A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain

Biomedical data are becoming increasingly complex and heterogeneous in nature. The data are stored in distributed information systems, using a variety of data models, and are processed by increasingly more complex tools that analyze and visualize them. We present in this paper our framework for integrating biomedical research data and tools into a unique Web front end. Our framework is applied to the University of Washington’s Human Brain Project. Specifically, we present solutions to four integration tasks: definition of complex mappings from relational sources to XML, distributed XQuery processing, generation of heterogeneous output formats, and the integration of heterogeneous data visualization and analysis tools

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys

Tricuspid valve replacement outcomes in a diverse variety of valve replacement cases: Mortality, mechanical versus biological – A single-center study

Background: The initial trial in tricuspid surgery is repair; however, replacement is done whenever the valve is badly diseased. Tricuspid valve replacement (TVR) as an isolated procedure and combined with other valve replacements presents a challenge as these patients are in the high-risk subset. Materials and Methods: The present retrospective study was performed using the medical records of 42 cases who underwent TVR since 2017 at our institute. The mean age of the participants was 36.3 ± 13.2 years and male–female was 66.7% and 33.3%, respectively. Isolated TVR was done in 35.7% of cases, associated with mitral valve replacement (MVR) in 38.1%, with aortic valve replacement (AVR) in 4.8%, triple-valve replacement (MV, TV, and AV) in 19.0%, and TVR associated with pulmonary valve replacement in 2.4% of cases. This diverse variety of valve replacement cases is the highlight of our study. About 30.9% of participants were undergoing the procedure as a redo surgery. Trial of repair was given in 33.3% of cases. Moreover, bioprosthesis and mechanical valve prosthesis were used in 73.8% and 26.2%, respectively. Results: Early mortality occurred in 8 (19.0%) cases. Cause of death common in all deaths was right ventricular failure in all cases 8/8 (100%) seconded by multi-organ failure in 7/8 cases (87.5%), previous cardiac surgery was a factor in 4/8 (50%) cases, mediastinitis occurred in 2/8 (25%) cases, and both arrhythmias and cerebrovascular accident happened in 1/8 (12.5%) case each. Mortality rate was 3/15 (20.0%) in cases of isolated TV surgery. Mortality rate for concomitant MVR was 3/15 (20.0%), and for concomitant AVR with MVR (triple-valve replacement) was 2/8 (25.0%). No early mortality happened in the concomitant AVR and concomitant pulmonary valve replacement group. Late mortality happened in 11/42 (26.2%) cases during follow-up. Total mortality as per the valve types has been 5/11 (45.5%) in the mechanical valve replacement group and 14/31 (45.2%) for the biological valve group. Conclusions: The patients who require TVR are usually high-risk surgical candidates with high early and late mortality. The most common cause of death was right ventricular failure in this study. TVR associated with other heart valve replacement increases the risk strata of the patient which is the highlight of our study. In the end, we conclude that we had 19.0% early (0–30 days) and 26.2% late mortality (0–1 year) making a composite of 45.2% mortality at the end of 1 year. No difference in the effect of mortality as per the valve type has been observed

Aneurysmal bone cyst of thoracic spine mimicking spinal tuberculosis

A 22-year-old female presented to our services with back pain and paraparesis for 11 months. She was earlier diagnosed with tuberculosis of spine, and antitubercular chemotherapy was started. However her condition had worsened. Plain and contrast-enhanced computed tomography scans of the thorax and magnetic resonance imaging of the thoracic spine showed heterogenous, lytic, expansile lesion involving third thoracic vertebra with epidural extension and large bilateral paraspinal and mediastinal components. Multiple variably sized loculations with fluid-fluid levels were seen within the lesion. These imaging findings suggestive of aneurysmal bone cyst of thoracic spine were compared with the findings seen 11 months earlier, which were mistaken for spinal tuberculosis. Histopathology confirmed the diagnosis of aneurysmal bone cyst. The imaging features, diagnostic challenges and the lessons learned have been briefly discussed

Bricks as historical record of heavy metals fallout: study on copper accumulation in Agra soils since 1910

Peat, ice deposits and aquatic sediments, which have been used as a geochemical monitor of atmospheric heavy metal pollution until now, are open and dynamic systems and can be easily affected by climatic variations. In contrast, bricks, which are more compact, can act as a better geochemical monitor. Analysis of Cu, Cr, Ni, Pb and Zn in scores of soil and brick (baked/unbaked) samples, collected from a large area in and around a rapidly growing Indian city, Agra, reveals approximately similar concentrations in soils and bricks, thereby showing insignificant fractionation of these metals during brick making. Further, metals concentration in the core of bricks remains unaffected by any significant amount of acidic and alkaline rain. Thus, the feasibility of a novel role of bricks as a geochemical monitor of atmospheric heavy metal pollution has been tested. Utilizing this concept, an attempt has also been made to trace the history of atmospheric copper depositions in the soils of Agra during the last 100 years

Supplemental Materials - A Theory for Polymicrogyria and Brain Arteriovenous Malformations in HHT

Methods, Table e-1, and Figures e-1, e-2, and e-3 for manuscrip

Data from: A theory for polymicrogyria and brain arteriovenous malformations in HHT

Hereditary hemorrhagic telangiectasia (HHT) is generally considered a disorder of endothelial dysfunction, characterized by the development of multiple systemic arteriovenous malformations (AVMs), including within the brain. However, there have recently been a number of reports correlating HHT with malformations of cortical development, of which polymicrogyria is the most common type. Here we present seven new cases demonstrating polymicrogyria in HHT, six of which demonstrate a brain AVM (bAVM) in close spatial proximity, with the aim of providing a common origin for the association. Upon reviewing patient genetics and imaging data and comparing with previously reported findings, we form two new conclusions: i) polymicrogyria in HHT appears exclusively associated with a subset of mutations in the transmembrane protein endoglin that is involved with blood flow related mechanotransduction signaling during angiogenesis, and ii) the polymicrogyria is characteristically unilateral, typically focal, and correlates with vascular regions experiencing low fluid shear stress during corticogenesis in utero. Integrating these with findings in the literature from genetics and molecular biology experiments, we propose a theory suggesting dominant-negative endoglin mutations may predispose focal, aberrant hypersprouting angiogenesis during corticogenesis that leads to the production of polymicrogyria. This hypoxic insult may further serve as the revealing trigger for later development of a spatially coincident bAVM. This hypothesis suggests an essential role for endoglin-mediated hemodynamic mechanotransduction in normal corticogenesis

Cardiovascular magnetic resonance based diagnosis of left ventricular non-compaction cardiomyopathy: impact of cine bSSFP strain analysis

Abstract Background Investigation of the myocardial strain characteristics of the left ventricular non-compaction (LVNC) phenotype with cardiovascular magnetic resonance (CMR) feature tracking. Methods CMR cine balanced steady-state free precession data sets of 59 retrospectively identified LVNC phenotype patients (40 years, IQR: 28–50 years; 51% male) and 36 healthy subjects (39 years, IQR: 30–47 years; 44% male) were evaluated for LV volumes, systolic function and mass. Hypertrabeculation in patients and healthy subjects was evaluated against established CMR diagnostic criteria. Global circumferential strain (GCS), global radial strain (GRS) and global longitudinal strain (GLS) were evaluated with feature-tracking software. Subgroup analyses were performed in patients (n = 25) and healthy subjects (n = 34) with normal LV volumetrics, and with healthy subjects (n = 18) meeting at least one LVNC diagnostic criteria. Results All LVNC phenotype patients, as well as a significant proportion of healthy subjects, met morphology-based CMR diagnostic criteria: non-compacted (NC): compacted myocardial diameter ratio > 2.3 (100% vs. 19.4%), NC mass > 20% (100% vs. 44.4%) and > 25% (100% vs. 13.9%), and NC mass indexed to body surface area > 15 g/m2 (100% vs. 41.7%). LVNC phenotype patients demonstrated reduced GRS (26.4% vs. 37.1%; p < 0.001), GCS (− 16.5% vs. -20.5%; p < 0.001) and GLS (− 14.6% vs. -17.1%; p < 0.001) compared to healthy subjects, with statistically significant differences persisting on subgroup comparisons of LVNC phenotype patients with healthy subjects meeting diagnostic criteria. GCS also demonstrated independent and incremental diagnostic value beyond each of the morphology-based CMR diagnostic criteria. Conclusions LVNC phenotype patients demonstrate impaired strain by CMR feature tracking, also present on comparison of subjects with normal LV volumetrics meeting diagnostic criteria. The high proportion of healthy subjects meeting morphology-based CMR diagnostic criteria emphasizes the important potential complementary diagnostic value of strain in differentiating LVNC from physiologic hypertrabeculation