Internet-based profiler system as integrative framework to support translational research

BACKGROUND: Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler. TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability. The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions. RESULTS: The generic design of this system makes it compatible with multiple organ system (e.g., prostate, breast, lung, renal, and hematopoietic system,). Studies and folders are restricted to authorized users as required. Over the past 5 years, investigators at 2 academic institutions have scanned 656 TMA experiments and collected 63,311 digital images of these tissue samples. 68 pathologists from 12 major user groups have accessed the system. Two groups directly link clinical data from over 500 patients for immediate access and the remaining groups choose to maintain clinical and pathology data on separate systems. Profiler currently has 170 K data points such as staining intensity, tumor grade, and nuclear size. Due to the relational database structure, analysis can be easily performed on single or multiple TMA experimental results. The TMA module of Profiler can maintain images acquired from multiple systems. CONCLUSION: We have developed a robust process to develop molecular biomarkers using TMA technology and an internet-based database system to track all steps of this process. This system is extendable to other types of molecular data as separate modules and is freely available to academic institutions for licensing

Developed in collaboration with and endorsed by the Heart Rhythm Society (HRS), the American College of Cardiology (ACC), the American Heart Association (AHA), and the Association for European Paediatric and Congenital Cardiology (AEPC). Endorsed by the Asia Pacific Heart Rhythm Society (APHRS), the Indian Heart Rhythm Society (IHRS), and the Latin American Heart Rhythm Society (LAHRS).

AbstractIn view of the increasing complexity of both cardiovascular implantable electronic devices (CIEDs) and patients in the current era, practice guidelines, by necessity, have become increasingly specific. This document is an expert consensus statement that has been developed to update and further delineate indications and management of CIEDs in pediatric patients, defined as ≤21 years of age, and is intended to focus primarily on the indications for CIEDs in the setting of specific disease categories. The document also highlights variations between previously published adult and pediatric CIED recommendations and provides rationale for underlying important differences. The document addresses some of the deterrents to CIED access in low- and middle-income countries and strategies to circumvent them. The document sections were divided up and drafted by the writing committee members according to their expertise. The recommendations represent the consensus opinion of the entire writing committee, graded by class of recommendation and level of evidence. Several questions addressed in this document either do not lend themselves to clinical trials or are rare disease entities, and in these instances recommendations are based on consensus expert opinion. Furthermore, specific recommendations, even when supported by substantial data, do not replace the need for clinical judgment and patient-specific decision-making. The recommendations were opened for public comment to Pediatric and Congenital Electrophysiology Society (PACES) members and underwent external review by the scientific and clinical document committee of the Heart Rhythm Society (HRS), the science advisory and coordinating committee of the American Heart Association (AHA), the American College of Cardiology (ACC), and the Association for European Paediatric and Congenital Cardiology (AEPC). The document received endorsement by all the collaborators and the Asia Pacific Heart Rhythm Society (APHRS), the Indian Heart Rhythm Society (IHRS), and the Latin American Heart Rhythm Society (LAHRS). This document is expected to provide support for clinicians and patients to allow for appropriate CIED use, appropriate CIED management, and appropriate CIED follow-up in pediatric patients

The Evolution of Extracellular Matrix

We present a perspective on the molecular evolution of the extracellular matrix (ECM) in metazoa that draws on research publications and data from sequenced genomes and expressed sequence tag libraries. ECM components do not function in isolation, and the biological ECM system or “adhesome” also depends on posttranslational processing enzymes, cell surface receptors, and extracellular proteases. We focus principally on the adhesome of internal tissues and discuss its origins at the dawn of the metazoa and the expansion of complexity that occurred in the chordate lineage. The analyses demonstrate very high conservation of a core adhesome that apparently evolved in a major wave of innovation in conjunction with the origin of metazoa. Integrin, CD36, and certain domains predate the metazoa, and some ECM-related proteins are identified in choanoflagellates as predicted sequences. Modern deuterostomes and vertebrates have many novelties and elaborations of ECM as a result of domain shuffling, domain innovations and gene family expansions. Knowledge of the evolution of metazoan ECM is important for understanding how it is built as a system, its roles in normal tissues and disease processes, and has relevance for tissue engineering, the development of artificial organs, and the goals of synthetic biology

Magnetic structures and turbulence in SN 1006 revealed with imaging X-ray polarimetry

Young supernova remnants (SNRs) strongly modify surrounding magnetic fields, which in turn play an essential role in accelerating cosmic rays (CRs). X-ray polarization measurements probe magnetic field morphology and turbulence at the immediate acceleration site. We report the X-ray polarization distribution in the northeastern shell of SN1006 from a 1 Ms observation with the Imaging X-ray Polarimetry Explorer (IXPE). We found an average polarization degree of $22.4\pm 3.5\%$ and an average polarization angle of $-45.4\pm 4.5^\circ$ (measured on the plane of the sky from north to east). The X-ray polarization angle distribution reveals that the magnetic fields immediately behind the shock in the northeastern shell of SN 1006 are nearly parallel to the shock normal or radially distributed, similar to that in the radio observations, and consistent with the quasi-parallel CR acceleration scenario. The X-ray emission is marginally more polarized than that in the radio band. The X-ray polarization degree of SN 1006 is much larger than that in Cas A and Tycho, together with the relatively tenuous and smooth ambient medium of the remnant, favoring that CR-induced instabilities set the turbulence in SN 1006 and CR acceleration is environment-dependent.Comment: 15 pages, 4 Figures, 2 Tables; accepted for publication in The Astrophysical Journa

The first X-ray polarimetric observation of the black hole binary LMC X-1

We report on an X-ray polarimetric observation of the high-mass X-ray binary LMC X-1 in the high/soft state, obtained by the Imaging X-ray Polarimetry Explorer (IXPE) in October 2022. The measured polarization is below the minimum detectable polarization of 1.1 per cent (at the 99 per cent confidence level). Simultaneously, the source was observed with the NICER, NuSTAR and SRG/ART-XC instruments, which enabled spectral decomposition into a dominant thermal component and a Comptonized one. The low 2-8 keV polarization of the source did not allow for strong constraints on the black-hole spin and inclination of the accretion disc. However, if the orbital inclination of about 36 degrees is assumed, then the upper limit is consistent with predictions for pure thermal emission from geometrically thin and optically thick discs. Assuming the polarization degree of the Comptonization component to be 0, 4, or 10 per cent, and oriented perpendicular to the polarization of the disc emission (in turn assumed to be perpendicular to the large scale ionization cone orientation detected in the optical band), an upper limit to the polarization of the disc emission of 1.0, 0.9 or 0.9 per cent, respectively, is found (at the 99 per cent confidence level).Comment: 12 pages, 9 figures, 4 tables. Accepted for publication in MNRA

Magnetic Field Properties inside the Jet of Mrk 421: Multiwavelength Polarimetry Including the Imaging X-ray Polarimetry Explorer

We conducted a polarimetry campaign from radio to X-ray wavelengths of the high-synchrotron-peak (HSP) blazar Mrk 421, including Imaging X-ray Polarimetry Explorer (IXPE) measurements on 2022 December 6-8. We detected X-ray polarization of Mrk 421 with a degree of $\Pi_{\rm X}$=14$\pm$1$\%$ and an electric-vector position angle $\psi_{\rm X}$=107$\pm$3$^{\circ}$ in the 2-8 keV band. From the time variability analysis, we find a significant episodic variation in $\psi_{\rm X}$. During 7 months from the first IXPE pointing of Mrk 421 in 2022 May, $\psi_{\rm X}$ varied across the range of 0$^{\circ}$ to 180$^{\circ}$, while $\Pi_{\rm X}$ maintained similar values within $\sim$10-15$\%$. Furthermore, a swing in $\psi_{\rm X}$ in 2022 June was accompanied by simultaneous spectral variations. The results of the multiwavelength polarimetry show that the X-ray polarization degree was generally $\sim$2-3 times greater than that at longer wavelengths, while the polarization angle fluctuated. Additionally, based on radio, infrared, and optical polarimetry, we find that rotation of $\psi$ occurred in the opposite direction with respect to the rotation of $\psi_{\rm X}$ over longer timescales at similar epochs. The polarization behavior observed across multiple wavelengths is consistent with previous IXPE findings for HSP blazars. This result favors the energy-stratified shock model developed to explain variable emission in relativistic jets. The accompanying spectral variation during the $\psi_{\rm X}$ rotation can be explained by a fluctuation in the physical conditions, e.g., in the energy distribution of relativistic electrons. The opposite rotation direction of $\psi$ between the X-ray and longer-wavelength polarization accentuates the conclusion that the X-ray emitting region is spatially separated from that at longer wavelengths.Comment: 17 pages, 13 figures, 4 tables; Accepted for publication in A&

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Glaciers of the McMurdo Dry Valleys: Terrestrial analog for Martian polar sublimation

Abstract: The surfaces of the Martian north and south polar residual caps are marked by unusual ice features: dark spiralesque troughs up to 1 km deep, 10 km wide and 300 km long appear on both ice caps, and circular pits that make up the "swiss-cheese" terrain appear on the south polar cap

Modeling Wood Fibre Length in Black Spruce (Picea mariana (Mill.) BSP) Based on Ecological Land Classification

Effective planning to optimize the forest value chain requires accurate and detailed information about the resource; however, estimates of the distribution of fibre properties on the landscape are largely unavailable prior to harvest. Our objective was to fit a model of the tree-level average fibre length related to ecosite classification and other forest inventory variables depicted at the landscape scale. A series of black spruce increment cores were collected at breast height from trees in nine different ecosite groups within the boreal forest of northeastern Ontario, and processed using standard techniques for maceration and fibre length measurement. Regression tree analysis and random forests were used to fit hierarchical classification models and find the most important predictor variables for the response variable area-weighted mean stem-level fibre length. Ecosite group was the best predictor in the regression tree. Longer mean fibre-length was associated with more productive ecosites that supported faster growth. The explanatory power of the model of fitted data was good; however, random forests simulations indicated poor generalizability. These results suggest the potential to develop localized models linking wood fibre length in black spruce to landscape-level attributes, and improve the sustainability of forest management by identifying ideal locations to harvest wood that has desirable fibre characteristics