Updating and profiling the natural product-likeness of Latin American compound libraries.

Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.

Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB.

The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries.

Effects of intense storm events on dolphin occurrence and foraging behavior.

As storms become increasingly intense and frequent due to climate change, we must better understand how they alter environmental conditions and impact species. However, storms are ephemeral and provide logistical challenges that prevent visual surveys commonly used to understand marine mammal ecology. Thus, relatively little is known about top predators' responses to such environmental disturbances. In this study, we utilized passive acoustic monitoring to characterize the response of bottlenose dolphins to intense storms offshore Maryland, USA between 2015 and 2017. During and following four autumnal storms, dolphins were detected less frequently and for shorter periods of time. However, dolphins spent a significantly higher percentage of their encounters feeding after the storm than they did before or during. This change in foraging may have resulted from altered distributions and behavior of their prey species, which are prone to responding to environmental changes, such as varied sea surface temperatures caused by storms. It is increasingly vital to determine how these intense storms alter oceanography, prey movements, and the behavior of top predators.

Chemical induction of silent biosynthetic pathway transcription in Aspergillus niger.

Manipulation of the fungal epigenome is hypothesized to be an effective method for accessing natural products from silent biosynthetic pathways. A library of epigenetic modifiers was tested using the fungus Aspergillus niger to determine the impact of small-molecule inhibitors on reversing the transcriptional suppression of biosynthetic genes involved in polyketide (PKS), non-ribosomal peptide (NRPS), and hybrid PKS-NRPS (HPN) production. Examination of expressed sequence tag libraries from A. niger demonstrated that >70% of its PKS-, NRPS-, and HPN-encoding gene clusters were transcriptionally suppressed under standard laboratory culture conditions. Using a chemical epigenetic methodology, we showed that treatment of A. niger with suberoylanilide hydroxamic acid and 5-azacytidine led to the transcriptional upregulation of many secondary-metabolite-encoding biosynthetic gene clusters. Chemical epigenetic modifiers exhibited positional biases for upregulating chromosomally distal gene clusters. In addition, a phylogenetic-based preference was noted in the upregulation of reducing clade I PKS gene clusters, while reducing clade IV PKS gene clusters were largely unaffected. Manipulating epigenetic features in fungi is a powerful method for accessing the products of silent biosynthetic pathways. Moreover, this approach can be readily incorporated into modern microbial screening operations.

Gamma-ray imaging with a Si/CsI(Tl) Compton detector.

We present results from Compton imaging of gamma-ray sources using an instrument constructed from thin silicon scattering detectors and CsI(Tl) absorbing detectors. We have successfully imaged single and double point sources for several common radioactive isotopes ((137)Cs, (60)Co, (22)Na, (54)Mn). The measured angular resolution is 11.6( composite function) FWHM at 662keV. In parallel with the hardware effort, a GEANT4-based simulation code was developed. Comparisons between real and simulated data are discussed.

A three-part study to investigate the incidence and potential etiologies of tadalafil-associated back pain or myalgia.

The potential mechanisms underlying back pain and/or myalgia experienced by men taking tadalafil were investigated. An integrated analysis of 10 placebo-controlled tadalafil clinical trials (N=1846) showed that the incidence of back pain and/or myalgia was 9.4% in patients receiving tadalafil 10 mg (N=394), 8.3% in patients receiving tadalafil 20 mg (N=883) and 3.7% in placebo-treated patients (N=569). One (0.3%) patient receiving tadalafil 10 mg, six (0.7%) patients receiving tadalafil 20 mg, and no patients receiving placebo discontinued treatment due to back pain and/or myalgia. In a prospective study in healthy volunteers, no substantial changes were observed in laboratory markers indicative of inflammation or muscle damage, and tadalafil did not affect renal plasma flow nor produce lumbar or gluteal myositis by positron emission tomography scan or magnetic resonance imaging. Although the mechanism of back pain and/or myalgia remains unknown, these events appear to be self-limiting and a general effect of phosphodiesterase 5 inhibition.

Laser plasma x-ray source for ultrafast time-resolved x-ray absorption spectroscopy.

We describe a laser-driven x-ray plasma source designed for ultrafast x-ray absorption spectroscopy. The source is comprised of a 1 kHz, 20 W, femtosecond pulsed infrared laser and a water target. We present the x-ray spectra as a function of laser energy and pulse duration. Additionally, we investigate the plasma temperature and photon flux as we vary the laser energy. We obtain a 75 µm FWHM x-ray spot size, containing ∼10(6) photons/s, by focusing the produced x-rays with a polycapillary optic. Since the acquisition of x-ray absorption spectra requires the averaging of measurements from >10(7) laser pulses, we also present data on the source stability, including single pulse measurements of the x-ray yield and the x-ray spectral shape. In single pulse measurements, the x-ray flux has a measured standard deviation of 8%, where the laser pointing is the main cause of variability. Further, we show that the variability in x-ray spectral shape from single pulses is low, thus justifying the combining of x-rays obtained from different laser pulses into a single spectrum. Finally, we show a static x-ray absorption spectrum of a ferrioxalate solution as detected by a microcalorimeter array. Altogether, our results demonstrate that this water-jet based plasma source is a suitable candidate for laboratory-based time-resolved x-ray absorption spectroscopy experiments.

Locating blood vessels in retinal images by piecewise threshold probing of a matched filter response.

We describe an automated method to locate and outline blood vessels in images of the ocular fundus. Such a tool should prove useful to eye care specialists for purposes of patient screening, treatment evaluation, and clinical study. Our method differs from previously known methods in that it uses local and global vessel features cooperatively to segment the vessel network. We evaluate our method using hand-labeled ground truth segmentations of 20 images. A plot of the operating characteristic shows that our method reduces false positives by as much as 15 times over basic thresholding of a matched filter response (MFR), at up to a 75% true positive rate. For a baseline, we also compared the ground truth against a second hand-labeling, yielding a 90% true positive and a 4% false positive detection rate, on average. These numbers suggest there is still room for a 15% true positive rate improvement, with the same false positive rate, over our method. We are making all our images and hand labelings publicly available for interested researchers to use in evaluating related methods.

A new objective digital computerized vision screening system.

PURPOSE: Fewer than 40% of children in the crucial younger-than-4 age group are evaluated for visual problems by pediatricians. This is due to impracticality from either a clinical or practice efficiency standpoint. Current photoscreening methods require trained readers and suffer from significant subjectivity and interobserver variability. We report a cross-sectional, double-masked study using new digital imaging with objective, automated, computerized image analysis. METHODS: Two-hundred six children aged 9 months to 16 years were prospectively studied in a University-based pediatric ophthalmology practice. Images were taken by volunteers with a modified digital camera which, when downloaded, were analyzed within 35 seconds by new image analysis software. The analysis was compared to a masked review of a complete pediatric ophthalmic exam. RESULTS: Overall agreement between physician and the objective computerized analysis was 86.9%. Positive predictive value was 91%, sensitivity was 89%, and specificity was 83%. CONCLUSIONS: This automated digital imaging screening system eliminates human bias and provides accurate and immediate results. The system requires no special expertise.

Egomotion estimation of a range camera using the space envelope.

In this paper we present a method to compute the egomotion of a range camera using the space envelope. The space envelope is a geometric model that provides more information than a simple segmentation for correspondences and motion estimation. We describe a novel variation of the maximal matching algorithm that matches surface normals to find correspondences. These correspondences are used to compute rotation and translation estimates of the egomotion. We demonstrate our methods on two image sequences containing 70 images. We also discuss the cases where our methods fail, and additional possible methods for exploiting the space envelope.

Tips for testifying.

The author offers practical suggestions for the witness to help improve effectiveness without compromising truthfulness when testifying in depositions and trial. The guidelines are designed to reduce the podiatrist's apprehension when venturing into the legal arena and to serve as resource material.

Note: Operation of gamma-ray microcalorimeters at elevated count rates using filters with constraints.

Microcalorimeter sensors operated near 0.1 K can measure the energy of individual x- and gamma-ray photons with significantly more precision than conventional semiconductor technologies. Both microcalorimeter arrays and higher per pixel count rates are desirable to increase the total throughput of spectrometers based on these devices. The millisecond recovery time of gamma-ray microcalorimeters and the resulting pulse pileup are significant obstacles to high per pixel count rates. Here, we demonstrate operation of a microcalorimeter detector at elevated count rates by use of convolution filters designed to be orthogonal to the exponential tail of a preceding pulse. These filters allow operation at 50% higher count rates than conventional filters while largely preserving sensor energy resolution.

A high resolution gamma-ray spectrometer based on superconducting microcalorimeters.

Improvements in superconductor device fabrication, detector hybridization techniques, and superconducting quantum interference device readout have made square-centimeter-sized arrays of gamma-ray microcalorimeters, based on transition-edge sensors (TESs), possible. At these collecting areas, gamma microcalorimeters can utilize their unprecedented energy resolution to perform spectroscopy in a number of applications that are limited by closely-spaced spectral peaks, for example, the nondestructive analysis of nuclear materials. We have built a 256 pixel spectrometer with an average full-width-at-half-maximum energy resolution of 53 eV at 97 keV, a useable dynamic range above 400 keV, and a collecting area of 5 cm(2). We have demonstrated multiplexed readout of the full 256 pixel array with 236 of the pixels (91%) giving spectroscopic data. This is the largest multiplexed array of TES microcalorimeters to date. This paper will review the spectrometer, highlighting the instrument design, detector fabrication, readout, operation of the instrument, and data processing. Further, we describe the characterization and performance of the newest 256 pixel array.

Impaired PTPN13 phosphatase activity in spontaneous or HPV-induced squamous cell carcinomas potentiates oncogene signaling through the MAP kinase pathway.

Human papillomaviruses (HPVs) are a causative factor in over 90% of cervical and 25% of head and neck squamous cell carcinomas (HNSCCs). The C terminus of the high-risk HPV 16 E6 oncoprotein physically associates with and degrades a non-receptor protein tyrosine phosphatase (PTPN13), and PTPN13 loss synergizes with H-Ras(V12) or ErbB2 for invasive growth in vivo. Oral keratinocytes that have lost PTPN13 and express H-Ras(V12) or ErbB2 show enhanced Ras/RAF/MEK/Erk signaling. In co-transfection studies, wild-type PTPN13 inhibited Ras/RAF/MEK/Erk signaling in HEK 293 cells that overexpress ErbB2, EGFR or H-Ras(V12), whereas an enzymatically inactive PTPN13 did not. Twenty percent of HPV-negative HNSCCs had PTPN13 phosphatase mutations that did not inhibit Ras/RAF/MEK/Erk signaling. Inhibition of Ras/RAF/MEK/Erk signaling using MEK inhibitor U0126 blocked anchorage-independent growth in cells lacking PTPN13. These findings show that PTPN13 phosphatase activity has a physiologically significant role in regulating MAP kinase signaling.

Locating blood vessels in retinal images by piece-wise threshold probing of a matched filter response.

We describe an automated method to locate and outline blood vessels in images of the ocular fundus. Such a tool should prove useful to eyecare specialists for purposes of patient screening, treatment evaluation, and clinical study. Our method differs from previously known methods in that it uses local and global vessel features cooperatively to segment the vessel network. A comparison of our method against hand-labeled ground truth segmentations of five images yielded 65% sensitivity and 81% specificity. A previously known technique yielded 69% sensitivity and 63% specificity. For a baseline, we also compared the ground truth against a second hand labeling, yielding 80% sensitivity and 90% specificity. These numbers indicate our method improves upon the previously known technique, but that further improvement is still possible.

Effects of genetic, epigenetic, and environmental factors on taxol content in Taxus brevifolia and related species.

The demand for taxol, a promising cancer chemotherapeutic agent, far exceeds supply. Presently, taxol is derived from the bark of the Pacific yew, Taxus brevifolia, a small, slow-growing evergreen tree native to the northwestern United States. Knowledge of the distribution and magnitude of genetic and non-genetic sources of variation in taxol content in the genus Taxus is necessary if supply issues are to be met through plant harvesting. Analytical determinations of taxol, cephalomannine, and baccatin III in more than 200 trees representing several populations of T. brevifolia and other yew taxa indicate that (1) significant variation in taxane content exists among and within populations and species, (2) taxol levels exceeding those reported for T. brevifolia bark were found in shoots of individual trees from most taxa studied, and (3) the season in which samples are collected and handling procedures can influence taxane content.