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At least 91 records · Page 5

Adaptive pruning-based optimization of parameterized quantum circuits

Abstract Variational hybrid quantum–classical algorithms are powerful tools to maximize the use of noisy intermediate-scale quantum devices. While past studies have developed powerful and expressive ansatze, their near-term applications have been limited by the difficulty of optimizing in the vast parameter space. In this work, we propose a heuristic optimization strategy for such ansatze used in variational quantum algorithms, which we call ‘parameter-efficient circuit training (PECT)’. Instead of optimizing all of the ansatz parameters at once, PECT launches a sequence of variational algorithms, in which each iteration of the algorithm activates and optimizes a subset of the total parameter set. To update the parameter subset between iterations, we adapt the Dynamic Sparse Reparameterization scheme which was originally proposed for training deep convolutional neural networks. We demonstrate PECT for the Variational Quantum Eigensolver, in which we benchmark unitary coupled-cluster ansatze including UCCSD and k -UpCCGSD, as well as the Low-Depth Circuit Ansatz (LDCA), to estimate ground state energies of molecular systems. We additionally use a layerwise variant of PECT to optimize a hardware-efficient circuit for the Sycamore processor to estimate the ground state energy densities of the one-dimensional Fermi-Hubbard model. From our numerical data, we find that PECT can enable optimizations of certain ansatze that were previously difficult to converge and more generally can improve the performance of variational algorithms by reducing the optimization runtime and/or the depth of circuits that encode the solution candidate(s).

Physics↗

Salmonella enterica Serovar Typhi Lipopolysaccharide O-Antigen Modification Impact on Serum Resistance and Antibody Recognition

Salmonella enterica serovar Typhi is a human-restricted Gram-negative bacterial pathogen responsible for causing an estimated 27 million cases of typhoid fever annually, leading to 217,000 deaths, and current vaccines do not offer full protection. The O-antigen side chain of the lipopolysaccharide is an immunodominant antigen, can define host-pathogen interactions, and is under consideration as a vaccine target for some Gram-negative species. The composition of the O-antigen can be modified by the activity of glycosyltransferase (gtr) operons acquired by horizontal gene transfer. Here we investigate the role of two gtr operons that we identified in the S. Typhi genome. Strains were engineered to express specific gtr operons. Full chemical analysis of the O-antigens of these strains identified gtr-dependent glucosylation and acetylation. The glucosylated form of the O-antigen mediated enhanced survival in human serum and decreased complement binding. A single nucleotide deviation from an epigenetic phase variation signature sequence rendered the expression of this glucosylating gtr operon uniform in the population. In contrast, the expression of the acetylating gtrC gene is controlled by epigenetic phase variation. Acetylation did not affect serum survival, but phase variation can be an immune evasion mechanism, and thus, this modification may contribute to persistence in a host. In murine immunization studies, both O-antigen modifications were generally immunodominant. Our results emphasize that natural O-antigen modifications should be taken into consideration when assessing responses to vaccines, especially O-antigen-based vaccines, and that the Salmonella gtr repertoire may confound the protective efficacy of broad-ranging Salmonella lipopolysaccharide conjugate vaccines.

59 BASIC BIOLOGICAL SCIENCES↗

The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5

Here, the first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5). Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI) is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction. A role for capturing reducing equivalents released as hydrogen during nitrogen fixation has been proposed for the second hydrogenase, CpII. Biochemical characterization of CpI and CpII indicated CpI has extremely high hydrogen production activity in comparison to CpII, while CpII has elevated hydrogen oxidation activity in comparison to CpI when assayed under the same conditions. This suggests that these enzymes have evolved a catalytic bias to support their respective physiological functions. Using the published genome of C. pasteurianum (strain W5) hydrogenase sequences were identified, including the already known [NiFe]-hydrogenase, CpI, and CpII sequences, and a third hydrogenase, CpIII was identified in the genome as well. Quantitative real-time PCR experiments were performed in order to analyze transcript abundance of the hydrogenases under diazotrophic and non-diazotrophic growth conditions. There is a markedly reduced level of CpI gene expression together with concomitant increases in CpII gene expression under nitrogen-fixing conditions. Structure-based analyses of the CpI and CpII sequences reveal variations in their catalytic sites that may contribute to their alternative physiological roles. This work demonstrates that the physiological roles of CpI and CpII are to evolve and to consume hydrogen, respectively, in concurrence with their catalytic activities in vitro , with CpII capturing excess reducing equivalents under nitrogen fixation conditions. Comparison of the primary sequences of CpI and CpII and their homologs provides an initial basis for identifying key structural determinants that modulate hydrogen production and hydrogen oxidation activities.

09 BIOMASS FUELS↗

Neoproterozoic variations in the C-isotopic composition of seawater: stratigraphic and biogeochemical implications

The recent proliferation of stratigraphic studies of delta 13C variation in carbonates and organic C in later Neoproterozoic and basal Cambrian successions (approximately 850-530 Ma) indicates a strong oscillating trend in the C-isotopic composition of surface seawater. Alone, this trend does not adequately characterize discrete intervals in Neoproterozoic time. However, integrated with the vectorial signals provided by fossils and Sr-isotopic variations, C isotope chemostratigraphy facilitates the interbasinal correlation of later Neoproterozoic successions. Results of these studies are evaluated in terms of four stratigraphic intervals: (1) the Precambrian/Cambrian boundary, (2) the post-Varanger terminal Proterozoic, (3) the late Cryogenian, and (4) the early Cryogenian. Where biostratigraphic or radiometric data constrain the age of Neoproterozoic sedimentary sequences, secular variations in C and Sr isotopes can provide a level of stratigraphic resolution exceeding that provided by fossils alone. Isotopic data place strong constraints on the chemical evolution of seawater, linking it to major tectonic and paleoclimatic events. They also provide a biogeochemical framework for the understanding of the initial radiation of macroscopic metazoans, which is associated stratigraphically, and perhaps causally, with a global increase in the burial of organic C and a concomitant rise of atmospheric O2.

NASA Discipline Exobiology↗

Community detection in sequence similarity networks based on attribute clustering

Networks are powerful tools for the presentation and analysis of interactions in multi-component systems. A commonly studied mesoscopic feature of networks is their community structure, which arises from grouping together similar nodes into one community and dissimilar nodes into separate communities. Here in this paper, the community structure of protein sequence similarity networks is determined with a new method: Attribute Clustering Dependent Communities (ACDC). Sequence similarity has hitherto typically been quantified by the alignment score or its expectation value. However, pair alignments with the same score or expectation value cannot thus be differentiated. To overcome this deficiency, the method constructs, for pair alignments, an extended alignment metric, the link attribute vector, which includes the score and other alignment characteristics. Rescaling components of the attribute vectors qualitatively identifies a systematic variation of sequence similarity within protein superfamilies. The problem of community detection is then mapped to clustering the link attribute vectors, selection of an optimal subset of links and community structure refinement based on the partition density of the network. ACDC-predicted communities are found to be in good agreement with gold standard sequence databases for which the "ground truth" community structures (or families) are known. ACDC is therefore a community detection method for sequence similarity networks based entirely on pair similarity information. A serial implementation of ACDC is available from https://cmb.ornl.gov/resources/developments

59 BASIC BIOLOGICAL SCIENCES↗

Polymorphism in Self-Assembly of Short Peptoid Sequences

Due to various applications enabled by diverse morphologies of self-assembled sequence-defined polymers, controlling the self-assembly of synthetic peptidomimetics into designed morphologies has emerged as a promising route for the development of bioinspired functional materials. Herein, we report morphological control over the assembly of a series of short peptoids, or poly-N-substituted glycines, that contain asymmetric hydrophobic domains. We demonstrate that the inherent flexibility of amphiphilic peptoid bilayers drives assembly polymorphism, resulting in the coexistence of nanosheets, twisted ribbons, and nanofibers three distinct morphologies. By tuning peptoid molecular interactions through variations in sequence design, solution pH, and temperature, we demonstrate precise control over the twisting and folding of peptoid bilayers, enabling the formation of well-defined nanosheets and nanohelices. Molecular dynamics simulations further unravel how the introduction of asymmetric hydrophobic domains enables the flexibility of peptoid bilayers and results in peptoid assembly polymorphism. By tuning peptoid molecular interactions through heating, we further demonstrate the transformation of nanosheets into nanohelices. We envision that our mechanistic investigation of peptoid assembly polymorphism provides a strong foundation for leveraging peptoid sequences and chemistries to achieve controlled molecular interactions, driving the creation of biomimetic materials with tailored morphologies and functionalities.

assembly polymorphism↗

Persistent Sub-Yearly Chromospheric Variations in Lower Main-Sequence Stars: Tau Booe and alpha Com

The recent discoveries of extrasolar planetary systems around lower main-sequence stars such as tau Booe (HD 120136) has prompted further investigation into their stellar activity. A cursory analysis of tau Booe for cyclic chromospheric activity, based on its 30-yr record of Ca 2 H and K fluxes obtained as part of the HK Project from Mount Wilson Observatory, finds an intermediate, sub-yearly period (approximately 117 d) in chromospheric activity in addition to, and separate from, both its rotation (3.3 d) and long-term variability. As a persistent subyearly period in surface magnetic activity is unprecedented, we investigate this apparent anomaly further by examining chromospheric activity levels of other stars with similar mass, searching for variability in chromospheric activity with periods of less than one year, but longer than measured or predicted rotation. An examination of the time series of 40 mid-to-late F dwarfs yielded one other star for further analysis: alpha Com (HD 114378, P approximately 132 d). The variations for these two stars were checked for persistence and coherence. Based on these determinations, we eliminate the possibilities of rotation, long-term activity cycle, and the evolution of active regions as the cause of this variation in both stars. In particular, for tau Booe we infer that the phenomenon may be chromospheric in origin; however, beyond this, it is difficult to identify anything further regarding the cause of the activity variations, or even whether the observed modulation in the two stars have the same origin.

Maulik, Davesh↗

Lipocalin Blc is a potential heme-binding protein

Lipocalins are a superfamily of functionally diverse proteins defined by a well-conserved tertiary structure despite variation in sequence. Lipocalins bind and transport small hydrophobic molecules in organisms of all kingdoms. However, there is still uncertainty regarding the function of some members of the family, including bacterial lipocalin Blc from Escherichia coli. Here, we present evidence that lipocalin Blc may be involved in heme binding, trans-periplasmic transport, or heme storage. This conclusion is supported by a cocrystal structure, mass-spectrometric data, absorption titration, and in silico analysis. Binding of heme is observed at low micromolar range with one-to-one ligand-to-protein stoichiometry. However, the absence of classical coordination to the iron atom leaves the possibility that the primary ligand of Blc is another tetrapyrrole.

59 BASIC BIOLOGICAL SCIENCES↗

A study of mechanistic mapping of novel SNPs to male breast cancer

Alterations in BRCA2, PALB2, CHEK2, and p53 genes have been identified for their association with male breast cancer in various studies. The incidence of male breast cancer in India is consistent with its global rate. The present study was carried out with an aim to evaluate the genetic alterations in male breast cancer patients from Malwa region of Punjab, India. Four male breast cancer patients belonging to different families were recruited from Guru Gobind Singh Medical College and Hospital, Faridkot, India. A total of 51 genes reported with implications in the pathogenesis of breast cancer were screened using next generation sequencing. Germline variations were found in BRCA1, BRCA2, PMS2, p53, and PALB2 genes, previously reported to be associated with MBC as well as FBC. In addition to these, 13 novel missense alterations were detected in eight genes including STK11, FZR1, PALB2, BRCA2, NF2, BAP1, BARD1, and CHEK2. Impact of these missense alterations on structure and function of protein was also analyzed through molecular dynamics simulation. Structural analysis of these single nucleotide polymorphisms (SNPs) revealed significant impact on the encoded protein functioning.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Fast heating of fuel assembled in a spherical deuterated polystyrene shell target by counter-irradiating tailored laser pulses delivered by a HAMA 1 Hz ICF driver

Fast heating is a method of heating an assembled high-density plasma into a hot state by irradiating it with short-duration (sub-picosecond), high-intensity ($>$ $10^{18}$ W ${\rm cm}^{-2}$ ) laser pulses before the plasma expands and dissolves hydrodynamically. In this paper, we present detailed experimental results of fast heating fuel assembled in a spherical deuterated polystyrene shell target of 500 ${\mu}$ m diameter and 7 μm thickness with counterbeam illumination by using a HAMA 1 Hz, 5.9 J inertial confinement fusion laser driver with pulse tailoring. These tailored pulses contain three pulses in sequence: a 'foot' pulse of 2.4 J/25 ns, a 'spike' pulse of 0.5 J/300 ps and a 'heater' pulse of 0.4 J/110 fs; these pulses are designed to assemble the fuel and heat it. By varying the energy of the foot pulse, we find that fast heating the fuel is achieved only if the fuel is weakly ablated by the foot pulse and then shock-assembled by the spike pulse into the target centre so that the heater pulse can access the fuel with a focal intensity greater than $10^{18}$ W ${\rm cm}^{-2}$ . Without a foot pulse, the heater pulse contributes to assembling the fuel. For higher foot-pulse energies, the heater pulse drives a hydrodynamic motion with speeds of the order 107 cm ${\rm s}^{-1}$ with intensities of the order $10^{17}$ W ${\rm cm}^{-2}$ , resulting in re-assembling and additional heating of the pre-assembled fuel. Once a shock-assembled core is achieved at the target centre, we succeed qualitatively in fast heating the core for shots in sequence with variations of laser energy within 18%. The coupling efficiency from the heating laser to the core is inferred to be $(10 \pm 2)$ % in total: $(8 \pm 1.6)$ % for the ionized bulk electrons and $(2 \pm 0.4)$ % for the bulk ions. The fusion neutron spectrum detected on the laser axis exhibits peaks at 1.0 MeV, 1.7 MeV and 3.8 MeV. These peaks are attributed to the $C(d, n){\hspace{0pt}}^{13}$ N and $d(d, n){\hspace{0pt}}^3$ He reactions induced by counterpropagating fast deuterons accelerated by the photon pressure of the heating pulses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient

Abstract Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.

59 BASIC BIOLOGICAL SCIENCES↗

Bacterial hemophilin homologs and their specific type eleven secretor proteins have conserved roles in heme capture and are diversifying as a family

Cellular life relies on enzymes that require metals, which must be acquired from extracellular sources. Bacteria utilize surface and secreted proteins to acquire such valuable nutrients from their environment. These include the cargo proteins of the type eleven secretion system (T11SS), which have been connected to host specificity, metal homeostasis, and nutritional immunity evasion. This Sec-dependent, Gram-negative secretion system is encoded by organisms throughout the phylum Proteobacteria, including human pathogens Neisseria meningitidis, Proteus mirabilis, Acinetobacter baumannii, and Haemophilus influenzae. Experimentally verified T11SS-dependent cargo include transferrin-binding protein B (TbpB), the hemophilin homologs heme receptor protein C (HrpC), hemophilin A (HphA), the immune evasion protein factor-H binding protein (fHbp), and the host symbiosis factor nematode intestinal localization protein C (NilC). Here, we examined the specificity of T11SS systems for their cognate cargo proteins using taxonomically distributed homolog pairs of T11SS and hemophilin cargo and explored the ligand binding ability of those hemophilin cargo homologs. In vivo expression in Escherichia coli of hemophilin homologs revealed that each is secreted in a specific manner by its cognate T11SS protein. Sequence analysis and structural modeling suggest that all hemophilin homologs share an N-terminal ligand-binding domain with the same topology as the ligand-binding domains of the Haemophilus haemolyticus heme binding protein (Hpl) and HphA. We term this signature feature of this group of proteins the hemophilin ligand-binding domain. Network analysis of hemophilin homologs revealed five subclusters and representatives from four of these showed variable heme-binding activities, which, combined with sequence-structure variation, suggests that hemophilins are diversifying in function.

59 BASIC BIOLOGICAL SCIENCES↗

Usefulness of LANDSAT data for monitoring plant development and range conditions in California's annual grassland

A network of sampling sites throughout the annual grassland region of California was established to correlate plant growth stages and forage production to climatic and other environmental factors. Plant growth and range conditions were further related to geographic location and seasonal variations. A sequence of LANDSAT data was obtained covering critical periods in the growth cycle. This was analyzed by both photointerpretation and computer aided techniques. Image characteristics and spectral reflectance data were then related to forage production, range condition, range site and changing growth conditions. It was determined that repeat sequences with LANDSAT color composite images do provide a means for monitoring changes in range condition. Spectral radiance data obtained from magnetic tape can be used to determine quantitatively the critical stages in the forage growth cycle. A computer ratioing technique provided a sensitive indicator of changes in growth stages and an indication of the relative differences in forage production between range sites.

Carneggie, D. M.↗

Usefulness of LANDSAT data for monitoring plant development and range conditions in California's annual grassland

A network of sampling sites throughout the annual grassland region was established to correlate plant growth in stages and forage production to climatic and other environmental factors. Plant growth and range conditions were further related to geographic location and seasonal variations. A sequence of LANDSAT data was obtained covering critical periods in the growth cycle. Data were analyzed by both photointerpretation and computer aided techniques. Image characteristics and spectral reflectance data were then related to forage production, range condition, range site, and changing growth conditions.

Carneggie, D. M.↗

N-15/N-14 variations in Cretaceous Atlantic sedimentary sequences - Implication for past changes in marine nitrogen biogeochemistry

Unusually low delta N-15 found in early to middle Cretaceous beds rich in marine organic matter from two separate eastern Atlantic Ocean basins is reported. These findings constitute unambiguous evidence that the N contained in these strata is the end result of biogeochemical processes that differed substantially from those that operated on the N contained in intervening organic carbon-poor strata and younger marine sediments. The data indicate that the low N-15 relative abundance is the consequence of pelagic rather than postdepositional processes. Reduced ocean circulation, increased denitrification, and hence, reduced euphotic zone nitrate availability may have led to Cretaceous phytoplankton assemblages that were periodically dominated by N2-fixing blue-green algae, a possible source of the sedimentary N-15 depletion.

Rau, Greg H.↗

Identification of a rare homozygous c.790C>T variation in the TFB2M gene in Korean patients with autism spectrum disorder

Highlights: • TFB2M have been known to critical in mitochondrial DNA gene expression. • We identified a variation of TFB2M gene sequence in Korean autism patients. • The variation caused increased mitochondrial DNA gene expression. • Increased mitochondrial biogenesis resulted in ROS production and damaged cells. • Structural changes of variant TFB2M seems to delay unloading of DNA from TFB2M. Mitochondrial dysfunction and subsequent enhanced oxidative stress is implicated in the pathogenesis of autism spectrum disorder (ASD). Mitochondrial transcription factor B2 (TFB2M) is an essential protein in mitochondrial gene expression. No reports have described TFB2M mutations and variations involved in any human diseases. We identified a rare homozygous c.790C>T (His264Tyr) variation in TFB2M gene in two Korean siblings with ASD by whole-exome sequencing. The roles of the TFB2M variation in the pathogenesis of ASD were investigated. Patient fibroblasts revealed increased transcription of mitochondrial genes and mitochondrial function in terms of ATP, membrane potential, oxygen consumption, and reactive oxygen species (ROS). Overexpression of the TFB2M variant in primary-cultured fibroblasts demonstrated significantly increased transcription of mitochondrial genes and mitochondrial function compared with overexpression of wild-type TFB2M. Molecular dynamics simulation of the TFB2M variant protein suggested an increase in the rigidity of the hinge region, which may cause alterations in loading and/or unloading of TFB2M on target DNA. Our results suggest that augmentation of mitochondrial gene expression and subsequent enhancement of mitochondrial function may be associated with the pathogenesis of ASD in Korean patients.

60 APPLIED LIFE SCIENCES↗

Using the XMM-Newton Optical Monitor to Study Cluster Galaxy Evolution

We explore the application of XMM Newton Optical Monitor (XMM-OM) ultraviolet (UV) data to study galaxy evolution. Our sample is constructed as the intersection of all Abell clusters with z < 0.05 and having archival XMM-OM data in either the UVM2 or UVW1 filters, plus optical and UV photometry from the Sloan Digital Sky Survey and GALEX, respectively. The 11 resulting clusters include 726 galaxies with measured redshifts, 520 of which have redshifts placing them within their parent Abell clusters. We develop procedures for manipulating the XMM-OM images and measuring galaxy photometry from them, and we confirm our results via comparison with published catalogs. Color-magnitude diagrams (CMDs) constructed using the XMM-OM data along with SDSS optical data show promise for evolutionary studies, with good separation between red and blue sequences and real variation in the width of the red sequence that is likely indicative of differences in star formation history. This is particularly true for UVW1 data, as the relative abundance of data collected using this filter and its depth make it an attractive choice. Available tools that use stellar synthesis libraries to fit the UV and optical photometric data may also be used, thereby better describing star formation history within the past billion years and providing estimates of total stellar mass that include contributions from young stars. Finally, color-color diagrams that include XMM-OM UV data appear useful to the photometric identification of both extragalactic and stellar sources.

Miller, Neal A.↗