Search NASA⌕ Search

SEARCH · Search NASA

Results for “References”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12

Preliminary assessment of stable nitrogen and oxygen isotopic composition of USGS51 and USGS52 nitrous oxide reference gases and perspectives on calibration needs

Rationale: Despite a long history and growing interest in isotopic analyses of N 2 O, there is a lack of isotopically characterized N 2 O isotopic reference materials (standards) to enable normalization and reporting of isotope-delta values. Here, in this paper we report the isotopic characterization of two pure N 2 O gas reference materials, USGS51 and USGS52, which are now available for laboratory calibration (https://isotopes.usgs.gov/lab/referencematerials.html). Methods: A total of 400 sealed borosilicate glass tubes of each N 2 O reference gas were prepared from a single gas filling of a high vacuum line. We demonstrated isotopic homogeneity via dual-inlet isotope-ratio mass spectrometry. Isotopic analyses of these reference materials were obtained from eight laboratories to evaluate interlaboratory variation and provide preliminary isotopic characterization of their δ 15 N, δ 18 O, δ 15 N α , δ 15 N β and site preference (S P ) values. Results: The isotopic homogeneity of both USGS51 and USGS52 was demonstrated by one-sigma standard deviations associated with the determinations of their δ 15 N, δ 18 O, δ 15 N α , δ 15 N β and S P values of 0.12 mUr or better. The one-sigma standard deviations of SP measurements of USGS51 and USGS52 reported by eight laboratories participating in the interlaboratory comparison were 1.27 and 1.78 mUr, respectively. Conclusions: The agreement of isotope-delta values obtained in the interlaboratory comparison was not sufficient to provide reliable accurate isotope measurement values for USGS51 and USGS52. Lastly, we propose that provisional values for the isotopic composition of USGS51 and USGS52 determined at the Tokyo Institute of Technology can be adopted for normalizing and reporting sample data until further refinements are achieved through additional calibration efforts.

54 ENVIRONMENTAL SCIENCES↗

Large-Volume Injection and Assessment of Reference Standards for n -Alkane δD and δ 13 C Analysis via Gas Chromatography Isotope Ratio Mass Spectrometry

Compound-specific stable isotope analysis of hydrogen (δD) and carbon (δ 13 C) in organic compounds is a valuable tool in biogeochemical research. A key limitation of this method is the relatively large amount of sample required to achieve desirable precision. We developed a large-volume (20 μL) injection method that allows for high throughput analysis of less concentrated samples and tested it for δ 13 C and δD measurements of n-alkanes. We also conducted a comparison of reference standards and assessed several methods to normalize and correct n-alkane δD and δ13C measurements. The mean precision of the δD method based on 233 environmental n-alkane samples (two to three replications per sample) is 4.0‰ (1σ, estimated from the weighted mean of the pooled unbiased standard deviations) and 0.46‰ (1σ) for δ 13 C from 37 environmental samples (two to three replications per sample). The evaluation of reference standards shows that the use of n-alkane standards with large offsets in δD values in adjacent n-alkane chains can lead to biases in measurement correction. The large-volume injection method shows good reproducibility of δ 13 C and δD measurements of n-alkanes and reduces the required sample concentration by about 80%. We propose that for δD measurements, a reference standard set should be used in which each reference standard has a limited range of δD values and no adjacent n-alkane chains, to minimize memory effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum mechanics in noninertial reference frames: Violations of the nonrelativistic equivalence principle

In previous work we have developed a formulation of quantum mechanics in non-inertial reference frames. This formulation is grounded in a class of unitary cocycle representations of what we have called the Galilean line group, the generalization of the Galilei group that includes transformations amongst non-inertial reference frames. These representations show that in quantum mechanics, just as is the case in classical mechanics, the transformations to accelerating reference frames give rise to fictitious forces. A special feature of these previously constructed representations is that they all respect the non-relativistic equivalence principle, wherein the fictitious forces associated with linear acceleration can equivalently be described by gravitational forces. In this paper we exhibit a large class of cocycle representations of the Galilean line group that violate the equivalence principle. Nevertheless the classical mechanics analogue of these cocycle representations all respect the equivalence principle. -- Highlights: •A formulation of Galilean quantum mechanics in non-inertial reference frames is given. •The key concept is the Galilean line group, an infinite dimensional group. •A large class of general cocycle representations of the Galilean line group is constructed. •These representations show violations of the equivalence principle at the quantum level. •At the classical limit, no violations of the equivalence principle are detected.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Advances in benchmarking and round robin testing for PEM water electrolysis: Reference protocol and hardware

While the number of publications in the PEM water electrolysis community increases each year, no common ground concerning reference hardware (test cells and test bench) and testing protocols has been yet established. This would, however, be necessary for the comparability of experimental results. First attempts for such reference hardware and procedures have been made in the framework of the Task 30 Electrolysis within the Technology Collaboration Programme on Advanced Fuel Cells (AFC TCP) of the International Energy Agency (IEA). Since then, improvements of both the test hardware (test cell and components) as well as the measurement protocol were identified, and a revised methodology and key results based on a comprehensive measurement series have been obtained. A detailed protocol for testing commercial reference components with a reference laboratory test cell developed in-house by Fraunhofer ISE is presented. For evaluation of the protocol and the hardware, it was tested at three different institutions at the same time. Impedance spectroscopic and polarization data was acquired and analyzed. The obtained differences in performance were calculated to give the community an expectation window to compare own data to. Finally, the importance of a thorough temperature control and the conditioning phase are demonstrated.

08 HYDROGEN↗

The oxygen stable isotope composition of CRM 125-A UO 2 standard reference material

While there is a clear need for standardized reference materials for analytical calibrations and for inter-laboratory comparisons, there are not currently any for the oxygen stable isotopic composition of uranium oxides. In this paper we summarize the results from four laboratories by seven different methods of oxygen stable isotope analyses using fluorination techniques of CRM 125-A UO 2 Standard Reference Material. We synthesize these data and methods to arrive at a consensus oxygen stable isotope composition for CRM 125-A $δ$ 18 O = -9.63‰ (±0.29‰) VSMOW. We discuss methodological differences between analytical approaches, including furnace vs laser heating, fluorination using BrF 5 or ClF 3 , as well as calibration strategies. We highlight the potential effects of calibration scale compression from single-point calibrations using reference material with $δ$ 18 O values having a large relative difference from the sample being analyzed. We demonstrate how calibration scale compression can yield differences in calibrated $δ$ 18 O values up to ~2‰ for samples with ~20‰ difference from a single reference material, if the calibration slope of different analytical systems differs by 0.1. In conclusion, we suggest the use of liquid water calibration standards sealed in silver capillary tubes for multi-point calibrations of fluorination analysis systems.

07 ISOTOPE AND RADIATION SOURCES↗

A library of calcium mineral reference spectra recorded by parallel imaging using NEXAFS spectromicroscopy

Calcium minerals are ubiquitous in geology and life chemistry. Understanding the phase and chemical state of calcium minerals is important for numerous processes including materials chemistry, hard tissue biogenesis and geological processes. Photoemission spectroscopies such as near edge X-ray absorption fine structure (NEXAFS) and scanning transmission X-ray microscopy have been instrumental in identifying and characterizing calcium minerals in all these areas. In this work, we have recorded reference spectra for a range of different calcium minerals including a series of calcium carbonates, calcium oxalates and calcium phosphates. While collections of reference spectra for several calcium minerals can be found in the literature, these spectra have been reported in different contexts using a variety of instruments. We, here, report a comprehensive list of references recorded in parallel in a single experiment by imaging an array of calcium minerals using a NEXAFS microscope. We present reference NEXAFS spectra at the calcium L-, carbon K- and oxygen K-edges.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Kernel reconstruction methods for Doppler broadening — Temperature interpolation by linear combination of reference cross sections at optimally chosen temperatures

This paper establishes a new family of methods to perform temperature interpolation of nuclear interactions cross sections, reaction rates, or cross sections times the energy. One of these quantities at temperature T is approximated as a linear combination of quantities at reference temperatures (T j ). The problem is formalized in a cross section independent fashion by considering the kernels of the different operators that convert cross section related quantities from a temperature T 0 to a higher temperature T — namely the Doppler broadening operation. Doppler broadening interpolation of nuclear cross sections is thus here performed by reconstructing the kernel of the operation at a given temperature T by means of linear combination of kernels at reference temperatures (T j ). The choice of the L 2 metric yields optimal linear interpolation coefficients in the form of the solutions of a linear algebraic system inversion. The optimization of the choice of reference temperatures (T j ) is then undertaken so as to best reconstruct, in the L∞ sense, the kernels over a given temperature range [T min ,T max ]. The performance of these kernel reconstruction methods is then assessed in light of previous temperature interpolation methods by testing them upon isotope 238 U. Temperature-optimized free Doppler kernel reconstruction significantly outperforms all previous interpolation-based methods, achieving 0.1% relative error on temperature interpolation of 238 U total cross section over the temperature range [300 K,3000 K] with only 9 reference temperatures.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Measuring residual stress in Ti-6Al-4V with HR-EBSD, using reference patterns from annealed material

In this study, elastic strain and residual stress values in an engineering material were determined by high-resolution EBSD (HR-EBSD) using reference patterns from annealed, recrystallized material. Specifically, rolled Ti-6Al-4V sheet was analyzed using HR EBSD in both an as-annealed and a strained state, the latter established via a static two-point bend fixture. The commercial software CrossCourt4 (CC4) was used to evaluate the relative intragranular strain tensor components of the alpha grains mapped by HR-EBSD. The intragranular reference patterns identified in each grain by the software were then replaced with similarly-oriented patterns from scans of the as-annealed, recrystallized material. The CC4 analysis was then repeated to provide calibrated strain and residual stress values. Elastic strains on the order of 10–3 were detected, with corresponding residual stress values on the order of 1 GPa. Subsequent analyses using high energy synchrotron x-ray diffraction showed good correlation with the elastic strains measured by HR-EBSD using the annealed reference patterns. Additionally, the maximum macroscopic stress analytically predicted for two-point bending was in agreement with the residual stress observed. Good repeatability of the methodology and insight into the state of individual grains were also observed. The findings provide encouraging evidence that accurate intragranular and long-range residual stress measurements of engineering significance can be made with HR-EBSD using a physical reference pattern library.

36 MATERIALS SCIENCE↗

Comparison of setup error using different reference images: a phantom and lung cancer patients study

The purpose of this study was to compare setup errors obtained with kilovoltage cone-beam computed tomography (CBCT) and 2 different kinds of reference images, free-breathing 3D localization CT images (FB-CT) and the average images of 4-D localization CT images (AVG-CT) for phantom and lung cancer patients. This study also explored the correlation between the difference of translational setup errors and the gross tumor volume (GTV) motion. A respiratory phantom and 14 patients were enrolled in this study. For phantom and each patient, 3D helical CT and 4D CT images were acquired, and AVG-CT images were generated from the 4D CT. The setup errors were determined based on the image registration between the CBCT and the 2 different reference images, respectively. The data for both translational and rotational setup errors were analyzed and compared. The GTV centroid movement as well as its correlation with the translational setup error differences was also evaluated. In the phantom study, the AVG-CT method was more accurate than the FB-CT method. For patients, the translational setup errors based on FB-CT were significantly larger than those from AVG-CT in the left-right (LR), superior-inferior (SI), and anterior-posterior (AP) directions (p < 0.05). Translational setup errors differed by >1 mm in 32.6% and >2 mm in 12.9% of CBCT scans. The rotational setup errors from FB-CT were significantly different from those from AVG-CT in the LR and AP directions (p < 0.05). The correlation coefficient of the translational setup error differences and the GTV centroid movement in the LR, SI, and AP directions was 0.515 (p = 0.060), 0.902 (p < 0.001), and 0.510 (p = 0.062), respectively. For lung cancer patients, respiration may affect the on-line target position location. AVG-CT provides different reference information than FB-CT. The difference in SI direction caused by the 2 methods increases with the GTV movement. Therefore, AVG-CT should be the prefered choice of reference images.

61 RADIATION PROTECTION AND DOSIMETRY↗

Block correlated second order perturbation theory with a generalized valence bond reference function

The block correlated second-order perturbation theory with a generalized valence bond (GVB) reference (GVB-BCPT2) is proposed. In this approach, each geminal in the GVB reference is considered as a “multi-orbital” block (a subset of spin orbitals), and each occupied or virtual spin orbital is also taken as a single block. The zeroth-order Hamiltonian is set to be the summation of the individual Hamiltonians of all blocks (with explicit two-electron operators within each geminal) so that the GVB reference function and all excited configuration functions are its eigenfunctions. The GVB-BCPT2 energy can be directly obtained without iteration, just like the second order Møller–Plesset perturbation method (MP2), both of which are size consistent. We have applied this GVB-BCPT2 method to investigate the equilibrium distances and spectroscopic constants of 7 diatomic molecules, conformational energy differences of 8 small molecules, and bond-breaking potential energy profiles in 3 systems. GVB-BCPT2 is demonstrated to have noticeably better performance than MP2 for systems with significant multi-reference character, and provide reasonably accurate results for some systems with large active spaces, which are beyond the capability of all CASSCF-based methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Note: Improved calibration of atomic force microscope cantilevers using multiple reference cantilevers

Overall precision of the simplified calibration method in J. E. Sader et al., Rev. Sci. Instrum. 83, 103705 (2012), Sec. III D, is dominated by the spring constant of the reference cantilever. The question arises: How does one take measurements from multiple reference cantilevers, and combine these results, to improve uncertainty of the reference cantilever’s spring constant and hence the overall precision of the method? This question is addressed in this note. Its answer enables manufacturers to specify of a single set of data for the spring constant, resonant frequency, and quality factor, from measurements on multiple reference cantilevers. With this data set, users can trivially calibrate cantilevers of the same type.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Extension of frozen natural orbital approximation to open-shell references: Theory, implementation, and application to single-molecule magnets

Natural orbitals are often used to achieve a more compact representation of correlated wave-functions. Using natural orbitals computed as eigenstates of the virtual–virtual block of the state density matrix instead of the canonical Hartree–Fock orbitals results in smaller errors when the same fraction of virtual space is frozen. This strategy, termed frozen natural orbital (FNO) approach, is effective in reducing the cost of regular coupled-cluster (CC) calculations and some multistate methods, such as EOM-IP-CC (equation-of-motion CC for ionization potentials). This contribution extends the FNO approach to the EOM-SF-CC ansatz (EOM-CC with spin-flip). In contrast to EOM-IP-CCSD, EOM-SF-CCSD relies on high-spin open-shell references. Using FNOs computed for an open-shell reference leads to an erratic behavior of the EOM-SF-CC energies and properties due to an inconsistent truncation of the α and β orbital spaces. A general solution to problems arising in the EOM-CC calculations utilizing open-shell references, termed OSFNO (open-shell FNO), is proposed. Furthermore, by means of singular value decomposition (SVD) of the overlap matrix of the α and β orbitals, the OSFNO algorithm identifies the corresponding orbitals and determines virtual orbitals corresponding to the singly occupied space. This is followed by SVD of the singlet part of the state density matrix in the remaining virtual orbital subspace. The so-computed FNOs preserve the spin purity of the open-shell orbital subspace to the extent allowed by the original reference, thus facilitating a safe truncation of the virtual space. The performance of OSFNO is benchmarked for selected diradicals and triradicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Proton deflectometry with in situ x-ray reference for absolute measurement of electromagnetic fields in high-energy-density plasmas

In this work, we report a technique of proton deflectometry that uses a grid and an in situ reference x-ray grid image for precise measurements of magnetic fields in high-energy-density plasmas. A D 3 He fusion implosion provides a bright point source of both protons and x-rays, which is split into beamlets by a grid. The protons undergo deflections as they propagate through the plasma region of interest, whereas the x-rays travel along straight lines. The x-ray image, therefore, provides a zero-deflection reference image. The line-integrated magnetic fields are inferred from the shifts of beamlets between the deflected (proton) and reference (x-ray) images. We developed a system for analysis of these data, including automatic algorithms to find beamlet locations and to calculate their deflections from the reference image. The technique is verified in an experiment performed at OMEGA to measure a nonuniform magnetic field in vacuum and then applied to observe the interaction of an expanding plasma plume with the magnetic field.

47 OTHER INSTRUMENTATION↗

VLBI FOR GRAVITY PROBE B. II. MONITORING OF THE STRUCTURE OF THE REFERENCE SOURCES 3C 454.3, B2250+194, AND B2252+172

We used 8.4 GHz very long baseline interferometry images obtained at up to 35 epochs between 1997 and 2005 to examine the radio structures of the main reference source, 3C 454.3, and two secondary reference sources, B2250+194 and B2252+172, for the guide star for the NASA/Stanford relativity mission Gravity Probe B (GP-B). For one epoch in 2004 May, we also obtained images at 5.0 and 15.4 GHz. The 35 8.4 GHz images for quasar 3C 454.3 confirm a complex, evolving, core-jet structure. We identified at each epoch a component, C1, near the easternmost edge of the core region. Simulations of the core region showed that C1 is located, on average, 0.18 {+-} 0.06 mas west of the unresolved 'core' identified in 43 GHz images. We also identified in 3C 454.3 at 8.4 GHz several additional components that moved away from C1 with proper motions ranging in magnitude between 0.9 c and 5 c. The detailed motions of the components exhibit two distinct bends in the jet axis located {approx}3 and {approx}5.5 mas west of C1. The spectra between 5.0 and 15.4 GHz for the 'moving' components are steeper than those for C1. The 8.4 GHz images of B2250+194 and B2252+172, in contrast to those of 3C 454.3, reveal compact structures. The spectrum between 5.0 and 15.4 GHz for B2250+194 is inverted while that for B2252+172 is flat. Based on its position near the easternmost edge of the 8.4 GHz radio structure, close spatial association with the 43 GHz core, and relatively flat spectrum, we believe 3C 454.3 component C1 to be the best choice for the ultimate reference point for the GP-B guide star. The compact structures and inverted-to-flat spectra of B2250+194 and B2252+172 make these objects valuable secondary reference sources.

79 ASTRONOMY AND ASTROPHYSICS↗

Specific absorbed fractions for a revised series of the UF/NCI pediatric reference phantoms: internal photon sources

Assessment of radiation absorbed dose to internal organs of the body from the intake of radionuclides, or in the medical setting through the injection of radiopharmaceuticals, is generally performed based upon reference biokinetic models or patient imaging data, respectively. Biokinetic models estimate the time course of activity localized to source organs. The time-integration of these organ activity profiles are then scaled by the radionuclide S-value, which defines the absorbed dose to a target tissue per nuclear transformation in various source tissues. S-values are computed using established nuclear decay information (particle energies and yields), and a parameter termed the specific absorbed fraction (SAF). The SAF is the ratio of the absorbed fraction—fraction of particle energy emitted in the source tissue that is deposited in the target tissue—and the target organ mass. While values of the SAF may be computed using patient-specific or individual-specific anatomic models, they have been more widely available through the use of computational reference phantoms. In this study, we report on an extensive series of photon SAFs computed in a revised series of the University of Florida and the National Cancer Institute pediatric reference phantoms which have been modified to conform to the specifications embodied in the ICRP reference adult phantoms of Publication 110 (e.g. organs modeled, organ ID numbers, blood contribution to elemental compositions). Following phantom anatomical revisions, photon radiation transport simulations were performed using MCNPX v2.7 in each of the ten phantoms of the series—male and female newborn, 1 year old, 5 year old, 10 year old, and 15 year old—for 60 different tissues serving as source and/or target regions. A total of 25 photon energies were considered from 10 keV to 10 MeV along a logarithm energy grid. Detailed analyses were conducted of the relative statistical errors in the Monte Carlo target tissue energy deposition tallies at low photon energies and over all energies for source–target combinations at large intra-organ separation distances. Based on these analyses, various data smoothing algorithms were employed, including multi-point weighted data smoothing, and log–log interpolation at low energies (1 keV and 5 keV) using limiting SAF values based upon target organ mass to bound the interpolation interval. The final dataset is provided in a series of ten electronic supplemental files in MS Excel format. Finally, the results of this study were further used as the basis for assessing the radiative component of internal electron source SAFs as described in our companion paper (Schwarz et al 2021) for this same pediatric phantom series.

61 RADIATION PROTECTION AND DOSIMETRY↗

Specific absorbed fractions for a revised series of the UF/NCI pediatric reference phantoms: internal electron sources

Assessment of radiation absorbed dose to internal organs of the body from the intake of radionuclides, or in the medical setting through the injection of radiopharmaceuticals, is generally performed based upon reference biokinetic models or patient imaging data, respectively. Biokinetic models estimate the time course of activity localized to source organs. The time-integration of these organ activity profiles are then scaled by the radionuclide S-value, which defines the absorbed dose to a target tissue per nuclear transformation in various source tissues. S-values are computed using established nuclear decay information (particle energies and yields), and a parameter termed the specific absorbed fraction (SAF). The SAF is the ratio of the absorbed fraction—fraction of particle energy emitted in the source tissue that is deposited in the target tissue—and the target organ mass. While values of the SAF may be computed using patient-specific or individual-specific anatomic models, they have been more widely available through the use of computational reference phantoms. In this study, we report on an extensive series of photon SAFs computed in a revised series of the University of Florida and the National Cancer Institute pediatric reference phantoms which have been modified to conform to the specifications embodied in the ICRP reference adult phantoms of Publication 110 (e.g. organs modeled, organ ID numbers, blood contribution to elemental compositions). Following phantom anatomical revisions, photon radiation transport simulations were performed using MCNPX v2.7 in each of the ten phantoms of the series—male and female newborn, 1 year old, 5 year old, 10 year old, and 15 year old—for 60 different tissues serving as source and/or target regions. A total of 25 photon energies were considered from 10 keV to 10 MeV along a logarithm energy grid. Detailed analyses were conducted of the relative statistical errors in the Monte Carlo target tissue energy deposition tallies at low photon energies and over all energies for source–target combinations at large intra-organ separation distances. Based on these analyses, various data smoothing algorithms were employed, including multi-point weighted data smoothing, and log–log interpolation at low energies (1 keV and 5 keV) using limiting SAF values based upon target organ mass to bound the interpolation interval. The final dataset is provided in a series of ten electronic supplemental files in MS Excel format. Finally, the results of this study were further used as the basis for assessing the radiative component of internal electron source SAFs as described in our companion paper (Schwarz et al 2021) for this same pediatric phantom series.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.

59 BASIC BIOLOGICAL SCIENCES↗

The Release 6 reference sequence of the Drosophila melanogaster genome

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy and middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.

59 BASIC BIOLOGICAL SCIENCES↗