Validation and Comparison Study for Fourth Generation HIV Test Kit

Introduction/Objective

CDC recommends the use of 4th generation HIV test as the first line of screening. Alere Determine HIV – 1/2 Ag/Ab Combo (Abbott Diagnostics Scarborough, Inc., Scarborough, Maine) (Alere) is a qualitative 4thgeneration assay that detects HIV 1/2 antibodies and p24 antigen. In this validation study, Alere was compared with OraQuick Advance Rapid HIV 1/2 Antibody test (OraSure Technologies, Inc., Bethlehem, PA) (Oraquick), a qualitative 3rd generation test and BioPlex (Bio-Rad Laboratories, Hercules, California) a 5th generation test that detects and differentiates between HIV 1 and 2 antibodies and p24 antigen.

Methods/Case Report

Comparison study: Forty-five samples were tested simultaneously on the three assays. Results for the patient samples were confirmed with Geenius (Bio- Rad Marnes-La-Coquette, France) or PCR assays for antibody or antigen positive cases respectively.

Precision study

A HIV-1 antibody positive and an all-negative sample were tested 10 times each to validate the precision of the Alere test.

Dilution study

A positive sample for HIV-1 antibody was used for dilution with a HIV negative serum sample. Diluted samples from 1:10 to 1:1000 were tested using Alere and BioPlex.

Results (if a Case Study enter NA)

Comparison study revealed that sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for Alere test were 100%. Sensitivity for Oraquick was 86.6% and NPV was 77.77%. Specificity and PPV were 100%. BioPlex showed sensitivity and NPV of 100%, but specificity was 78.5% and PPV was 90.90%. Precision study showed reproducible results on the Alere test. Dilution study revealed that Alere assay gave positive results up to 1:300 dilution, and BioPlex assay was positive up to 1:500 dilution.

Conclusion

Our studies showed that Alere had the sensitivity and specificity of 100% making it an effective screening test in acute settings. BioPlex assay demonstrated that it was the most sensitive test with quantitative index for the HIV 1 and 2 antibodies and p24 antigen. Therefore, both Alere and BioPlex tests are good initial screening tests

Diffuse Pulmonary Meningotheliomatosis: A Case Report

Introduction/Objective

Diffuse pulmonary meningotheliomatosis (DPM) is a pulmonary disease characterized by the presence of widespread bilateral minute pulmonary meningothelial-like nodules (MPMNs). It is exceedingly rare and predominantly seen in females. The nodules are typically asymptomatic and detected incidentally on imaging.

Methods/Case Report

We present a case of a 57-year-old woman with a history of chronic cough and CT imaging findings of bilateral multiple ground-glass nodules. Wedge resections from the right upper and right lower lobes were obtained, which revealed gross changes suggestive of interstitial lung disease. Histologic evaluation of the wedges showed similar morphology, consisting of discrete areas with variable interstitial expansion of the stroma with ovoid/spindle cells, collagen, elastosis, and mild chronic inflammatory cells, in a somewhat perivascular pattern. Some areas were also cystic. This appeared in a background of emphysematous change and focal foreign body giant cell reaction to non-polarizable material. Immunohistochemical stains were diffusely positive for vimentin, EMA , and PR, and CD163 highlighted increased cells that were S100 and CD1a negative. Additionally, the ovoid/spindle cells were negative for desmin, SMM, HMB-45, HHV8, pan-CK, chromogranin, and multiplex SOX10-MART1.

Results (if a Case Study enter NA)

NA

Conclusion

Diffuse pulmonary meningotheliomatosis is a rare entity that requires sufficient histological evaluation to identify the ovoid/spindle cell component histologically and immunohistochemically. This disease should be considered in the differential for cases of diffuse interstitial pulmonary infiltrates. Few cases have been reported in the literature, requiring further research to understand the mechanisms of this disease and its clinical significance.

Search for Subsolar-Mass Binaries in the First Half of Advanced LIGO's and Advanced Virgo's Third Observing Run

We report on a search for compact binary coalescences where at least one binary component has a mass between 0.2  M_{⊙} and 1.0  M_{⊙} in Advanced LIGO and Advanced Virgo data collected between 1 April 2019 1500 UTC and 1 October 2019 1500 UTC. We extend our previous analyses in two main ways: we include data from the Virgo detector and we allow for more unequal mass systems, with mass ratio q≥0.1. We do not report any gravitational-wave candidates. The most significant trigger has a false alarm rate of 0.14  yr^{-1}. This implies an upper limit on the merger rate of subsolar binaries in the range [220-24200]  Gpc^{-3} yr^{-1}, depending on the chirp mass of the binary. We use this upper limit to derive astrophysical constraints on two phenomenological models that could produce subsolar-mass compact objects. One is an isotropic distribution of equal-mass primordial black holes. Using this model, we find that the fraction of dark matter in primordial black holes in the mass range 0.2  M_{⊙}<m_{PBH}<1.0  M_{⊙} is f_{PBH}≡Ω_{PBH}/Ω_{DM}≲6%. This improves existing constraints on primordial black hole abundance by a factor of ∼3. The other is a dissipative dark matter model, in which fermionic dark matter can collapse and form black holes. The upper limit on the fraction of dark matter black holes depends on the minimum mass of the black holes that can be formed: the most constraining result is obtained at M_{min}=1  M_{⊙}, where f_{DBH}≡Ω_{DBH}/Ω_{DM}≲0.003%. These are the first constraints placed on dissipative dark models by subsolar-mass analyses.

Enhanced medium-range order in vapor-deposited germania glasses at elevated temperatures

Glasses are nonequilibrium solids with properties highly dependent on their method of preparation. In vapor-deposited molecular glasses, structural organization could be readily tuned with deposition rate and substrate temperature. Here, we show that the atomic arrangement of strong network-forming GeO₂ glass is modified at medium range (<2 nm) through vapor deposition at elevated temperatures. Raman spectral signatures distinctively show that the population of six-membered GeO₄ rings increases at elevated substrate temperatures. Deposition near the glass transition temperature is more efficient than postgrowth annealing in modifying atomic structure at medium range. The enhanced medium-range organization correlates with reduction of the room temperature internal friction. Identifying the microscopic origin of room temperature internal friction in amorphous oxides is paramount to design the next-generation interference coatings for mirrors of the end test masses of gravitational wave interferometers, in which the room temperature internal friction is a main source of noise limiting their sensitivity.

Low Mechanical Loss TiO_{2}:GeO_{2} Coatings for Reduced Thermal Noise in Gravitational Wave Interferometers

The sensitivity of current and planned gravitational wave interferometric detectors is limited, in the most critical frequency region around 100 Hz, by a combination of quantum noise and thermal noise. The latter is dominated by Brownian noise: thermal motion originating from the elastic energy dissipation in the dielectric coatings used in the interferometer mirrors. The energy dissipation is a material property characterized by the mechanical loss angle. We have identified mixtures of titanium dioxide (TiO_{2}) and germanium dioxide (GeO_{2}) that show internal dissipations at a level of 1×10^{-4}, low enough to provide improvement of almost a factor of 2 on the level of Brownian noise with respect to the state-of-the-art materials. We show that by using a mixture of 44% TiO_{2} and 56% GeO_{2} in the high refractive index layers of the interferometer mirrors, it would be possible to achieve a thermal noise level in line with the design requirements. These results are a crucial step forward to produce the mirrors needed to meet the thermal noise requirements for the planned upgrades of the Advanced LIGO (Laser Interferometer Gravitational-Wave Observatory) and Virgo detectors.

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

Analysis of two-level systems and mechanical loss in amorphous ZrO2-doped Ta2O5 by non-cage-breaking and cage-breaking transitions

The energy landscape of ZrO₂-doped amorphous Ta₂O₅ is explored in this work. With models corresponding to experimental concentrations of 50% Zr and 50% Ta cations, we search for, gather, and analyze two-level systems (TLSs) from molecular dynamic simulations. The mechanical loss function is calculated for each TLS individually. The results show that TLS with low asymmetry and large elastic coupling constants contribute the most to mechanical loss. We identify these as "bad actors." The higher barriers relate to the mechanical loss at higher temperatures. The concept of the oxygen cage that describes the local structural environment surrounding a metal ion is introduced. The existence of a drastic change in local environment, or a cage-breaking process, enables us to understand the double peaks present in the asymmetry distribution and provides a pictorial interpretation to distinguish two types of TLS. Quantitatively, a cage-breaking event is related to at least one large distance change in an atom-atom pair, and non-cage-breaking transitions have only small rearrangements. The majority of TLSs are cage-breaking transitions, but non-cage-breaking TLS transitions show higher average mechanical loss in ZrO₂-doped Ta₂O₅. By decomposing the contributions to mechanical loss, we find that the low temperature loss peak near 40 K mainly comes from non-cage-breaking TLS transitions and the second loss peak near 120 K originates from cage-breaking TLS transitions. This finding is important for understanding the interplay between the atomic structure of TLS and mechanical loss.

GW190521: A Binary Black Hole Merger with a Total Mass of 150 M_{⊙}

On May 21, 2019 at 03:02:29 UTC Advanced LIGO and Advanced Virgo observed a short duration gravitational-wave signal, GW190521, with a three-detector network signal-to-noise ratio of 14.7, and an estimated false-alarm rate of 1 in 4900 yr using a search sensitive to generic transients. If GW190521 is from a quasicircular binary inspiral, then the detected signal is consistent with the merger of two black holes with masses of 85_{-14}^{+21}  M_{⊙} and 66_{-18}^{+17}  M_{⊙} (90% credible intervals). We infer that the primary black hole mass lies within the gap produced by (pulsational) pair-instability supernova processes, with only a 0.32% probability of being below 65  M_{⊙}. We calculate the mass of the remnant to be 142_{-16}^{+28}  M_{⊙}, which can be considered an intermediate mass black hole (IMBH). The luminosity distance of the source is 5.3_{-2.6}^{+2.4}  Gpc, corresponding to a redshift of 0.82_{-0.34}^{+0.28}. The inferred rate of mergers similar to GW190521 is 0.13_{-0.11}^{+0.30}  Gpc^{-3} yr^{-1}.

Prospects for observing and localizing gravitational-wave transients with Advanced LIGO, Advanced Virgo and KAGRA

We present our current best estimate of the plausible observing scenarios for the Advanced LIGO, Advanced Virgo and KAGRA gravitational-wave detectors over the next several years, with the intention of providing information to facilitate planning for multi-messenger astronomy with gravitational waves. We estimate the sensitivity of the network to transient gravitational-wave signals for the third (O3), fourth (O4) and fifth observing (O5) runs, including the planned upgrades of the Advanced LIGO and Advanced Virgo detectors. We study the capability of the network to determine the sky location of the source for gravitational-wave signals from the inspiral of binary systems of compact objects, that is binary neutron star, neutron star-black hole, and binary black hole systems. The ability to localize the sources is given as a sky-area probability, luminosity distance, and comoving volume. The median sky localization area (90% credible region) is expected to be a few hundreds of square degrees for all types of binary systems during O3 with the Advanced LIGO and Virgo (HLV) network. The median sky localization area will improve to a few tens of square degrees during O4 with the Advanced LIGO, Virgo, and KAGRA (HLVK) network. During O3, the median localization volume (90% credible region) is expected to be on the order of 10 5 , 10 6 , 10 7 Mpc 3 for binary neutron star, neutron star-black hole, and binary black hole systems, respectively. The localization volume in O4 is expected to be about a factor two smaller than in O3. We predict a detection count of 1 - 1 + 12 ( 10 - 10 + 52 ) for binary neutron star mergers, of 0 - 0 + 19 ( 1 - 1 + 91 ) for neutron star-black hole mergers, and 17 - 11 + 22 ( 79 - 44 + 89 ) for binary black hole mergers in a one-calendar-year observing run of the HLV network during O3 (HLVK network during O4). We evaluate sensitivity and localization expectations for unmodeled signal searches, including the search for intermediate mass black hole binary mergers.

Search for Subsolar Mass Ultracompact Binaries in Advanced LIGO's Second Observing Run

We present a search for subsolar mass ultracompact objects in data obtained during Advanced LIGO's second observing run. In contrast to a previous search of Advanced LIGO data from the first observing run, this search includes the effects of component spin on the gravitational waveform. We identify no viable gravitational-wave candidates consistent with subsolar mass ultracompact binaries with at least one component between 0.2  M_{⊙}-1.0  M_{⊙}. We use the null result to constrain the binary merger rate of (0.2  M_{⊙}, 0.2  M_{⊙}) binaries to be less than 3.7×10^{5}  Gpc^{-3} yr^{-1} and the binary merger rate of (1.0  M_{⊙}, 1.0  M_{⊙}) binaries to be less than 5.2×10^{3}  Gpc^{-3} yr^{-1}. Subsolar mass ultracompact objects are not expected to form via known stellar evolution channels, though it has been suggested that primordial density fluctuations or particle dark matter with cooling mechanisms and/or nuclear interactions could form black holes with subsolar masses. Assuming a particular primordial black hole (PBH) formation model, we constrain a population of merging 0.2  M_{⊙} black holes to account for less than 16% of the dark matter density and a population of merging 1.0  M_{⊙} black holes to account for less than 2% of the dark matter density. We discuss how constraints on the merger rate and dark matter fraction may be extended to arbitrary black hole population models that predict subsolar mass binaries.

Detecting episomal or integrated human papillomavirus 16 DNA using an exonuclease V-qPCR-based assay

Screening for human papillomavirus (HPV) integration into host cell chromosomes typically requires large amounts of time and reagents. We developed a rapid and sensitive assay based on exonuclease V (ExoV) and quantitative polymerase chain reaction (qPCR) to determine HPV genome configurations in cell lines and tissues. We established the assay using genomic DNA from cell lines known to harbor integrated or episomal HPV16. DNA was incubated with ExoV, which is specific for linear DNA, and the DNA fraction resistant to digestion was measured by qPCR. The percent of DNA resistant to ExoV digestion was calculated relative to undigested DNA for determination of episomal or integrated HPV16. The ExoV assay was accurate, capable of distinguishing episomal from integrated HPV16 in cell lines and tissues. Future applications of the ExoV assay may include screening of HPV genome configurations in the progression of HPV-associated cancers.

High Precision Detection of Change in Intermediate Range Order of Amorphous Zirconia-Doped Tantala Thin Films Due to Annealing

Understanding the local atomic order in amorphous thin film coatings and how it relates to macroscopic performance factors, such as mechanical loss, provides an important path towards enabling the accelerated discovery and development of improved coatings. High precision x-ray scattering measurements of thin films of amorphous zirconia-doped tantala (ZrO_{2}-Ta_{2}O_{5}) show systematic changes in intermediate range order (IRO) as a function of postdeposition heat treatment (annealing). Atomic modeling captures and explains these changes, and shows that the material has building blocks of metal-centered polyhedra and the effect of annealing is to alter the connections between the polyhedra. The observed changes in IRO are associated with a shift in the ratio of corner-sharing to edge-sharing polyhedra. These changes correlate with changes in mechanical loss upon annealing, and suggest that the mechanical loss can be reduced by developing a material with a designed ratio of corner-sharing to edge-sharing polyhedra.

Sculpting the band gap: a computational approach

Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations.

Simulations of silver-doped germanium-selenide glasses and their response to radiation

Chalcogenide glasses doped with silver have many applications including their use as a novel radiation sensor. In this paper, we undertake the first atomistic simulation of radiation damage and healing in silver-doped Germanium-selenide glass. We jointly employ empirical potentials and ab initio methods to create and characterize new structural models and to show that they are in accord with many experimental observations. Next, we simulate a thermal spike and track the evolution of the radiation damage and its eventual healing by application of a simulated annealing process. The silver network is strongly affected by the rearrangements, and its connectivity (and thus contribution to the electrical conductivity) change rapidly in time. The electronic structure of the material after annealing is essentially identical to that of the initial structure.

Thermal properties of holmium-implanted gold films for a neutrino mass experiment with cryogenic microcalorimeters

In a microcalorimetric neutrino mass experiment using the radioactive decay of (163)Ho, the radioactive material must be fully embedded in the microcalorimeter absorber. One option that is being investigated is to implant the radioactive isotope into a gold absorber, as gold is successfully used in other applications. However, knowing the thermal properties at the working temperature of microcalorimeters is critical for choosing the absorber material and for optimizing the detector performance. In particular, it is paramount to understand if implanting the radioactive material in gold changes its heat capacity. We used a bolometric technique to measure the heat capacity of gold films, implanted with various concentrations of holmium and erbium (a byproduct of the (163)Ho fabrication), in the temperature range 70 mK-300 mK. Our results show that the specific heat capacity of the gold films is not affected by the implant, making this a viable option for a future microcalorimeter holmium experiment.

Note: Thermal properties of magnesium in the 60-150 mK range

Refrigerators for space and other applications working around 100 mK require lightweight components with good thermal properties. We have measured the thermal properties of high-purity (99.95%) magnesium, which is five times lighter than copper, over the 60-150 mK range and found that it is well-behaved down to these temperatures. Both conductivity and heat capacity are in good agreement with extrapolations from measurements at higher temperatures. The heat capacity per unit volume is about the same as copper and the thermal conductivity about 2.7 times lower than copper of similar residual resistivity ratio, as expected from magnesium's higher room-temperature resistivity.