DNA methylation profiling to assess pathogenicity of BRCA1 unclassified variants in breast cancer

Germline pathogenic mutations in BRCA1 increase risk of developing breast cancer. Screening for mutations in BRCA1 frequently identifies sequence variants of unknown pathogenicity and recent work has aimed to develop methods for determining pathogenicity. We previously observed that tumor DNA methylation can differentiate BRCA1-mutated from BRCA1-wild type tumors. We hypothesized that we could predict pathogenicity of variants based on DNA methylation profiles of tumors that had arisen in carriers of unclassified variants. We selected 150 FFPE breast tumor DNA samples [47 BRCA1 pathogenic mutation carriers, 65 BRCAx (BRCA1-wild type), 38 BRCA1 test variants] and analyzed a subset (n=54) using the Illumina 450K methylation platform, using the remaining samples for bisulphite pyrosequencing validation. Three validated markers (BACH2, C8orf31, and LOC654342) were combined with sequence bioinformatics in a model to predict pathogenicity of 27 variants (independent test set). Predictions were compared with standard multifactorial likelihood analysis. Prediction was consistent for c.5194-12G>A (IVS 19-12 G>A) (P>0.99); 13 variants were considered not pathogenic or likely not pathogenic using both approaches. We conclude that tumor DNA methylation data alone has potential to be used in prediction of BRCA1 variant pathogenicity but is not independent of estrogen receptor status and grade, which are used in current multifactorial models to predict pathogenicity

Comparison of human uterine cervical electrical impedance measurements derived using two tetrapolar probes of different sizes

BACKGROUND We sought to compare uterine cervical electrical impedance spectroscopy measurements employing two probes of different sizes, and to employ a finite element model to predict and compare the fraction of electrical current derived from subepithelial stromal tissue. METHODS Cervical impedance was measured in 12 subjects during early pregnancy using 2 different sizes of the probes on each subject. RESULTS Mean cervical resistivity was significantly higher (5.4 vs. 2.8 Ωm; p < 0.001) with the smaller probe in the frequency rage of 4–819 kHz. There was no difference in the short-term intra-observer variability between the two probes. The cervical impedance measurements derived in vivo followed the pattern predicted by the finite element model. CONCLUSION Inter-electrode distance on the probes for measuring cervical impedance influences the tissue resistivity values obtained. Determining the appropriate probe size is necessary when conducting clinical studies of resistivity of the cervix and other human tissues

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Sex identification of ancient DNA samples using a microfluidic device.

Ancient DNA is the name given to the degraded, fragmented, and chemically damaged biomolecules that can be recovered from archaeological remains of plants, animals, and humans. Where ancient human DNA has survived at archaeological sites, it can give valuable information and is especially useful for its potential to identify kinship, population affinities, pathogens, and biological sex. Here, we describe the operation of a microfluidic device for the sex identification of ancient DNA samples using an efficient sample handling process. DNA is extracted from powdered bone samples and abasic sites labeled with biotin. Streptavidin-coated superparamagnetic particles are used to isolate the labeled DNA prior to amplification of the Amelogenin sex marker

Ecological studies of vegetation in short-tailed shearwater colonies in Tasmania

Extensive modification of coastal vegetation at the Pineapples and Cape Deslacs rookeries is related to the burrowing,trampling and guano deposition of short-tailed shearwaters (Puffinus tenuirodtris).Ordination and classification of the associated vegetation and measurement of soil nutrient levels demonstrate two distinct but interactin phases of vegetation succession. These are affected by coastal influence, edaphic factors and the presence or absence of nesting areas

The spectral energy distributions of active galactic nuclei

We present spectral energy distributions (SEDs) of 41 active galactic nuclei, derived from multiwavelength photometry and archival spectroscopy. All of the SEDs span at least 0.09 to 30 μm, but in some instances wavelength coverage extends into the X-ray, far-infrared, and radio. For some active galactic nuclei (AGNs) we have fitted the measured far-infrared photometry with greybody models, while radio flux density measurements have been approximated by power laws or polynomials. We have been able to fill some of the gaps in the spectral coverage using interpolation or extrapolation of simple models. In addition to the 41 individual AGN SEDs, we have produced 72 Seyfert SEDs by mixing SEDs of the central regions of Seyferts with galaxy SEDs. Relative to the literature, our templates have broader wavelength coverage and/or higher spectral resolution. We have tested the utility of our SEDs by using them to generate photometric redshifts for 0 < z ≤ 6.12 AGNs in the Boötes field (selected with X-ray, IR, and optical criteria) and, relative to SEDs from the literature, they produce comparable or better photometric redshifts with reduced flux density residuals

Instantaneous monitoring of heart beat dynamics during anesthesia and sedation

Anesthesia-induced altered arousal depends on drugs having their effect in specific brain regions. These effects are also reflected in autonomic nervous system (ANS) outflow dynamics. To this extent, instantaneous monitoring of ANS outflow, based on neurophysiological and computational modeling, may provide a more accurate assessment of the action of anesthetic agents on the cardiovascular system. This will aid anesthesia care providers in maintaining homeostatic equilibrium and help to minimize drug administration while maintaining antinociceptive effects. In previous studies, we established a point process paradigm for analyzing heartbeat dynamics and have successfully applied these methods to a wide range of cardiovascular data and protocols. We recently devised a novel instantaneous nonlinear assessment of ANS outflow, also suitable and effective for real-time monitoring of the fast hemodynamic and autonomic effects during induction and emergence from anesthesia. Our goal is to demonstrate that our framework is suitable for instantaneous monitoring of the ANS response during administration of a broad range of anesthetic drugs. Specifically, we compare the hemodynamic and autonomic effects in study participants undergoing propofol (PROP) and dexmedetomidine (DMED) administration. Our methods provide an instantaneous characterization of autonomic state at different stages of sedation and anesthesia by tracking autonomic dynamics at very high time-resolution. Our results suggest that refined methods for analyzing linear and nonlinear heartbeat dynamics during administration of specific anesthetic drugs are able to overcome nonstationary limitations as well as reducing inter-subject variability, thus providing a potential real-time monitoring approach for patients receiving anesthesia

New records of marine invertebrates from Ascension Island (central Atlantic)

The sea anemone Telmatactis forskalii, the zoanthid Isaurus tuberculatus, the nemertine Baseodiscus delineatus, the echinoderms Ophiocoma wendtii and Mithrodia clavigera, the molluscs Colubraria canariensis, Glyphepithema turtoni, Tonna pennata, Trivia candidula, Melanella eburnea, Melanella n.sp., Echineulima leucophaes, Stylocheilus striatus, Limaria hians, Pteria hirundo and Callistoctopus macropus, and the crustaceans Tetraclitella sp., Oxynaspis celata, Thor amboinensis and Parribacus antarcticus are recorded from Ascension Island for the first time. A new depth record is given for the sea anemone Telmatactis cricoides. An undescribed shrimp species of the genus Lysmata and the shrimp Lysmata moorei were observed to clean fish at night

Clinical impact of early post-transplant red cell transfusions in kidney transplantation: a systematic review and meta-analysis

Introduction: Red blood cell transfusions (RBCT) represent a potentially modifiable risk factor for HLA sensitisation and adverse outcomes post transplantation. Evidence of the clinical impact of post-transplant RBCT has been infrequently reported. Herein, we performed a systematic review of available literature to assess the prevalence of RBCT post kidney transplant, and the effect of transfusion on transplant outcomes. Methods: We included studies from 2000 to July 2022, published on Medline, Embase and the Transplant Library. Results: Ten studies were analysed which included a total of 32,817 kidney transplant recipients, with a median transfusion prevalence of 40% (range 18-64%). There was significant heterogeneity between studies in terms of patient and allograft characteristics, immunological risk, and immunosuppression protocols. Analysis of unadjusted outcomes showed that post-transplant RBCTs are associated with inferior patient survival, allograft loss, rejection and donor specific antibodies. Adjusted outcomes were described where available, and supported the adverse associations seen in the unadjusted models in many studies. Discussion: This review demonstrates that RBCT post-transplant are common and maybe associated with inferior outcomes, highlighting the urgent need for high quality prospective evidence of the effect of RBCTs on transplant outcomes. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/, identifier, CRD42022348763767