may have one or more controls or a control may have one or more treated units. Optimal 1 — k matching is compared to optimal full matching, finding that optimal full matching is often much better. (3) Distances: Matching involves defining a distance between covariate vectors, and several such distances exist. Three recent proposals are compared. Practical advice is summarized in a final section.     

Mycotoxin profile of Fusarium langsethiae isolated from wheat in Italy: production of type‐A trichothecenes and relevant glucosyl derivatives

Fusarium langsethiae, formally described as a new species over a decade ago, has been identified as the main producer of HT‐2 (HT2) and T‐2 (T2) toxins in Europe in small cereal grains. Mycotoxin contamination caused by this Fusarium species can represent a food safety hazard that deserves further attention. In the present work, the mycotoxin profile in wheat cultures of F. langsethiae is presented with particular reference to the production of major type‐A trichothecenes and their glucosyl derivatives. F. langsethiae isolates, representative of the major Italian wheat cultivation areas, were tested for the production of T2, HT2, diacetoxyscirpenol (DAS) and neosolaniol (NEO), and relevant glucosyl derivatives. Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) was used for the identification and chemical characterization of these metabolites. F. langsethiae isolates under investigation resulted to be potent producers of T2, HT2 and NEO. Furthermore, a well‐defined set of isolates, all originating from Central Italy, produced also DAS. All isolates were found to be able to produce HT2 glucosyl derivatives, whereas only traces of T2 glucoside were detected in one sample. Furthermore, two mono‐glucosyl derivatives of NEO and one mono‐glucoside derivative of DAS were identified and characterized. The screening for the presence/absence of glucosylated trichothecenes in analyzed fungal extracts revealed a general co‐occurrence of these derivatives with the parent toxin at levels that could be roughly estimated to account up to 37% of the relevant unconjugated toxin. This is the first report of the production of glucosylated trichothecenes by F. langsethiae cultured on small grains. Copyright © 2013 John Wiley & Sons, Ltd.     

NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41

Due to the inherently flexible nature of a protein–protein interaction surface, it is difficult both to inhibit the association with a small molecule, and to predict how it might bind to the surface. In this study, we have examined small molecules that mediate the interaction between a WWI motif on the C-helix of HIV-1 glycoprotein-41 (gp41) and a deep hydrophobic pocket contained in the interior N-helical trimer. Association between these two components of gp41 leads to virus–cell and cell–cell fusion, which could be abrogated in the presence of an inhibitor that binds tightly in the pocket. We have studied a comprehensive combinatorial library of α-helical peptidomimetics, and found that compounds with strongly hydrophobic side chains had the highest affinity. Computational docking studies produced multiple possible binding modes due to the flexibility of both the binding site and the peptidomimetic compounds. We applied a transferred paramagnetic relaxation enhancement experiment to two selected members of the library, and showed that addition of a few experimental constraints enabled definitive identification of unique binding poses. Computational docking results were extremely sensitive to side chain conformations, and slight variations could preclude observation of the experimentally validated poses. Different receptor structures were required for docking simulations to sample the correct pose for the two compounds. The study demonstrated the sensitivity of predicted poses to receptor structure and indicated the importance of experimental verification when docking to a malleable protein–protein interaction surface.     

X‐Band DNP Hyperpolarization of Viscous Liquids and Polymer Melts

NMR studies of synthetic polymers and biomacromolecules, which provide insight into the conformation and dynamics of these materials, can benefit strongly from the increased sensitivity offered by dynamic nuclear polarization (DNP) and other hyperpolarizing methods. In this study ¹H DNP nuclear spin hyperpolarization of two polybutadiene samples, representing a supercooled liquid and an entangled polymer melt, is demonstrated at 0.35 T magnetic field strength and at temperatures between −80 and +50 °C. Electron spin polarization transfer from the α,γ‐bisdiphenylene‐β‐phenylallyl radical to the sample nuclei is achieved by the Overhauser and solid effect. DNP signal enhancements are studied, varying the electron spin resonance offset, microwave power, and sample temperature. The influence of spin relaxation times, line widths, and molecular dynamics are discussed. The results show promising, up to 15‐fold NMR signal enhancements using noncryogenic temperatures and an inexpensive setup that is less technically demanding than current high‐field DNP setups.

     

Antioxidant capacity and antibacterial activity from Annona cherimola phytochemicals by ultrasound-assisted extraction and its comparison to conventional methods

In recent years, the food, pharmacy, and cosmetic industries have focused on the search of natural compounds with antimicrobial and antioxidant properties; commonly, these compounds are obtained from Kingdom plantae. The aim of the present work is comparing antibacterial and antioxidant capacity of Annona cherimola Mill leaves, using different extraction methods. The ultrasound assisted extraction technique (UAE) was compared with conventional techniques: Soxhlet and maceration. Water and ethanol were used as solvents for leaves extractions performed with these three methods. The main acetogenins reported in Annona cherimola Mill and Annona muricata L. species were simulated using the functional hybrid B3LYP and to confirm its presence, analysis of the compound composition was performed using FT-IR, UV–Vis and HPLC. Total phenolics (TP) and flavonoids (TF) were determined by spectroscopy techniques and novel Differential Pulse Voltammetry (DPV) electrochemical technique. Total Antioxidant Capacity (TAC) of the extracts was measured, using the DPPH, FRAP and CUPRAC techniques. The highest antioxidant content was found in the Soxhlet water extracts; even so, the UAE technique presented an attractive alternative due to considerable reduction in extraction time, which was greater than 99%, and possible selectivity in compounds extraction. Finally, antibacterial activity of the extracts was evaluated, obtaining the best results against gram-positive bacteria using UAE water extract. In this way, the UAE technique presents an excellent extraction option due to the considerable reduction in time and energy, as well as the increase in antibacterial activity.     

Intramyocellular lipid quantification: comparison between 3.0- and 1.5-T (1)H-MRS

OBJECTIVE: This study aimed to prospectively compare measurement precision of calf intramyocellular lipid (IMCL) quantification at 3.0 and 1.5 T using (1)H magnetic resonance spectroscopy ((1)H-MRS). MATERIALS AND METHODS: We examined the soleus and tibialis anterior (TA) muscles of 15 male adults [21-48 years of age, body mass index (BMI)=21.9-38.0 kg/m(2)]. Each subject underwent 3.0- and 1.5-T single-voxel, short-echo-time, point-resolved (1)H-MRS both at baseline and at 31-day follow-up. The IMCL methylene peak (1.3 ppm) was scaled to unsuppressed water peak (4.7 ppm) using the LCModel routine. Full width at half maximum (FWHM) and signal-to-noise ratios (SNRs) of unsuppressed water peak were measured using jMRUI software. Measurement precision was tested by comparing interexamination coefficients of variation (CV) between different field strengths using Wilcoxon matched pairs signed rank test in all subjects. Overweight subjects (BMI>25 kg/m(2)) were analyzed separately to examine the benefits of 3.0-T acquisitions in subjects with increased adiposity. RESULTS: No significant difference between 3.0 and 1.5 T was noted in CVs for IMCL of soleus (P=.5). CVs of TA were significantly higher at 3.0 T (P=.02). SNR was significantly increased at 3.0 T for soleus (64%, P<.001) and TA (62%, P<.001) but was lower than the expected improvement of 100%. FWHM at 3.0 T was significantly increased for soleus (19%, P<.001) and TA (7%, P<.01). Separate analysis of overweight subjects showed no significant difference between 3.0- and 1.5-T CVs for IMCL of soleus (P=.8) and TA (P=.4). CONCLUSION: Using current technology, (1)H-MRS for IMCL at 3.0 T did not improve measurement precision, as compared with 1.5 T.