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  1. Diffusion State Distance (DSD) is a data-dependent metric that compares data points using a data-driven diffusion process and provides a powerful tool for learning the underlying structure of high-dimensional data. While finding the exact nearest neighbors in the DSD metric is computationally expensive, in this paper, we propose a new random-walk based algorithm that empirically finds approximate k-nearest neighbors accurately in an efficient manner. Numerical results for real-world protein-protein interaction networks are presented to illustrate the efficiency and robustness of the proposed algorithm. The set of approximate k-nearest neighbors performs well when used to predict proteins’ functional labels. 
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  2. Background While increased CD8 counts and low CD4/CD8 ratio during treated HIV correlate with immunosenescence, their additional predictive values to identify individuals with HIV at higher risk of clinical events remain controversial. Methods We selected treatment-naive individuals initiating ART from ACTG studies 384, 388, A5095, A5142, A5202, and A5257 who had achieved viral suppression at year 2. We examined the effect of CD8+ T cell counts and CD4/CD8 at year 2 on the probability of AIDS and serious non-AIDS events in years 37. We used inverse probability weighting methods to address informative censoring, combined with multivariable logistic regression models. Findings We analyzed 5133 participants with a median age of 38 years; 959 (19%) were female, pre-ART median CD4 counts were 249 (Q1-Q3 91372) cell/µL. Compared to participants with CD8 counts between 500/µL and 1499/µL, those with >1500/µL had a higher risk of clinical events during years 37 (aOR 1.75; 95%CI 1.332.32). CD4/CD8 ratio was not predictive of greater risk of events through year 7. Additional analyses revealed consistent CD8 count effect sizes for the risk of AIDS events and noninfectious non-AIDS events, but opposite effects for the risk of severe infections, which were more frequent among individuals with CD8 counts <500/µL (aOR 1.70; 95%CI 1.092.65). Interpretation The results of this analysis with pooled data from clinical trials support the value of the CD8 count as a predictor of clinical progression. People with very high CD8 counts during suppressive ART might benefit from closer monitoring and may be a target population for novel interventions. 
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  3. We report on a comprehensive analysis of simultaneous X-ray polarimetric and spectral data of the bright atoll source GX 9+9 with the Imaging X-ray Polarimetry Explorer (IXPE) and NuSTAR . The source is significantly polarized in the 4–8 keV band, with a degree of 2.2%  ±  0.5% (uncertainty at the 68% confidence level). The NuSTAR broad-band spectrum clearly shows an iron line, and is well described by a model including thermal disc emission, a Comptonized component, and reflection. From a spectro-polarimetric fit, we obtain an upper limit to the polarization degree of the disc of 4% (at the 99% confidence level), while the contribution of Comptonized and reflected radiation cannot be conclusively separated. However, the polarization is consistent with resulting from a combination of Comptonization in a boundary or spreading layer, plus reflection off the disc, which significantly contributes in any realistic scenario. 
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    Free, publicly-accessible full text available August 1, 2024
  4. ABSTRACT X Persei is a persistent low-luminosity X-ray pulsar of period of ≈ 835 s in a Be binary system. The field strength at the neutron star surface is not known precisely, but indirect signs indicate a magnetic field above 1013 G, which makes the object one of the most magnetized known X-ray pulsars. Here we present the results of observations X Persei performed with the Imaging X-ray Polarimetry Explorer (IXPE). The X-ray polarization signal was found to be strongly dependent on the spin phase of the pulsar. The energy-averaged polarization degree in 3–8 keV band varied from several to ∼20 per cent over the pulse with a phase dependence resembling the pulse profile. The polarization angle shows significant variation and makes two complete revolutions during the pulse period, resulting in nearly nil pulse-phase averaged polarization. Applying the rotating vector model to the IXPE data we obtain the estimates for the rotation axis inclination and its position angle on the sky, as well as for the magnetic obliquity. The derived inclination is close to the orbital inclination, reported earlier for X Persei. The polarimetric data imply a large angle between the rotation and magnetic dipole axes, which is similar to the result reported recently for the X-ray pulsar GRO J1008−57. After eliminating the effect of polarization angle rotation over the pulsar phase using the best-fitting rotating vector model, the strong dependence of the polarization degree with energy was discovered, with its value increasing from 0 at ∼2 keV to 30per cent at 8 keV. 
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    Free, publicly-accessible full text available July 12, 2024
  5. ABSTRACT We present an X-ray spectropolarimetric analysis of the bright Seyfert galaxy NGC 4151. The source has been observed with the Imaging X-ray Polarimetry Explorer (IXPE) for 700 ks, complemented with simultaneous XMM–Newton (50 ks) and NuSTAR (100 ks) pointings. A polarization degree Π = 4.9 ± 1.1 per cent and angle Ψ = 86° ± 7° east of north (68 per cent confidence level) are measured in the 2–8 keV energy range. The spectropolarimetric analysis shows that the polarization could be entirely due to reflection. Given the low reflection flux in the IXPE band, this requires, however, a reflection with a very large (>38 per cent) polarization degree. Assuming more reasonable values, a polarization degree of the hot corona ranging from ∼4 to ∼8 per cent is found. The observed polarization degree excludes a ‘spherical’ lamppost geometry for the corona, suggesting instead a slab-like geometry, possibly a wedge, as determined via Monte Carlo simulations. This is further confirmed by the X-ray polarization angle, which coincides with the direction of the extended radio emission in this source, supposed to match the disc axis. NGC 4151 is the first active galactic nucleus with an X-ray polarization measure for the corona, illustrating the capabilities of X-ray polarimetry and IXPE in unveiling its geometry. 
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    Free, publicly-accessible full text available June 8, 2024
  6. We describe WiSER, a clean-slate search engine designed to exploit high-performance SSDs with the philosophy "read as needed". WiSER utilizes many techniques to deliver high throughput and low latency with a relatively small amount of main memory; the techniques include an optimized data layout, a novel two-way cost-aware Bloom filter, adaptive prefetching, and space-time trade-offs. In a system with memory that is significantly smaller than the working set, these techniques increase storage space usage (up to 50%), but reduce read amplification by up to 3x, increase query throughput by up to 2.7x, and reduce latency by 16x when compared to the state-of-the-art Elasticsearch. We believe that the philosophy of "read as needed" can be applied to more applications as the read performance of storage devices keeps improving. 
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  7. ABSTRACT We report spectro-polarimetric results of an observational campaign of the bright neutron star low-mass X-ray binary Cyg X-2 simultaneously observed by IXPE, NICER, and INTEGRAL. Consistently with previous results, the broad-band spectrum is characterized by a lower-energy component, attributed to the accretion disc with kTin ≈ 1 keV, plus unsaturated Comptonization in thermal plasma with temperature kTe = 3 keV and optical depth τ ≈ 4, assuming a slab geometry. We measure the polarization degree in the 2–8 keV band P = 1.8 ± 0.3 per cent and polarization angle ϕ = 140° ± 4°, consistent with the previous X-ray polarimetric measurements by OSO-8 as well as with the direction of the radio jet which was earlier observed from the source. While polarization of the disc spectral component is poorly constrained with the IXPE data, the Comptonized emission has a polarization degree P = 4.0 ± 0.7 per cent and a polarization angle aligned with the radio jet. Our results strongly favour a spreading layer at the neutron star surface as the main source of the polarization signal. However, we cannot exclude a significant contribution from reflection off the accretion disc, as indicated by the presence of the iron fluorescence line. 
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  8. A bio-orthogonal chemistry-based approach for fluorescent labelling of ribosomal RNA is described. It involves an adenosine analogue modified with trans -cyclooctene and masked 5′-phosphate group using aryl phosphoramidate. The incorporation into rRNA has been confirmed using agarose gel electrophoresis, as well as a highly sensitive UHPLC-MS/MS method. Fluorescent labelling of rRNA has been achieved in live HeLa cells via an inverse electron demand Diels–Alder reaction with a tetrazine conjugated to an Oregon Green fluorophore. This communication describes the stepwise approach that led to the development and characterization of the probe. The results demonstrate a new strategy towards development of future fluorescent probes to investigate the biochemistry of nucleic acids. 
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