Prevalence of Chlamydia infection among women visiting a gynaecology outpatient department: evaluation of an in-house PCR assay for detection of Chlamydia trachomatis

<p>Abstract</p> <p>Background</p> <p>Screening women for <it>Chlamydia trachomatis </it>infection in developing countries is highly desirable because of asymptomatic infection. The existing diagnostic methods in developing countries are not effective and their sensitivity fall below 45.0% which leads to further spread of infection. There is an urgent need for improved and cost effective diagnostic tests that will reduce the burden of sexually transmitted infections in the developing world.</p> <p>Methods</p> <p>Prevalence of <it>C. trachomatis </it>infection among women visiting gynaecology department of Hindu Rao hospital in Delhi, India was determined using Roche Amplicor Multi Well Plate kit (MWP) as well as using in-house PCR assay. We used 593 endocervical swabs for clinical evaluation of the in-house developed assay against Direct Fluorescence Assay (DFA; Group I n = 274) and Roche Amplicor MWP kit (Group II, n = 319 samples) and determined the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) of the in-house developed assay.</p> <p>Results</p> <p>We detected 23.0% positive cases and there was a higher representation of women aged 18-33 in this group. An in-house PCR assay was developed and evaluated by targeting unique sequence within the <it>gyrA </it>gene of <it>C. trachomatis</it>. Specificity of the reaction was confirmed by using genomic DNA of human and other STI related microorganisms as template. Assay is highly sensitive and can detect as low as 10 fg of <it>C. trachomatis </it>DNA. The resolved sensitivity of in-house PCR was 94.5% compared with 88.0% of DFA assay. The high specificity (98.4%) and sensitivity (97.1%) of the in-house assay against Roche kit and availability of test results within 3 hours allowed for immediate treatment and reduced the risk of potential onward transmission.</p> <p>Conclusions</p> <p>The in-house PCR method is cost effective (~ 20.0% of Roche assay) and hence could be a better alternative for routine diagnosis of genital infection by <it>C. trachomatis </it>to facilitate improved screening and treatment management.</p

A binary tree approach to template placement for searches for gravitational waves from compact binary mergers

We demonstrate a new geometric method for fast template placement for searches for gravitational waves from the inspiral, merger and ringdown of compact binaries. The method is based on a binary tree decomposition of the template bank parameter space into non-overlapping hypercubes. We use a numerical approximation of the signal overlap metric at the center of each hypercube to estimate the number of templates required to cover the hypercube and determine whether to further split the hypercube. As long as the expected number of templates in a given cube is greater than a given threshold, we split the cube along its longest edge according to the metric. When the expected number of templates in a given hypercube drops below this threshold, the splitting stops and a template is placed at the center of the hypercube. Using this method, we generate aligned-spin template banks covering the mass range suitable for a search of Advanced LIGO data. The aligned-spin bank required ~24 CPU-hours and produced 2 million templates. In general, we find that other methods, namely stochastic placement, produces a more strictly bounded loss in match between waveforms, with the same minimal match between waveforms requiring about twice as many templates with our proposed algorithm. Though we note that the average match is higher, which would lead to a higher detection efficiency. Our primary motivation is not to strictly minimize the number of templates with this algorithm, but rather to produce a bank with useful geometric properties in the physical parameter space coordinates. Such properties are useful for population modeling and parameter estimation

An Early-warning System for Electromagnetic Follow-up of Gravitational-wave Events

Binary neutron stars (BNSs) will spend ≃10–15 minutes in the band of Advanced Laser Interferometer Gravitational-Wave Observatory (LIGO) and Virgo detectors at design sensitivity. Matched-filtering of gravitational-wave (GW) data could in principle accumulate enough signal-to-noise ratio (S/N) to identify a forthcoming event tens of seconds before the companions collide and merge. Here we report on the design and testing of an early-warning GW detection pipeline. Early-warning alerts can be produced for sources that are at low enough redshift so that a large enough S/N accumulates ~10–60 s before merger. We find that about 7% (49%) of the total detectable BNS mergers will be detected 60 s (10 s) before the merger. About 2% of the total detectable BNS mergers will be detected before merger and localized to within 100 deg² (90% credible interval). Coordinated observing by several wide-field telescopes could capture the event seconds before or after the merger. LIGO–Virgo detectors at design sensitivity could facilitate observing at least one event at the onset of merger

Template bank for compact binary mergers in the fourth observing run of Advanced LIGO, Advanced Virgo, and KAGRA

Template banks containing gravitational wave (GW) waveforms are essential for matched-filtering GW search pipelines. We describe the generation method, the design, and validation of the template bank used by the GstLAL-based inspiral pipeline to analyze data from the fourth observing run of LIGO scientific, Virgo, and KAGRA collaboration. This paper presents a template bank containing $1.8 \times 10^6$ templates that include merging neutron star - neutron star, neutron star - black hole, and black hole - black hole systems up to a total mass of $400$ $M_\odot$. Motivated by observations, component masses below $3$ $M_\odot$ have dimensionless spins ranging between $\pm 0.05$, while component masses between $3$ to $200$ $M_\odot$ have dimensionless spins ranging between $\pm 0.99$, where we assume spin-aligned systems. The low-frequency cutoff is $15$ Hz. The templates are placed in the parameter space according to the metric via a binary tree approach which took $\mathcal{O}\left(10\right)$ minutes when jobs were parallelized. The template bank generated with this method has a $98\%$ match or higher for $90\%$ of the injections, thus being as effective as the template placement method used for the previous observation runs. The volumes of the templates are computed prior to template placement and the nearby templates have similar volumes in the coordinate space, henceforth, enabling a more efficient and less biased implementation of population models. SVD sorting of the O4 template bank has been renewed to use post-Newtonian phase terms, which improved the computational efficiency of SVD by nearly $4 \sim 5$ times as compared to conventional SVD sorting schemes. Template banks and searches focusing on the sub-solar mass parameter space and intermediate-mass black hole parameter space are conducted separately

An early warning system for electromagnetic follow-up of gravitational-wave events

Binary neutron stars (BNSs) will spend $\simeq 10$ -- 15 minutes in the band of Advanced LIGO and Virgo detectors at design sensitivity. Matched-filtering of gravitational-wave (GW) data could in principle accumulate enough signal-to-noise ratio (SNR) to identify a forthcoming event tens of seconds before the companions collide and merge. Here we report on the design and testing of an early warning gravitational-wave detection pipeline. Early warning alerts can be produced for sources that are at low enough redshift so that a large enough SNR accumulates $\sim 10 - 60\,\rm s$ before merger. We find that about 7% (respectively, 49%) of the total detectable BNS mergers will be detected $60\, \rm s$ ($10\, \rm s$) before the merger. About 2% of the total detectable BNS mergers will be detected before merger and localized to within $100\, \rm \text{deg}^2$ (90% credible interval). Coordinated observing by several wide-field telescopes could capture the event seconds before or after the merger. LIGO-Virgo detectors at design sensitivity could facilitate observing at least one event at the onset of merger.Comment: small update in numbers caused by using a more updated local BNS rate estimat

When to Point Your Telescopes: Gravitational Wave Trigger Classification for Real-Time Multi-Messenger Followup Observations

We develop a robust and self-consistent framework to extract and classify gravitational wave candidates from noisy data, for the purpose of assisting in real-time multi-messenger follow-ups during LIGO-Virgo-KAGRA's fourth observing run~(O4). Our formalism implements several improvements to the low latency calculation of the probability of astrophysical origin~(\PASTRO{}), so as to correctly account for various factors such as the sensitivity change between observing runs, and the deviation of the recovered template waveform from the true gravitational wave signal that can strongly bias said calculation. We demonstrate the high accuracy with which our new formalism recovers and classifies gravitational wave triggers, by analyzing replay data from previous observing runs injected with simulated sources of different categories. We show that these improvements enable the correct identification of the majority of simulated sources, many of which would have otherwise been misclassified. We carry out the aforementioned analysis by implementing our formalism through the \GSTLAL{} search pipeline even though it can be used in conjunction with potentially any matched filtering pipeline. Armed with robust and self-consistent \PASTRO{} values, the \GSTLAL{} pipeline can be expected to provide accurate source classification information for assisting in multi-messenger follow-up observations to gravitational wave alerts sent out during O4.Comment: v2 upload was accidental. revert back to v