Logical Majorana fermions for fault-tolerant quantum simulation

We show how to absorb fermionic quantum simulation's expensive fermion-to-qubit mapping overhead into the overhead already incurred by surface-code-based fault-tolerant quantum computing. The key idea is to process information in surface-code twist defects, which behave like logical Majorana fermions. Our approach implements a universal set of fault-tolerant gates on these logical Majorana fermions by effecting encoded measurement-based topological quantum computing with them. A critical feature of our approach is the use of code deformations between logical tetron and logical hexon surface-code-patch encodings, which enables one to move beyond the limitations of a wholly square-patch tetronic surface-code approach. To motivate near-term implementations, we also show how one could realize each of a universal set of logical Majorana gates on a small-scale testbed using noisy intermediate scale quantum (NISQ) technology on as few as 13 qubits.Comment: 14 pages, 15 figure

The cytochrome P450 family in the parasitic nematode <i>Haemonchus contortus</i>

&lt;i&gt;Haemonchus contortus&lt;/i&gt;, a highly pathogenic and economically important parasitic nematode of sheep, is particularly adept at developing resistance to the anthelmintic drugs used in its treatment and control. The basis of anthelmintic resistance is poorly understood for many commonly used drugs with most research being focused on mechanisms involving drug targets or drug efflux. Altered or increased drug metabolism is a possible mechanism that has yet to receive much attention despite the clear role of xenobiotic metabolism in pesticide resistance in insects. The cytochrome P450s (CYPs) are a large family of drug-metabolising enzymes present in almost all living organisms, but for many years thought to be absent from parasitic nematodes. In this paper, we describe the CYP sequences encoded in the &lt;i&gt;H. Contortus&lt;/i&gt; genome and compare their expression in different parasite life-stages, sexes and tissues. We developed a novel real-time PCR approach based on partially assembled CYP sequences “tags” and confirmed findings in the subsequent draft genome with RNA-seq. Constitutive expression was highest in larval stages for the majority of CYPs, although higher expression was detected in the adult male or female for a small subset of genes. Many CYPs were expressed in the worm intestine. A number of &lt;i&gt;H. Contortus&lt;/i&gt; genes share high identity with &lt;i&gt;Caenorhabditis elegans&lt;/i&gt; CYPs and the similarity in their expression profiles supports their classification as putative orthologues. Notably, &lt;i&gt;H. Contortus&lt;/i&gt; appears to lack the dramatic CYP subfamily expansions seen in &lt;i&gt;C. elegans&lt;/i&gt; and other species, which are typical of CYPs with exogenous roles. However, a small group of &lt;i&gt;H. Contortus&lt;/i&gt; genes cluster with the &lt;i&gt;C. elegans&lt;/i&gt; CYP34 and CYP35 subfamilies and may represent candidate xenobiotic metabolising genes in the parasite

The Efficacy of Video Cameras to Account for Northern Bobwhites Flushed, but Undetected During Aerial Surveys

Over the past 20 years, conventional distance sampling from a helicopter platform has been used to estimate northern bobwhite (Colinus virginianus; hereafter, bobwhite) density over large areas of rangeland vegetation. However, it has been speculated that aerial surveys can complicate the ability to meet the distance sampling assumption of detecting 100% of the target objects on the transect line due to the restricted observer view from the helicopter. We attempted to use video cameras to determine whether missed detections occurred and whether digital methods could improve the precision of bobwhite density estimates. Our objectives were to 1) determine whether video cameras are a viable option to detect if coveys are flushing behind the helicopter and missed by observers, 2) determine whether coveys are flushing underneath the helicopter and missed by observers, and 3) explore the use of video cameras in a mark-recapture distance sampling (MRDS) framework. We recorded video while traversing line-transects with a helicopter during 4 distance-sampling surveys across 2 ranches in South Texas, USA. For objective 1, we reviewed footage from cameras with a backward-facing view and detected only 1 pair of bobwhites (0.001% of 889 coveys detected) that flushed on video footage recorded during the surveys but were unnoticed by observers. These results indicated that when coveys flushed, they rarely flushed behind the helicopter, and the helicopter flew at what seemed to be the proper speed and altitude to detect late flushes. For objective 2, we reviewed footage from a helicopter-mounted camera that was recorded within a swath underneath the helicopter’s center. We recorded 22 flushes within the swath, none of which was missed by the observers in the helicopter; as a result, we could not complete an MRDS analysis in Program Distance. This study improved confidence in fulfilling the assumptions of distance sampling and resulting density estimates but was limited to flushing birds only

Evolution of eukaryotic transcription : insights from the genome of Giardia lamblia

Author Posting. © Cold Spring Harbor Laboratory Press, 2004. This article is posted here by permission of Cold Spring Harbor Laboratory Press for personal use, not for redistribution. The definitive version was published in Genome Research 14 (2004): 1537-1547, doi:10.1101/gr.2256604.The Giardia lamblia genome sequencing project affords us a unique opportunity to conduct comparative analyses of core cellular systems between early and late-diverging eukaryotes on a genome-wide scale. We report a survey to identify canonical transcription components in Giardia, focusing on RNA polymerase (RNAP) subunits and transcription-initiation factors. Our survey revealed that Giardia contains homologs to 21 of the 28 polypeptides comprising eukaryal RNAPI, RNAPII, and RNAPIII; six of the seven RNAP subunits without giardial homologs are polymerase specific. Components of only four of the 12 general transcription initiation factors have giardial homologs. Surprisingly, giardial TATA-binding protein (TBP) is highly divergent with respect to archaeal and higher eukaryotic TBPs, and a giardial homolog of transcription factor IIB was not identified. We conclude that Giardia represents a transition during the evolution of eukaryal transcription systems, exhibiting a relatively complete set of RNAP subunits and a rudimentary basal initiation apparatus for each transcription system. Most class-specific RNAP subunits and basal initiation factors appear to have evolved after the divergence of Giardia from the main eukaryotic line of descent. Consequently, Giardia is predicted to be unique in many aspects of transcription initiation with respect to paradigms derived from studies in crown eukaryotes.This work was supported in part by NIH grant AI43273 to M.L.S., by NIH grant AI51089 to A.G.M, and DOE grant DE-FG02-01ER63201 to G.J.O. Additional support was provided by the G. Unger Vetlesen Foundation and LI-COR Biotechnology

ASTER, a multinational Earth observing concept

The Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) is a facility instrument selected for launch in 1998 on the first in a series of spacecraft for NASA's Earth Observing System (EOS). The ASTER instrument is being sponsored and built in Japan. It is a three telescope, high spatial resolution imaging instrument with 15 spectral bands covering the visible through to the thermal infrared. It will play a significant role within EOS providing geological, biological, land hydrological information necessary for intense study of the Earth. The operational capabilities for ASTER, including the necessary interfaces and operational collaborations between the US and Japanese participants, are under development. EOS operations are the responsibility of the EOS Project at NASA's Goddard Space Flight Center (GSFC). Although the primary EOS control center is at GSFC, the ASTER control facility will be in Japan. Other aspects of ASTER are discussed

A Gaussian distribution for refined DT invariants and 3D partitions

We show that the refined Donaldson-Thomas invariants of C3, suitably normalized, have a Gaussian distribution as limit law. Combinatorially these numbers are given by weighted counts of 3D partitions. Our technique is to use the Hardy-Littlewood circle method to analyze the bivariate asymptotics of a q-deformation of MacMahon's function. The proof is based on that of E.M. Wright who explored the single variable case.Comment: 11 pages and 3 figure

Separation of rhodium from iridium through synergistic solvent extraction

There are currently few effective processes for the solvent extraction of rhodium from hydrochloric acid streams, and none that allow rhodium to be selectively extracted over iridium. Realizing this goal could allow rhodium to be recovered earlier in a typical platinum group metal (PGM) refining flowsheet and reduce the environmental impact of PGM refining. In this work, we show that a synergistic combination of a tert-alkyl primary amine LA and various inner-sphere ligands L can be used to recover rhodium via the complex [RhCl5L].HLA2. Although we show that rhodium is extracted by several extractant combinations, it is only readily stripped from the amine/amide synergistic mixture. As this extraction relies on the inner-sphere coordination of the amide to the metal, this process also demonstrates a route to obtain preferential extraction of rhodium over more inert iridium chloridometalates under industrially relevant conditions.</p

Site-Selective Excitation And Polarized Absorption Spectra Of Nd3+ In Sr-5(Po4)(3)F And Ca-5(Po4)(3)F

Polarized absorption and fluorescence spectra were analyzed to establish individual energy (Stark) levels of Nd3+ ions in host crystals of Sr-5(PO4)(3)F (SFAP) and Ca-5(PO4)(3)F (FAP). Site-selective excitation and fluorescence facilitated differentiation between Nd3+ ions in emitting sites-associated with 1.06 mu m stimulated emission, and nonemitting Nd3+ ions in other sites. Measurements were made on samples containing different concentrations of Nd3+ at 4 K and higher temperatures. Substitution of Nd3+ for Sr2+ or Ca2+ was accompanied by passive charge compensation during crystal growth. Crystal-field splitting calculations were performed according to site for Stark levels of Nd3+ ions identified spectroscopically. We obtained a final set of crystal-field parameters B-nm for Nd3+ ions in fluorescing sites with a rms, deviation of 7 cm(-1) (52 levels in Nd:SFAP) and 8 cm(-1) (59 levels in Nd:FAP). For one of the nonemitting sites in Nd:FAP we obtained a final set of B-nm parameters which gave a rms deviation of 6 cm(-1) between 46 experimental and calculated levels

Dietary fibres differentially impact on the production of phenolic acids from rutin in an in vitro fermentation model of the human gut microbiota

Polyphenols are often ingested alongside dietary fibres. They are both catabolised by, and may influence, the intestinal microbiota; yet, interactions between them and the impact on their resultant microbial products are poorly understood. Dietary fibres (inulin, pectin, psyllium, pyrodextrin, wheat bran, cellulose—three doses) were fermented in vitro with human faeces (n = 10) with and without rutin (20 µg/mL), a common dietary flavonol glycoside. Twenty-eight phenolic metabolites and short chain fatty acids (SCFA) were measured over 24 h. Several phenolic metabolites were produced during fibre fermentation, without rutin. With rutin, 3,4-dihydroxyphenylacetic acid (3,4diOHPAA), 3-hydroxyphenylacetic acid (3OHPAA), 3-(3 hydroxyphenyl)propionic acid (3OHPPA) and 3-(3,4-dihydroxyphenyl)propionic acid (3,4diOHPPA; DOPAC) were produced, with 3,4diOHPAA the most abundant, confirmed by fermentation of 13C labelled quercetin. The addition of inulin, wheat bran or pyrodextrin increased 3,4diOHPAA 2 2.5-fold over 24 h (p &lt; 0.05). Rutin affected SCFA production, but this depended on fibre, fibre concentration and timepoint. With inulin, rutin increased pH at 6 h from 4.9 to 5.6 (p = 0.01) but increased propionic, butyric and isovaleric acid (1.9, 1.6 and 5-fold, p &lt; 0.05 at 24 h). Interactions between fibre and phenolics modify production of phenolic acids and SCFA and may be key in enhancing health benefits