Examination of Amphibian Community and Environmental Relationships in South Texas Using Environmental DNA (eDNA)

Developing more efficient tools to assess amphibian biodiversity and understanding what environmental variables drive amphibian biodiversity are top priorities, as amphibians are facing extinction events across the globe. Environmental DNA (eDNA) surveys are a promising new tool to asses amphibian biodiversity. Throughout the study eDNA metabarcoding along with a targeted eDNA assay and traditional survey methods were used to provide foundational information on amphibian community assemblages throughout South Texas. Water quality, habitat characteristics and soil composition data were collected and used to examine environmental relationships. eDNA metabarcoding detected significantly more amphibian taxonomic units compared to traditional survey methods. eDNA metabarcoding was less sensitive at detecting DNA from a rare-cryptic amphibian compared to a targeted eDNA assay. There were no significant groupings of amphibian communities, some environmental variables were found to be correlated to amphibian community structure

C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenosine and its derivatives

We report that photo-excitation of one-electron-oxidized adenine [A(-H)•] in dAdo and its 2′-deoxyribonucleotides leads to formation of deoxyribose sugar radicals in remarkably high yields. Illumination of A(-H)• in dAdo, 3′-dAMP and 5′-dAMP in aqueous glasses at 143 K leads to 80-100% conversion to sugar radicals at C5′ and C3′. The position of the phosphate in 5′- and 3′-dAMP is observed to deactivate radical formation at the site of substitution. In addition, the pH has a crucial influence on the site of sugar radical formation; e.g. at pH ∼5, photo-excitation of A(-H)• in dAdo at 143 K produces mainly C5′• whereas only C3′• is observed at high pH ∼12. (13)C substitution at C5′ in dAdo yields (13)C anisotropic couplings of (28, 28, 84) G whose isotropic component 46.7 G identifies formation of the near planar C5′•. A β-(13)C 16 G isotropic coupling from C3′• is also found. These results are found to be in accord with theoretically calculated (13)C couplings at C5′ [DFT, B3LYP, 6-31(G) level] for C5′• and C3′•. Calculations using time-dependent density functional theory [TD-DFT B3LYP, 6-31G(d)] confirm that transitions in the near UV and visible induce hole transfer from the base radical to the sugar group leading to sugar radical formation

Health-Related Quality of Life After Stereotactic Body Radiation Therapy for Localized Prostate Cancer: Results From a Multi-institutional Consortium of Prospective Trials

PurposeTo evaluate the early and late health-related quality of life (QOL) outcomes among prostate cancer patients following stereotactic body radiation therapy (SBRT).Methods and MaterialsPatient self-reported QOL was prospectively measured among 864 patients from phase 2 clinical trials of SBRT for localized prostate cancer. Data from the Expanded Prostate Cancer Index Composite (EPIC) instrument were obtained at baseline and at regular intervals up to 6 years. SBRT delivered a median dose of 36.25 Gy in 4 or 5 fractions. A short course of androgen deprivation therapy was given to 14% of patients.ResultsMedian follow-up was 3 years and 194 patients remained evaluable at 5 years. A transient decline in the urinary and bowel domains was observed within the first 3 months after SBRT which returned to baseline status or better within 6 months and remained so beyond 5 years. The same pattern was observed among patients with good versus poor baseline function and was independent of the degree of early toxicities. Sexual QOL decline was predominantly observed within the first 9 months, a pattern not altered by the use of androgen deprivation therapy or patient age.ConclusionLong-term outcome demonstrates that prostate SBRT is well tolerated and has little lasting impact on health-related QOL. A transient and modest decline in urinary and bowel QOL during the first few months after SBRT quickly recovers to baseline levels. With a large number of patients evaluable up to 5 years following SBRT, it is unlikely that unexpected late adverse effects will manifest themselves

Accurate EELS background subtraction – an adaptable method in MATLAB

Electron energy-loss spectroscopy (EELS) is a technique that can give useful information on elemental composition and bonding environments. However in practice, the complexity of the background contributions, which can arise from multiple sources, can hamper the interpretation of the spectra. As a result, background removal is both an essential and difficult part of EELS analysis, especially during quantification of elemental composition. Typically, a power law is used to fit the background but this is often not suitable for many spectra such as in the low-loss region (< 50 eV) and when there are overlapping EELS edges. In this article, we present a series of scripts written in MATLAB v. R2019b that aims to provide statistical information on the model used to fit the background, allowing the user to determine the accuracy of background subtraction. The scripts were written for background subtraction of vibrational EELS in the ultralow-loss region near the zero-loss peak but can also be applied to other kinds of EEL spectra. The scripts can use a range of models for fitting, provided by the Curve Fitting Toolbox of MATLAB, and the user is able to precisely define the window for fitting as well as for edge integration. We demonstrate the advantages of using these scripts by comparing their background subtraction of example spectra to the most commonly used software, Gatan Microscopy Suite 3. The example spectra include those containing multiple scattering, multiple overlapping peaks, as well as vibrational EELS. Additionally, a comprehensive guide to using the scripts has been included in the Supplementary Information

Directional Sinogram Inpainting for Limited Angle Tomography

In this paper we propose a new joint model for the reconstruction of tomography data under limited angle sampling regimes. In many applications of Tomography, e.g. Electron Microscopy and Mammography, physical limitations on acquisition lead to regions of data which cannot be sampled. Depending on the severity of the restriction, reconstructions can contain severe, characteristic, artefacts. Our model aims to address these artefacts by inpainting the missing data simultaneously with the reconstruction. Numerically, this problem naturally evolves to require the minimisation of a non-convex and non-smooth functional so we review recent work in this topic and extend results to fit an alternating (block) descent framework. \oldtext{We illustrate the effectiveness of this approach with numerical experiments on two synthetic datasets and one Electron Microscopy dataset.} \newtext{We perform numerical experiments on two synthetic datasets and one Electron Microscopy dataset. Our results show consistently that the joint inpainting and reconstruction framework can recover cleaner and more accurate structural information than the current state of the art methods

Rationale for Stereotactic Body Radiation Therapy in Treating Patients with Oligometastatic Hormone-Naïve Prostate Cancer

Despite advances in treatment for metastatic prostate cancer, patients eventually progress to castrate-resistant disease and ultimately succumb to their cancer. Androgen deprivation therapy (ADT) is the standard treatment for metastatic prostate cancer and has been shown to improve median time to progression and median survival time. Research suggests that castrate-resistant clones may be present early in the disease process prior to the initiation of ADT. These clones are not susceptible to ADT and may even flourish when androgen-responsive clones are depleted. Stereotactic body radiation therapy (SBRT) is a safe and efficacious method of treating clinically localized prostate cancer and metastases. In patients with a limited number of metastatic sites, SBRT may have a role in eliminating castrate-resistant clones and possibly delaying progression to castrate-resistant disease

Mantle deformation beneath the Chicxulub impact crater

Accepted versio

Rationale for Utilization of Hydrogel Rectal Spacers in Dose Escalated SBRT for the Treatment of Unfavorable Risk Prostate Cancer

In this review we outline the current evidence for the use of hydrogel rectal spacers in the treatment paradigm for prostate cancer with external beam radiation therapy. We review their development, summarize clinical evidence, risk of adverse events, best practices for placement, treatment planning considerations and finally we outline a framework and rationale for the utilization of rectal spacers when treating unfavorable risk prostate cancer with dose escalated Stereotactic Body Radiation Therapy (SBRT)

High-throughput, quantitative analyses of genetic interactions in E. coli.

Large-scale genetic interaction studies provide the basis for defining gene function and pathway architecture. Recent advances in the ability to generate double mutants en masse in Saccharomyces cerevisiae have dramatically accelerated the acquisition of genetic interaction information and the biological inferences that follow. Here we describe a method based on F factor-driven conjugation, which allows for high-throughput generation of double mutants in Escherichia coli. This method, termed genetic interaction analysis technology for E. coli (GIANT-coli), permits us to systematically generate and array double-mutant cells on solid media in high-density arrays. We show that colony size provides a robust and quantitative output of cellular fitness and that GIANT-coli can recapitulate known synthetic interactions and identify previously unidentified negative (synthetic sickness or lethality) and positive (suppressive or epistatic) relationships. Finally, we describe a complementary strategy for genome-wide suppressor-mutant identification. Together, these methods permit rapid, large-scale genetic interaction studies in E. coli