Publications

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

An emerging challenge in modern distributed querying is to efficiently process multiple continuous aggregation queries simultaneously. Processing each query independently may be infeasible, so multi-query optimizations are critical for sharing work across queries. The challenge is to identify overlapping computations that may not be obvious in the queries themselves. In this paper, we reveal new opportunities for sharing work in the context of distributed aggregation queries that vary in their selection predicates. We identify settings in which a large set of q such queries can be answered by executing k . The k queries are revealed by analyzing a boolean matrix capturing the connection between data and the queries that they satisfy, in a manner akin to familiar techniques like Gaussian elimination. Indeed, we identify a class of linear aggregate functions (including SUM, COUNT and AVERAGE), and show that the sharing potential for such queries can be optimally recovered using standard matrix decompositions from computational linear algebra. For some other typical aggregation functions (including MIN and MAX) we find that optimal sharing maps to the NP-hard set basis problem. However, for those scenarios, we present a family of heuristic algorithms and demonstrate that they perform well for moderate-sized matrices. We also present a dynamic distributed system architecture to exploit sharing opportunities, and experimentally evaluate the benefits of our techniques via a novel, flexible random workload generator we develop for this setting.

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Much excitement surrounds the intense mass loss that seems to take place in some massive stars immediately before core collapse. However, occurring too late, it has a negligible impact on the star's evolution or the final yields, which are influenced instead by the longer-term, quasi-steady mass loss taking place during H and He burning. Late-time observations of core-collapse supernovae interacting with the progenitor wind are one means to constrain this secular mass loss. Here, we present radiative transfer calculations for a Type II SN with and without this interaction power, focusing on the phase between 350 and 1000d after explosion. Without interaction power, the ejecta are powered through radioactive decay whose exponential decline produces an ever-fading SN. Instead, with a constant interaction power of $10^{40}$ erg s$^{-1}$ (representative of an SN II ramming into a steady-state $10^{-6} M_\odot$ yr$^{-1}$ wind), the spectrum morphs from decay powered at 350d, with narrow lines forming in the inner metal-rich ejecta, to interaction powered at 1000d, with broad boxy lines forming in the outer H-rich ejecta. Intermediate times are characterized by a hybrid and complex spectrum made of overlapping narrow and broad lines. While interaction boosts primarily the flux in the ultraviolet, which remains largely unobserved today, a knee in the $R$-band light curve or a $U$-band boost are clear signatures of interaction at late times. The model predictions compare favorably with a number of Type II supernovae including SN 2004et or SN 2017eaw at 500-1000d after explosion.

Herein we analyse late-time (post-plateau; 103 < t < 1229 d) optical spectra of low-redshift (z < 0.016), hydrogen-rich Type IIP supernovae (SNe IIP). Our newly constructed sample contains 91 nebular spectra of 38 SNe IIP, which is the largest dataset of its kind ever analysed in one study, and many of the objects have complementary photometric data. We determined the peak and total luminosity, velocity of the peak, HWHM intensity, and profile shape for many emission lines. Temporal evolution of these values and various flux ratios are studied. We also investigate the correlations between these measurements and photometric observables, such as the peak and plateau absolute magnitudes and the late-time light curve decline rates in various optical bands. The strongest and most robust result we find is that the luminosities of all spectral features (except those of helium) tend to be higher in objects with steeper late-time V-band decline rates. A steep late-time V-band slope likely arises from less efficient trapping of gamma-rays and positrons, which could be caused by multidimensional effects such as clumping of the ejecta or asphericity of the explosion itself. Furthermore, if gamma-rays and positrons can escape more easily, then so can photons via the observed emission lines, leading to more luminous spectral features. It is also shown that SNe IIP with larger progenitor stars have ejecta with a more physically extended oxygen layer that is well-mixed with the hydrogen layer. In addition, we find a subset of objects with evidence for asymmetric Ni-56 ejection, likely bipolar in shape. We also compare our observations to theoretical late-time spectral models of SNe IIP from two separate groups and find moderate-to-good agreement with both sets of models. Our SNe IIP spectra are consistent with models of 12-15 M_Sun progenitor stars having relatively low metallicity (Z $\le$ 0.01).

&lt;p&gt;PDF file - 226K, Relative Abundance of Indicator Bacterial Phylotypes in Mice Fecal bacteria of age- and litter-matched SPF-N and SPF-S mice (n = 4-5 for each type) were subjected to an indicator analysis.&lt;/p&gt;

&lt;p&gt;Abstract&lt;/p&gt;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&lt;p&gt;The AlkB family of non-heme-Fe(II)/2-oxoglutarate(2OG)-dependent oxygenases are essential regulators of RNA epigenetics by serving as erasers of one-carbon marks on RNA with release of formaldehyde (FA). Two major human AlkB family members, FTO and ALKBH5, both act as oxidative demethylases of N6 methyladenosine (m6A) but furnish different major products, N6 hydroxymethyladenosine (hm6A) and adenosine (A), respectively. Here we identify foundational mechanistic differences between FTO and ALKBH5 that promote these distinct biochemical outcomes. In contrast to FTO, which follows a traditional oxidative N-demethylation pathway to catalyze conversion of m6A to hm6A with subsequent slow release of A and FA, we find that ALKBH5 catalyzes a direct&lt;/p&gt;&lt;p&gt;m6A-to-A transformation with rapid FA release. We identify a catalytic R130/K132/Y139 triad within ALKBH5 that facilitates release of FA via an unprecedented covalent-based demethylation mechanism with direct detection of a covalent intermediate. Importantly, a K132Q mutant furnishes an ALKBH5 enzyme with an m6A demethylation profile that resembles that of FTO, establishing the importance of this residue in the proposed covalent mechanism. Finally, we show that ALKBH5 is an endogenous source of FA in the cell by activity-based sensing of FA fluxes perturbed via ALKBH5 knockdown. This work provides a fundamental biochemical rationale for non-redundant roles of these RNA demethylases beyond different substrate preferences and cellular localization, where m6A demethylation by ALKBH5 versus FTO results in release of FA, an endogenous one-carbon unit but potential genotoxin, at different rates in living systems.&lt;/p&gt;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&lt;p&gt;Significance Statement&lt;/p&gt;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&lt;p&gt;Non-heme iron enzymes FTO and ALKBH5 play central roles in epigenetic RNA regulation by catalyzing the oxidation of N6-methyladenosine (m6A) to produce N6-hydroxymethyladenosine (hm6A) and adenosine (A), respectively. Here, we provide a mechanistic rationale for these distinct biochemical outcomes by identifying that ALKBH5 performs m6A demethylation via an unprecedented covalent-based mechanism with concomitant and rapid release of A and formaldehyde (FA), whereas FTO liberates hm6A to release A and FA over longer timescales. This work reveals foundational biochemical differences between these closely related but non-redundant epigenetic enzymes and identifies ALKBH5 as an endogenous source of rapid formaldehyde generation in cells.&lt;/p&gt;

In this paper we propose a new mem-computing image processing architecture, called Memristor Cellular Nonlinear Network, which leverages the unique capability of nonvolatile memristors to compute and store data in the same physical nano-scale locations. Adopting a bistable-like memristor in place for the linear resistor in the standard realization of a cell of the nonlinear dynamic array, the resulting network is capable to process information by exploiting the time evolution of the voltages across the memristors as well as to store/retrieve results into/ from the memristances. This attractive feature, absent in a standard Cellular Nonlinear Network, may pave the way towards the future development of a new generation of visual processors with unprecedented spatial resolution.