Accurate Catalogue Research Articles

Data concepts and their relevance for data capture in large scale digitisation of biological collections

Logistically, the data associated with biological collections can be divided into three main categories for digitisation: i) Label Data: the data appearing on the specimen on a label or annotation; ii) Curatorial Data: the data appearing on containers, boxes, cabinets and folders which hold the collections; iii) Supplementary Data: the data held separately from the collections in indices, archives and literature. Each of these categories of data have fundamentally different properties within the digitisation framework which have implications for the data capture process. These properties were assessed in relation to alternative data entry workflows and methodologies to create a more efficient and accurate system of data capture. We see a clear benefit in the prioritisation of curatorial data in the data capture process. These data are often only available at the cabinets, they are in a format suitable for allowing rapid data entry, and they result in an accurate cataloguing of the collections. Finally, the capture of a high resolution digital image enables additional data entry to be separated into multiple sweeps, and optical character recognition (OCR) software can be used to facilitate sorting images for fuller data entry, and giving potential for more automated data entry in the future.

The use of laser ranging to measure space debris

Space debris is a major problem for all the nations that are currently active in space. Adopting high-precision measuring techniques will help produce a reliable and accurate catalog for space debris and collision avoidance. Laser ranging is a kind of real-time measuring technology with high precision for space debris observation. The first space-debris laser-ranging experiment in China was performed at the Shanghai Observatory in July 2008 with a ranging precision of about 60–80 cm. The experimental results showed that the return signals from the targets with a range of 900 km were quite strong, with a power of 40W (2J at 20 Hz) using a 10ns pulse width laser at 532nm wavelength. The performance of the preliminary laser ranging system and the observed results in 2008 and 2010 are also introduced.

The fine-scale architecture of structural variants in 17 mouse genomes

BackgroundAccurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact. Next generation sequencing methods for SV detection are an advance on array-based methods, but are almost exclusively limited to four basic types: deletions, insertions, inversions and copy number gains.ResultsBy visual inspection of 100 Mbp of genome to which next generation sequence data from 17 inbred mouse strains had been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR. These paired-end mapping patterns reveal a greater diversity and complexity in SVs than previously recognized. In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV sites reveal additional complexity at approximately a quarter of structural variants analyzed. We find micro-deletions and micro-insertions at SV breakpoints, ranging from 1 to 107 bp, and SNPs that extend breakpoint micro-homology and may catalyze SV formation.ConclusionsAn integrative approach using experimental analyses to train computational SV calling is essential for the accurate resolution of the architecture of SVs. We find considerable complexity in SV formation; about a quarter of SVs in the mouse are composed of a complex mixture of deletion, insertion, inversion and copy number gain. Computational methods can be adapted to identify most paired-end mapping patterns.

Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses

BackgroundIntegration of retroviral DNA into a germ cell may lead to a provirus that is transmitted vertically to that host's offspring as an endogenous retrovirus (ERV). In humans, ERVs (HERVs) comprise about 8% of the genome, the vast majority of which are truncated and/or highly mutated and no longer encode functional genes. The most recently active retroviruses that integrated into the human germ line are members of the Betaretrovirus-like HERV-K (HML-2) group, many of which contain intact open reading frames (ORFs) in some or all genes, sometimes encoding functional proteins that are expressed in various tissues. Interestingly, this expression is upregulated in many tumors ranging from breast and ovarian tissues to lymphomas and melanomas, as well as schizophrenia, rheumatoid arthritis, and other disorders.ResultsNo study to date has characterized all HML-2 elements in the genome, an essential step towards determining a possible functional role of HML-2 expression in disease. We present here the most comprehensive and accurate catalog of all full-length and partial HML-2 proviruses, as well as solo LTR elements, within the published human genome to date. Furthermore, we provide evidence for preferential maintenance of proviruses and solo LTR elements on gene-rich chromosomes of the human genome and in proximity to gene regions.ConclusionsOur analysis has found and corrected several errors in the annotation of HML-2 elements in the human genome, including mislabeling of a newly identified group called HML-11. HML-elements have been implicated in a wide array of diseases, and characterization of these elements will play a fundamental role to understand the relationship between endogenous retrovirus expression and disease.

Deep Amino Acid Sequencing of Native Brain GABAA Receptors Using High-Resolution Mass Spectrometry

Mass spectrometric sequencing of low abundance, integral membrane proteins, particularly the transmembrane domains, presents challenges that span the multiple phases of sample preparation including solubilization, purification, enzymatic digestion, peptide extraction, and chromatographic separation. We describe a method through which we have obtained high peptide coverage for 12 γ-aminobutyric acid type A receptor (GABAA receptor) subunits from 2 picomoles of affinity-purified GABAA receptors from rat brain neocortex. Focusing on the α1 subunit, we identified peptides covering 96% of the protein sequence from fragmentation spectra (MS2) using a database searching algorithm and deduced 80% of the amino acid residues in the protein from de novo sequencing of Orbitrap spectra. The workflow combined microscale membrane protein solubilization, protein delipidation, in-solution multi-enzyme digestion, multiple stationary phases for peptide extraction, and acquisition of high-resolution full scan and fragmentation spectra. For de novo sequencing of peptides containing the transmembrane domains, timed digestions with chymotrypsin were utilized to generate peptides with overlapping sequences that were then recovered by sequential solid phase extraction using a C4 followed by a porous graphitic carbon stationary phase. The specificity of peptide identifications and amino acid residue sequences was increased by high mass accuracy and charge state assignment to parent and fragment ions. Analysis of three separate brain samples demonstrated that 78% of the sequence of the α1 subunit was observed in all three replicates with an additional 13% covered in two of the three replicates, indicating a high degree of sequence coverage reproducibility. Label-free quantitative analysis was applied to the three replicates to determine the relative abundances of 11 γ-aminobutyric acid type A receptor subunits. The deep sequence MS data also revealed two N-glycosylation sites on the α1 subunit, confirmed two splice variants of the γ2 subunit (γ2L and γ2S) and resolved a database discrepancy in the sequence of the α5 subunit.

Thermospheric Density: An Overview of Temporal and Spatial Variations

Neutral density shows complicated temporal and spatial variations driven by external forcing of the thermosphere/ionosphere system, internal dynamics, and thermosphere and ionosphere coupling. Temporal variations include abrupt changes with a time scale of minutes to hours, diurnal variation, multi-day variation, solar-rotational variation, annual/semiannual variation, solar-cycle variation, and long-term trends with a time scale of decades. Spatial variations include latitudinal and longitudinal variations, as well as variation with altitude. Atmospheric drag on satellites varies strongly as a function of thermospheric mass density. Errors in estimating density cause orbit prediction error, and impact satellite operations including accurate catalog maintenance, collision avoidance for manned and unmanned space flight, and re-entry prediction. In this paper, we summarize and discuss these density variations, their magnitudes, and their forcing mechanisms, using neutral density data sets and modeling results. The neutral density data sets include neutral density observed by the accelerometers onboard the Challenging Mini-satellite Payload (CHAMP), neutral density at satellite perigees, and global-mean neutral density derived from thousands of orbiting objects. Modeling results are from the National Center for Atmospheric Research (NCAR) thermosphere-ionosphere-electrodynamics general circulation model (TIE-GCM), and from the NRLMSISE-00 empirical model.

The updated spectral catalogue of INTEGRAL gamma-ray bursts

We present a catalogue with the properties of all the bursts detected and localized by the IBIS instrument onboard the INTEGRAL satellite from November 2002 to September 2008. The sample is composed of 56 bursts, corresponding to a rate of ∼0.8 GRB per month. Thanks to the performances of the INTEGRAL Burst Alert System, 50% of the IBIS GRBs have detected afterglows, while 5% have redshift measurements. A spectral analysis of the 43 bursts in the INTEGRAL public archive has been carried out using the most recent software and calibration, deriving an updated, homogeneous and accurate catalogue with the spectral features of the sample. When possible a time-resolved spectral analysis also has been carried out. The GRBs in the sample have 20–200 keV fluences in the range 5 × 10 −8 –2.5 × 10 −4 erg cm −2 , and peak fluxes in the range 0.11–56 ph cm −2 s −1 . While most of the spectra are well fitted by a power law with photon index ∼1.6, we found that 9 bursts are better described by a cut-off power law, resulting in Ep values in the range 35–190 keV. Altough these results are comparable to those obtained with BAT onboard Swift, there is marginal evidence that ISGRI detects dimmer bursts than Swift/BAT. Using the revised spectral parameters and an updated sky exposure map that also takes into account the effects of the GRB trigger efficiency, we strengthen the evidence for a spatial correlation with the super galactic plane of the faint bursts with long spectral lag.

Is This Rule Necessary? A Discussion of New Rules for Rare Serials

ABSTRACT Rare serials have always been the stepchild of cataloging rules, in both the serials cataloging world and the rare book cataloging world. This article focuses on the problems raised by this history, including definition of “rare” in the serials world, a description of their special characteristics and of the problems rare serials pose for catalogers. Issues addressed include the inadequacy of present day rules for accurate cataloging and recommended solutions for these problems that have been developed and tested by the authors.

Making Sense of High-Throughput Protein-Protein Interaction Data

Accurate systems biology modeling requires a complete catalog of protein complexes and their constituent proteins. We discuss a graph-theoretic/statistical algorithm for local dynamic modeling of protein complexes using data from affinity purification-mass spectrometry experiments. The algorithm readily accommodates multicomplex membership by individual proteins and dynamic complex composition, two biological realities not accounted for in existing topological descriptions of the overall protein network. A likelihood-based objective function guides the protein complex modeling algorithm. With an accurate complex membership catalog in place, systems biology can proceed with greater precision.

Foreground Separation Methods for Satellite and Balloon Experiments

A combined technique using the maximum-entropy method (MEM) and the mexican hat wavelet (MHW) to separate and reconstruct the physical components of the microwave sky is presented. We apply this method to simulated observations by the ESA Planck satellite in small patches of the sky. The reconstructed maps of the CMB and foregrounds are improved as compared to those obtained with MEM on its own. Moreover, more accurate point source catalogues are produced at each observing frequency. This technique may also be extended to deal with other multifrequency CMB experiments, including all-sky data.

한국 역사서 속의 별똥비와 별똥 소나기의 목록

《삼국사기》, 《고려사》, 《조선왕조실록》, 《승정원일기》 등 정통 한국 사서 원전에 수록되어 있는 천문관측 자료에서 별똥비와 별똥 소나기 기록을 검색하여 천문학적인 검토를 거쳐 그 목록을 작성하였다. 한국 사서에 나오는 별똥비 기록은 현재 국제 학계에 1958년 Imoto와 Hasegawa가 영문으로 발표한 논문이 표준이 되고 있는데, 이 문헌은 주로 1917년에 조선총독부에서 주관한 연구과제의 일환으로 일본인 관구리길가 작성한 보고서를 바탕으로 하고 있다. 그가 만든 목록은 날짜나 원전 인용 상의 오류를 상당히 포함하고 있으므로 본 연구에서는 한국의 정사서 원전을 검색하여 철저한 고증을 거쳐 수정되고 확장된 별똥비 및 별똥 소나기 목록을 작성하였다. 그 결과 지난 2천년 동안 한국의 역사서에는 별똥 소나기가 25번, 센별똥비가 4번, 보통 별똥비가 5번 기록되어 있었다. 그 가운데 일부는 사자자리 별똥비, 페르세우스 별똥비, 핼리혜성의 의해 생기는 물병자리-/sub n/ 별똥비와 오리온자리 별똥비 등에 속한 것으로 보이는 것이 있었으나, 상당히 많은 기록들은 이에 속하지 않았다. 본 연구에서 제시한 목록은 추후 많은 천체물리학적 연구에 유용할 것이다. We present a more complete and accurate catalogue of astronomical records far meteor showers and meteor storms appeared in primary official Korean history books, such as Samguk-sagi, Koryo-sa, Seungjeongwon-ilgi, and Chosen-Wangjo-Sillok. So far the catalogue made by Imoto and Hasegawa in 1958 has been widely used in the international astryonomical society. The catalogue is based on a report by Sekiguchi in 1917 that is mainly based on secondary history books. We observed that the catalogue has a number of errors in either dates or sources of the records. We have thoroughly checked the primary official history books, instead of the secondary ones, in order to make a corrected and extended catalogue. The catalogue contains 25 records of meteor storms, four records of intense meteor-showers, and five records of usual showers in Korean history. We also find that some of those records seem to correspond to some presently active meteor showers such as the Leonids, the Perseids, and the n -Aquarids-Orionids pair. However, a large number of those records do not correspond to suck present showers. This catalogue we obtained can be useful for various astrophysical studies in the future.

ImprovedHipparcosParallaxes of Coma Berenices and NGC 6231

A method to reprocess the Hipparcos Intermediate Astrometry Data that reduces the propagation of the along-scan spacecraft attitude errors was developed and successfully used to obtain a more consistent parallax of the Pleiades (Makarov, published in 2002). The same technique is used now to correct the Hipparcos parallaxes of the Coma Berenices and NGC 6231 open clusters, which are also in error. The new mean parallax of Coma is 12.40 ± 0.17 mas (against previously 11.43 mas) and of NGC 6231 1.7 ± 0.4 mas (against previously -0.8 mas). The new data for Coma are in excellent agreement with the pre-Hipparcos main-sequence fitting estimates. All six members of NGC 6231 that have negative parallaxes in Hipparcos obtain positive parallaxes. These results suggest that the main source of astrometric error has been correctly identified, and that a more accurate Hipparcos catalog can be computed.

Seismicity and crustal structure beneath the western Ligurian Sea derived from local earthquake tomography

In this paper, we present and comment on the results of a tomographic inversion of P arrival times of local earthquakes to better understand the structure and features of the Ligurian Sea, an oceanic basin originated in the Oligocene–Miocene. This tomographic inversion is the last step in a long and careful revision of the data available for the Ligurian Sea. An accurate catalogue derived from a controlled compilation of data from the numerous stations monitoring seismic activity in this young oceanic basin has been used for computation of a one dimensional (1D) reference model. A high-quality subset of the new catalogue has been used for the non-linear 3D tomographic inversion by iteratively solving the coupled hypocenter-velocity problem in a least square sense. Careful analysis of the resolution capability of the used data set has revealed the better-resolved features for interpretation. The resulting 3D model shows a high-velocity layer extending from the northeastern side of the model, where it lays about 30 km deep, to the southwestern part where it shallows to 15 km. The shallow part of this high-velocity body is located near the original area of the opening of the Ligurian Sea that took place between the Oligocene and early Miocene. Its velocity is comparable with that of an oceanic Moho (around 7.8 km/s). A lens-shaped high-velocity body, about 25 km long, located at a depth of 8–15 km, is interpreted as a series of ophiolitic bodies intruded into the upper crust.

Pebbles for the Mosaic of Cataloging Expertise: What Do Problems in Expert Systems for Cataloging Reveal about Cataloging Expertise?

Twenty-five years of research in expert systems for descriptive cataloging and related areas are reviewed. Researchers who developed prototype expert cataloging systems in the 1980s found that cataloging rules are extremely comprehensive and complicated, but still insufficient to permit these systems accurate cataloging results. Those researchers also identified smaller areas that need to be pursued for successful implementation of expert cataloging systems. Subsequent research has focused on narrower areas. Cataloging rules were studied and more was learned about problems with their logic structure and organization. Another focus was optical reading of bibliographic elements in documents. Categories of responsibility and graphic design continue to pose problems. The visual characteristics of documents were studied to understand more about the automatic recognition of bibliographic elements necessary for the bibliographic description of documents. The systematic study of the cataloging process, necessary for development of expert systems, may result in improvement of manual working procedures and enrich the education of new catalogers.

S1 and S2 States of Apo- and Diapocarotenes

A series of apocarotenes with 5 to 11 conjugated double bonds were synthesized and all-trans isomers were isolated using HPLC techniques. Absorption, fluorescence, and fluorescence excitation spectra were obtained in 77 K glasses. As previously noted for other polyenes and carotenoids, fluorescence spectra of the apocarotenes exhibit a systematic crossover from S1(21Ag) → S0(11Ag) to S2(21Ag) → S0(11Ag) emissions and a sharp decrease in fluorescence yields with increasing conjugation. The apocarotene spectra have sufficient resolution to accurately locate the dominant vibronic bands of the S0(11Ag) → S2(11Bu) and S1(21Ag) → S0(11Ag) transitions, thus leading to an accurate catalog of S1 and S2 electronic energies as a function of conjugation length. We also have obtained the low-temperature absorption and fluorescence spectra of several model polyenes and diapocarotenes. Comparisons between these series allow a systematic exploration of the influence of terminal cyclohexenyl rings on the energies of carot...

Precision Low Earth Orbit Determination Using Atmospheric Density Calibration

Atmospheric drag is the largest uncertainty in determining orbits of low altitude satellites. Deficiencies in operational satellite drag models persist due to empirical model limitations as well as inadequacies of proxy indices used as model drivers. Satellite drag errors result in degraded accuracy, requirements for frequent updates and inadequate predictions of true positions for accurate catalog maintenance, collision avoidance and re-entry operations. Time-dependent global corrections to operational drag models have been derived based on assimilation of satellite tracking data. These corrected drag values circumvent the persisting deficiencies of current drag models and provide significant improvements in precision orbit determination and prediction for low-earth orbit satellites.

The Progress of The Reference Frame

F.W. Argelander proposed to a meeting of the Astronomischen Gessellschaft in 1867 that an accurate catalogue of all stars down to 9th magnitude should be compiled. The sky was divided into zones of declination and observations were undertaken with transit circles at a number of observatories in an international collaboration. The importance of fitting these zonal observations to one global reference frame was realized, and for this purpose A. Auwers produced a Fundamental Catalog (FC) for the Northern and Southern hemispheres in 1879 and 1883, respectively. The accuracy of the positions was about half of an arcsecond. This was the first international celestial reference frame.This reference frame was improved over the next hundred years by continued international cooperation which was later coordinated through the IAU. These efforts culminated in the FK5 which was issued in 1988. The progress in accuracy from the FC to the FK5 is shown in Figure 1. Meanwhile, radio astronomy through the technique of Very Long Baseline Interferometry (VLBI) began to produce positions of extragalactic sources with an accuracy of a milliarcsecond (mas), which is almost two orders of magnitude better than that of the optical positions of the stars in the FK5.

Cryptic Biodiversity: An Overlooked Species and New Subspecies of Antbird (Aves: Formicariidae) with a Revision of Cercomacra tyrannina in Northeastern South America

An undescribed population of antbirds in the Cercomacra tyranninalni- grescens complex that is sympatric with Cercomacra tyrannina was discovered north of Manaus, Brazil. The new population differs from Cercomacra tyrannina in plumage, certain mensural characters, and especially voice. Based on similarity of the song, the undescribed form from Manaus is considered conspecific with Cercomacra tyrannina laeta. However, because of the sympatry of the Manaus population with Cercomacra tyrannina, laeta must be elevated to full species level, with three subspecies: Cercomacra laeta laeta in extreme southeastern Amazonia; C. laeta sabinoi in northeastern Brazil; and a new subspecies described in this paper, known only from the vicinity of Manaus and eastern Roraima, approximately 650 km north Manaus. The population of Cercom- acra tyrannina north of the Amazon River and west of the Rio Negro, formerly assigned to Cercomacra tyrannina laeta, is shown to be allied with Cercomacra tyrannina rather than Cercomacra laeta. In this paper, we recognize a valid species and subspecies from two areas whose avifaunas are among the best known in tropical South America. The cryptic species, Cercomacra laeta, was already represented by many dozens of speci- mens in museum collections. Our findings demonstrate that the accurate cataloging of the planet's biodiversity will rely not only on expeditions to remote mountain valleys but also on a careful analysis of specimens and information already at our disposal.

Analysis of mosquito wing beat sound

Male mosquitos locate their appropriate mating partners by the detection of species-specific wing beat sounds emitted by their females in flight. The wing beat sounds of five military-relevant infectious disease-vector mosquito species—A. freeborni, A. stephensi, A. albimanus, A. gambi, and Ae. aegypti—were recorded and analyzed for amplitude and spectral variation during flight. The post-processing of the recordings resulted in audio files of approximately 1 s of flight suitable for reproduction using a sampling synthesizer and, additionally, matrices of amplitude and frequency data versus time for the fundamental and any useful higher-order harmonics. The accurate cataloging of these unique wing beat sounds can be used effectively in the design of improved sound traps and automatic electronic species identification devices. [Work supported by a Walter Reed Army Institute of Research ILIR award.]

An Ethogram of Body Patterning Behavior in the Squid Loligo vulgaris reynaudii on Spawning Grounds in South Africa.

Squids are capable of a high degree of visual signaling, most of which is expressed through the neurally controlled chromatophore organs in the skin. An accurate catalog (or ethogram) of these signals is an essential prerequisite to quantified behavioral analyses and experimentation. Body patterns such as those described here may also be useful for distinguishing between morphologically identical species or subspecies of commercial importance. The natural behavior of Loligo vulgaris reynaudii on spawning grounds was filmed by divers, and the body patterning repertoire was described in detail; 23 chromatic components, 4 postural components, and 9 locomotor components of body patterning were observed and correlated with different types of behaviors. Most of the chromatic components were expressed during intraspecific behaviors (e.g., agonistic behavior among males, courtship, mating) and, to a lesser extent, during interspecific interactions with fishes. Several of the most basic types of body patterns are described, the most distinctive of which are Lateral Display and White Flashing used between males in agonistic contests. This species is comparable to other Loligo spp. in its complexity of body patterning behavior.