Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis*,†,‡

Microbial communities have potential evidential utility for forensic applications. However, bioinformatic analysis of high‐throughput sequencing data varies widely among laboratories. These differences can potentially affect microbial community composition and downstream analyses. To illustrate the importance of standardizing methodology, we compared analyses of postmortem microbiome samples using several bioinformatic pipelines, varying minimum library size or minimum number of sequences per sample, and sample size. Using the same input sequence data, we found that three open‐source bioinformatic pipelines, MG‐RAST, mothur, and QIIME2, had significant differences in relative abundance, alpha‐diversity, and beta‐diversity, despite the same input data. Increasing minimum library size and sample size increased the number of low‐abundant and infrequent taxa detected. Our results show that bioinformatic pipeline and parameter choice affect results in important ways. Given the growing potential application of forensic microbiology to the criminal justice system, continued research on standardizing computational methodology will be important for downstream applications.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154468/1/jfo14213_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154468/2/jfo14213.pd

First results of a study of TeV emission from GRBs in Milagrito

Milagrito, a detector sensitive to γ-rays at TeV energies, monitored the northern sky during the period February 1997 through May 1998. With a large field of view and high duty cycle, this instrument was used to perform a search for TeV counterparts to γ-ray bursts. Within the Milagrito field of view 54 γ-ray bursts at keV energies were observed by the Burst And Transient Satellite Experiment (BATSE) aboard the Compton Gamma-Ray Observatory. This paper describes the results of a preliminary analysis to search for TeV emission correlated with BATSE detected bursts. Milagrito detected an excess of events coincident both spatially and temporally with GRB 970417a, with chance probability 2.8×10−5 within the BATSE error radius. No other significant correlations were detected. Since 54 bursts were examined the chance probability of observing an excess with this significance in any of these bursts is 1.5×10−3. The statistical aspects and physical implications of this result are discussed

Milagro: A TeV gamma-ray monitor of the Northern Hemisphere Sky

A new type of very high energy (\u3e a few 100 GeV) gamma-ray observatory, Milagro, has been built with a large field of view of \u3e1 steradian and nearly 24 hours/day operation. Milagrito, a prototype for Milagro, was operated from February 1997 to May 1998. During the summer of 1998, Milagrito was dismantled and Milagro was built. Both detectors use a 80 m×60 m×8 mpond of water in which a 3 m×3 m grid of photomultiplier tubes detects the Cherenkov light produced in the water by the relativistic particles in extensive air showers. Milagrito was smaller and had only one layer of photomultipliers, but allowed the technique to be tested. Milagrito observations of the Moon’s shadow and Mrk 501 are consistent with the Monte Carlo prediction of the telescopes parameters, such as effective area and angular resolution. Milagro is larger and consists of two layers of photomultiplier tubes. The bottom layer detects penetrating particles that are used to reject the background of cosmic-ray initiated showers

Results from the Milagrito experiment

The Milagro water Cherenkov detector near Los Alamos, New Mexico is the first air shower detector capable of continuously monitoring the sky at energies between 500 GeV and 20 TeV. Preliminary results of the Milagro experiment are presented. A predecessor of the Milagro detector, Milagrito, was operational from February 1997 to May 1998. Milagrito consisted of 228 8″ photomultiplier tubes (PMTs) arranged in a grid with a 2.8 meter spacing and submerged in 1–2 meters of water. During its operation, Milagrito collected in excess of 9 billion events with a median energy of about 3 TeV. The detector’s sensitivity extends below 1 TeV for showers from near zenith. The results of an all sky search for the Milagrito data for both transient and DC sources will be presented, including the Crab Nebula and active galaxies Markarian 501 and 421, which are known sources of TeV gamma-rays. Also presented will be a study of the TeV emission from gamma ray bursts (GRBs) in Milagrito’s field of view detected by the BATSE experiment on the Compton Gamma-Ray Observatory

Detection of 6 November 1997 ground level event by Milagrito

Solar Energetic Particles (SEPs) with energies exceeding 10 GeV associated with the 6 November 1997 solar flare/CME (coronal mass ejection) have been detected with Milagrito, a prototype of the Milagro Gamma Ray Observatory. While SEP acceleration beyond 1 GeV is well established, few data exist for protons or ions beyond 10 GeV. The Milagro observatory, a ground based water Cherenkov detector designed for observing very high energy gamma ray sources, can also be used to study the Sun. Milagrito, which operated for approximately one year in 1997/98, was sensitive to solar proton and neutron fluxes above ∼4 GeV. In its scaler mode, Milagrito registered a rate increase coincident with the 6 November 1997 ground level event observed by Climax and other neutron monitors. A preliminary analysis suggests the presence of \u3e10 GeV particles

The Milagro gamma-ray observatory

The Milagro water Cherenkov detector began full operation in January 2000. This detector is capable of monitoring the Northern sky at energies above 500 GeV for sources of equivalent strength to the Crab Nebula over one year of integration. We report on the current performance and sensitivity of Milagro

Milagro: A TeV observatory for gamma-ray bursts

Observation of prompt TeV γ-rays from GRBs requires a new type of detector to overcome the low duty factor and small field of view of current TeV observatories. Milagro is such a new type of very high energy (\u3e a few 100 GeV) gamma-ray observatory, which has a large field of view of \u3e1 steradian and 24 hours/day operation. Milagrito, a prototype for Milagro, was operated from February 1997 to May 1998. During the summer of 1998, Milagrito was dismantled and Milagro was built. Both detectors use a 80 m×60 m×8 m pond of water in which a 3 m×3 m grid of photomultiplier tubes detects the Cherenkov light produced in the water by the relativistic particles in extensive air showers. Milagrito was smaller and had only one layer of photomultipliers, but allowed the technique to be tested. Milagrito observations of the Moon’s shadow and Mrk 501 are consistent with the Monte Carlo prediction of the telescope’s parameters, such as effective area and angular resolution. Milagro will have improved flux sensitivity over Milagrito due to larger effective area, better angular resolution and cosmic-ray background rejection

Distribution of Mycobacterium ulcerans in Buruli Ulcer Endemic and Non-Endemic Aquatic Sites in Ghana

Mycobacterium ulcerans, the causative agent of Buruli ulcer, is an emerging environmental bacterium in Australia and West Africa. The primary risk factor associated with Buruli ulcer is proximity to slow moving water. Environmental constraints for disease are shown by the absence of infection in arid regions of infected countries. A particularly mysterious aspect of Buruli ulcer is the fact that endemic and non-endemic villages may be only a few kilometers apart within the same watershed. Recent studies suggest that aquatic invertebrate species may serve as reservoirs for M. ulcerans, although transmission pathways remain unknown. Systematic studies of the distribution of M. ulcerans in the environment using standard ecological methods have not been reported. Here we present results from the first study based on random sampling of endemic and non-endemic sites. In this study PCR-based methods, along with biofilm collections, have been used to map the presence of M. ulcerans within 26 aquatic sites in Ghana. Results suggest that M. ulcerans is present in both endemic and non-endemic sites and that variable number tandem repeat (VNTR) profiling can be used to follow chains of transmission from the environment to humans. Our results suggesting that the distribution of M. ulcerans is far broader than the distribution of human disease is characteristic of environmental pathogens. These findings imply that focal demography, along with patterns of human water contact, may play a major role in transmission of Buruli ulcer

Broadband Multi-wavelength Properties of M87 during the 2017 Event Horizon Telescope Campaign

Abstract: In 2017, the Event Horizon Telescope (EHT) Collaboration succeeded in capturing the first direct image of the center of the M87 galaxy. The asymmetric ring morphology and size are consistent with theoretical expectations for a weakly accreting supermassive black hole of mass ∼6.5 × 109 M ⊙. The EHTC also partnered with several international facilities in space and on the ground, to arrange an extensive, quasi-simultaneous multi-wavelength campaign. This Letter presents the results and analysis of this campaign, as well as the multi-wavelength data as a legacy data repository. We captured M87 in a historically low state, and the core flux dominates over HST-1 at high energies, making it possible to combine core flux constraints with the more spatially precise very long baseline interferometry data. We present the most complete simultaneous multi-wavelength spectrum of the active nucleus to date, and discuss the complexity and caveats of combining data from different spatial scales into one broadband spectrum. We apply two heuristic, isotropic leptonic single-zone models to provide insight into the basic source properties, but conclude that a structured jet is necessary to explain M87’s spectrum. We can exclude that the simultaneous γ-ray emission is produced via inverse Compton emission in the same region producing the EHT mm-band emission, and further conclude that the γ-rays can only be produced in the inner jets (inward of HST-1) if there are strongly particle-dominated regions. Direct synchrotron emission from accelerated protons and secondaries cannot yet be excluded