Correlation-informed ordered dictionary learning for imaging in complex media.

We propose a method for imaging in scattering media when large and diverse datasets are available. It has two steps. Using a dictionary learning algorithm the first step estimates the true Green's function vectors as columns in an unordered sensing matrix. The array data comes from many sparse sets of sources whose location and strength are not known to us. In the second step, the columns of the estimated sensing matrix are ordered for imaging using the multidimensional scaling algorithm with connectivity information derived from cross-correlations of its columns, as in time reversal. For these two steps to work together, we need data from large arrays of receivers so the columns of the sensing matrix are incoherent for the first step, as well as from sub-arrays so that they are coherent enough to obtain connectivity needed in the second step. Through simulation experiments, we show that the proposed method is able to provide images in complex media whose resolution is that of a homogeneous medium.

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.

MOTIVATION: In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. Existing tools generally return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low-abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, few tools account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome. RESULTS: We present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of ANI, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power and how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach. AVAILABILITY AND IMPLEMENTATION: The source code implementing this approach is available via Conda and at https://github.com/KoslickiLab/YACHT. We also provide the code for reproducing experiments at https://github.com/KoslickiLab/YACHT-reproducibles.

The Noise Collector for sparse recovery in high dimensions.

The ability to detect sparse signals from noisy, high-dimensional data is a top priority in modern science and engineering. It is well known that a sparse solution of the linear system [Formula: see text] can be found efficiently with an [Formula: see text]-norm minimization approach if the data are noiseless. However, detection of the signal from data corrupted by noise is still a challenging problem as the solution depends, in general, on a regularization parameter with optimal value that is not easy to choose. We propose an efficient approach that does not require any parameter estimation. We introduce a no-phantom weight τ and the Noise Collector matrix C and solve an augmented system [Formula: see text], where e is the noise. We show that the [Formula: see text]-norm minimal solution of this system has zero false discovery rate for any level of noise, with probability that tends to one as the dimension of [Formula: see text] increases to infinity. We obtain exact support recovery if the noise is not too large and develop a fast Noise Collector algorithm, which makes the computational cost of solving the augmented system comparable with that of the original one. We demonstrate the effectiveness of the method in applications to passive array imaging.

Diels-Alder/Ene Reactivities of 2-(1'-Cycloalkenyl)thiophenes and 2-(1'-Cycloalkenyl)benzo[b]thiophenes with N-Phenylmaleimides: Role of Cycloalkene Ring Size on Benzothiophene and Dibenzothiophene Product Distributions.

Scaffolds of thiophene and benzothiophene are the important class of bioactive compounds found abundant in nature. The Diels-Alder reactions of 2-(1'-cycloalkenyl)thiophenes and 2-(1'-cycloalkenyl)benzo[b]thiophenes having the alkene groups present in five-, six-, seven-, eight-, and twelve-membered rings with substituted N-phenylmaleimides are characterized. The size of the cycloalkene rings plays a critical role in dictating the product distributions of expected and isomerized Diels-Alder adducts. 2D NMR studies indicate that the isolated isomers for 2-(1'-cycloalkenyl)thiophenes having five-, six-, and seven-membered rings are aromatized benzothiophene products, whereas eight- and twelve-membered rings are un-rearranged adducts. In addition, the product of subsequent ene-reaction with the N-phenylmaleimide is isolated for the five- and six-membered ring cases. Interestingly, in the 2-(1'-cycloalkenyl)benzo[b]thiophene having five-, six-, seven-, eight-, and twelve-membered rings, the un-rearranged dibenzothiophene Diels-Alder adduct is isolated in every instance. Molecular mechanics and density functional theory (M06-2X and PBE0-D3) calculations are performed to understand the differential reactivity of the various dienes for both the initial Diels-Alder reaction and a possible, subsequent ene reaction.

Synthesis and biology of cyclic imine toxins, an emerging class of potent, globally distributed marine toxins.

From a small group of exotic compounds isolated only two decades ago, Cyclic Imine (CI) toxins have become a major class of marine toxins with global distribution. Their distinct chemical structure, biological mechanism of action, and intricate chemistry ensures that CI toxins will continue to be the subject of fascinating fundamental studies in the broad fields of chemistry, chemical biology, and toxicology. The worldwide occurrence of potent CI toxins in marine environments, their accumulation in shellfish, and chemical stability are important considerations in assessing risk factors for human health. This review article aims to provide an account of chemistry, biology, and toxicology of CI toxins from their discovery to the present day.

Oxidative conversion of δ-sultones to γ-lactones.

Delta-sultones, prepared by C-H insertion, can be oxidatively converted to gamma-lactones by treatment with t-BuOK/t-BuOOH. An intermediate in the synthesis of (-)-eburnamonin was prepared using this approach.

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.

In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. While tools exist to answer this question, all existing approaches to date return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, no tools to date account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome. In this work, we present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of average nucleotide identity, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power as well as quantify theoretically how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach. Code implementing this approach, as well as all experiments performed, is available at https://github.com/KoslickiLab/YACHT.

Synthesis of plakortethers F and G.

Synthesis of plakortethers F and G has been performed by taking advantage of the symmetry in the structure. The structures of the prepared compounds have been confirmed by COSY, 1D NOE, and chemical transformation studies. The synthetic plakortether F was found to match the natural product by all physical data. The synthetic plakortether G exhibited several disagreements in (13)C NMR data with the reported values. However, on the basis of an extremely close match in appearance of its (1)H NMR spectrum to the obtained (1)H NMR spectrum of the natural product, as well as matching optical rotations, the two compounds are believed to be identical.

Formation of six- vs. five-membered cyclic sulfones by C-H insertion.

Selectivity of six- vs. five- membered ring formation in C-H insertion on alkylsulfonyl diazoacetates is sensitive to the substrate structure and catalyst used.

Enantioselective synthesis of Bakuchiol using diazosulfonate C-H insertion to install the quaternary center.

Bakuchiol was prepared from commercial (-)-citronellol using the diazosulfonate C-H insertion to control the regioselectivity and install the quaternary center.

Selective formation of six-membered cyclic sulfones and sulfonates by C-H insertion.

[reaction: see text] Carbethoxy diazosulfones and sulfonates, easily available from corresponding sulfones and sulfonates, undergo C-H insertion with preferential formation of six membered cyclic sulfones and sulfonates.

Multislice computed tomography-guided surgical repair of acquired posterior left ventricular aneurysms: demonstration of mitral valve and left ventricular reverse remodelling.

OBJECTIVES: Involvement of the mitral valve (MV) apparatus represents a challenge in surgical ventricular repair (SVR) of posterior left ventricular (LV) aneurysms. This study sought to investigate whether multislice computed tomography (MSCT) assessment can be used to optimize the surgical procedure for posterior LV aneurysms. METHODS: Thirty patients (m : w = 24 : 6, age 38-78, median 66 years; mean New York Heart Association class 2.98) with posterior LV aneurysm were operated upon. MSCT was performed in 24 patients before and after surgery. End-diastolic and end-systolic volumes of LV and aneurysm were indexed to body surface area (LVEDVI/LVESVI, AEDVI/AESVI). The MV apparatus was characterized by coaptation distance (CD), tenting area (TA), MV closure angle (MVCA), MV annulus area (MVAA) and interpapillary muscle distance (IMD). RESULTS: Thirty-day mortality was 10% and 5-year survival rate was 83%. After surgery, LVEDVI decreased from 151.2 ± 84.1 to 85.7 ± 28.3 ml/m(2) (P = 0.001) and LVESVI from 110.6 ± 88.8 to 50.2 ± 22.9 ml/m(2) (P = 0.001). LV ejection fraction increased from 31.5 ± 15.1 to 43.4 ± 9.9% (P = 0.001). Preoperative MSCT showed significantly higher values of MVAA, CD and TA in patients who needed MV repair or replacement. Postoperative reduction of mitral regurgitation in patients without MV surgery corresponded with significant reduction in intercommissural diameter, anteroposterior diameter, MVAA, TA, CD, MVCA and IMD. CONCLUSIONS: MSCT represents an excellent diagnostic tool for the assessment of MV and LV geometry. MSCT-guided SVR of submitral LV aneurysms leads to excellent mid-term results. On the basis of the MSCT assessment, we propose an algorithm for surgical planning in posterior LV aneurysms.

Determination of trans-resveratrol and its metabolites in rat serum using liquid chromatography with high-resolution time of flight mass spectrometry.

In this study we developed a sensitive method using high performance liquid chromatography (HPLC) coupled to electrospray ionization (ESI) with high resolution time of flight (TOF) mass spectrometry (MS) for the determination of naturally occurring antioxidant trans-resveratrol (3,5,4'-trihydroxy-trans-stilbene, RES). This method enabled an investigation of a relationship between tumor growth in rats and concentration of RES and its primary metabolites, trans-resveratrol-3-O-sulfate-3-O-sulfate (R3S) and trans-resveratrol-3-O-ß-d-glucuronide (R3G), in rat serum after RES exposure (5 or 25mg/kg/day). RES levels in rat serum were near the limit of detection, showing concentrations of 4±1 and 12±4ng/mL for low and high-dose exposure, respectively. Compared to RES, higher concentrations were found for its metabolites (R3G:4.8±0.3 and 6.8±0.3µg/mL; R3S:0.27±0.09 and 0.34±0.04µg/mL, respectively). Using TOF, for the first time, we measured the matrix affected limits of detection (LODs) in plasma (3.7, 82.4, and 4.7ng/mL for RES, R3G, and R3S, respectively), which were comparable to those reported in previous work using HPLC tandem mass spectrometry, but with a benefit of a full mass spectral profile. The ability to acquire data in full scan mode also revealed other isomers of R3S. The additional novelty of our study is in synthesis and application of deuterated recovery standards enabling accurate and precise quantification. In order to develop a robust method, the ESI conditions were optimized using a multilevel full factorial design of experiments.

SYNTHETICALLY USEFUL INTERMEDIATES BY DIAZOSULFONE AND SULFONATE C-H INSERTION.

Intramolecular C-H insertion on diazosulfone and diazosulfonate substrates was used to prepare synthetically useful intermediates from easily available starting materials.

A 9,000 Year History of Seal Hunting on Lake Baikal, Siberia: The Zooarchaeology of Sagan-Zaba II.

Sagan-Zaba II, a habitation site on the shore of Siberia's Lake Baikal, contains a record of seal hunting that spans much of the Holocene, making it one of the longest histories of seal use in North Asia. Zooarchaeological analyses of the 16,000 Baikal seal remains from this well-dated site clearly show that sealing began here at least 9000 calendar years ago. The use of these animals at Sagan-Zaba appears to have peaked in the Middle Holocene, when foragers used the site as a spring hunting and processing location for yearling and juvenile seals taken on the lake ice. After 4800 years ago, seal use declined at the site, while the relative importance of ungulate hunting and fishing increased. Pastoralists began occupying Sagan-Zaba at some point during the Late Holocene, and these groups too utilized the lake's seals. Domesticated animals are increasingly common after about 2000 years ago, a pattern seen elsewhere in the region, but spring and some summer hunting of seals was still occurring. This use of seals by prehistoric herders mirrors patterns of seal use among the region's historic and modern groups. Overall, the data presented in the paper demonstrate that Lake Baikal witnessed thousands of years of human use of aquatic resources.

PRACTICAL PREPARATION OF RESVERATROL 3-O-ß-D-GLUCURONIDE.

A practical synthesis of resveratrol 3-O-ß-D-glucuronide, suitable for preparation of large quantities, was developed using selective deacetylation of resveratrol triacetate with ammonium acetate. A simplified procedure for large scale preparation of resveratrol is also reported.

Sulfur ylide-initiated thio-claisen rearrangements. The synthesis of highly substituted indolines.

The coupling of rhodium carbenoids from vinyl diazoacetates with 2-thio-3-alkyl indoles was found to generate C(3) quaternary substituted indolines via a thionium ylide-initiated [3,3]-sigmatropic rearrangement.