bluuebunny/crossref_metadata_2025 huggingface dataset:
Tracembler – software for in-silico chromosome walking in unassembled genomes
Authors: Dong Qunfeng , Wilkerson Matthew D , Brendel Volker
Published: May 2007

Background

Whole genome shotgun sequencing produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. We have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user.

Results

Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum number of rounds of recursion is reached. All the BLAST matching sequences are then assembled into contigs based on significant sequence overlaps using the CAP3 program. We demonstrate the validity of the concept and software implementation with an example of successfully recovering a full-length Chrm2 gene as well as its upstream and downstream genomic regions from Rattus norvegicus reads. In a second example, a query with two adjacent Medicago truncatula genes as seeds resulted in a contig that likely identifies the microsyntenic homologous soybean locus.

Conclusion

Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations.
Advancing translational research with the Semantic Web
Authors: Ruttenberg Alan , Clark Tim , Bug William , Samwald Matthias , Bodenreider Olivier , Chen Helen , Doherty Donald , Forsberg Kerstin , Gao Yong , Kashyap Vipul , Kinoshita June , Luciano Joanne , Marshall M Scott , Ogbuji Chimezie , Rees Jonathan , Stephens Susie , Wong Gwendolyn T , Wu Elizabeth , Zaccagnini Davide , Hongsermeier Tonya , Neumann Eric , Herman Ivan , Cheung Kei-Hoi
Published: May 2007

Background

A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthenTranslational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature.

Results

We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine.

Conclusion

Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work.
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics
Authors: Smith Andrew K , Cheung Kei-Hoi , Yip Kevin Y , Schultz Martin , Gerstein Mark B
Published: May 2007

Background

A key abstraction in representing proteomics knowledge is the notion of unique identifiers for individual entities (e.g. proteins) and the massive graph of relationships among them. These relationships are sometimes simple (e.g. synonyms) but are often more complex (e.g. one-to-many relationships in protein family membership).

Results

We have built a software system called LinkHub using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. For efficiency, we also provide relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; we have used LinkHub to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as "connecting glue" between different identifier spaces. We demonstrate this with example queries discovering "interologs" of yeast protein interactions in the worm and exploring the relationship between gene essentiality and pseudogene content. We also show how "protein family based" retrieval of documents can be achieved. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code.

Conclusion

LinkHub leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data.
Discovery and characterization of 91 novel transcripts expressed in cattle placenta
Authors: Kumar Charu G , Larson Joshua H , Band Mark R , Lewin Harris A
Published: May 2007

Background

Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian selection. Thus, the ruminant placenta may be a rich source of genes to explore adaptive evolutionary responses in mammals. The aim of our study was to identify novel transcripts expressed in ruminant placenta, and to characterize them with respect to their expression patterns, organization of coding sequences in the genome, and potential functions.

Results

A combination of bioinformatics, comparative genomics and transcript profiling was used to identify and characterize 91 novel transcripts (NTs) represented in a cattle placenta cDNA library. These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence. Proteins longer than 100 aa were predicted for 29 NTs, and 21 are candidate non-coding RNAs. Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome. The authenticity of the NTs was confirmed by their alignment to cattle genome sequence, 42 of which showed evidence of mRNA splicing. Analysis of the genomic context where NT genes reside revealed 61 to be in intergenic regions, whereas 30 are within introns of known genes. The genes encoding the NTs were found to be significantly associated with subtelomeric regions.

Conclusion

The 91 lineage-specific transcripts are a useful resource for studying adaptive evolutionary responses of the ruminant placenta. The presence of so many genes encoding NTs in cattle but not primates or rodents suggests that gene loss and gain are important mechanisms of genome evolution in mammals. Furthermore, the clustering of NT genes within subtelomeric regions suggests that such regions are highly dynamic and may foster the birth of novel genes. The sequencing of additional vertebrate genomes with defined phylogenetic relationships will permit the search for lineage-specific genes to take on a more evolutionary context that is required to understand their origins and functions.
Fibrillary glomerulonephritis with small fibrils in a patient with the antiphospholipid antibody syndrome successfully treated with immunosuppressive therapy
Authors: Javaid Muhammad M , Denley Helen , Tagboto Senyo
Published: May 2007

Background

Fibrillary glomerulonephritis is a rare cause of progressive renal dysfunction, often leading to the need for dialysis within a few years. The role of immunosuppressive treatment is still uncertain although this has been tried with variable success.

Case presentation

A 56 year old woman with the antiphospholipid antibody syndrome (IgM anticardiolipin antibodies) was seen in the nephrology clinic with haematuria, proteinuria, and worsening renal function. A renal biopsy demonstrated a mesangial proliferative glomerulonephritis on light microscopy and smaller fibrils (10.6–13.8 nm in diameter) than is usual for fibrillary glomerulonephritis (typically 18–22 nm) on electron microscopy. Amyloidosis was excluded following detailed evaluation. On account of rapidly worsening renal failure she was started on cyclophosphamide and prednisolone which led to the partial recovery and stabilization of her renal function.

Conclusion

This case highlights the need for routine electron microscopy in native renal biopsies, where the differential diagnosis is wide and varied and the light and immunofluorescence microscopic findings may be non specific.
Exploring the association of dual use of the VHA and Medicare with mortality: separating the contributions of inpatient and outpatient services
Authors: Wolinsky Fredric D , An Hyonggin , Liu Li , Miller Thomas R , Rosenthal Gary E
Published: May 2007

Background

Older veterans may use both the Veterans Health Administration (VHA) and Medicare, but the association of dual use with health outcomes is unclear. We examined the association of indirect measures of dual use with mortality.

Methods

Our secondary analysis used survey, claims, and National Death Index data from the Survey on Assets and Health Dynamics among the Oldest Old. The analytic sample included 1,521 men who were Medicare beneficiaries. Veterans were classified as dual users when their self-reported number of hospital episodes or physician visits exceeded that in their Medicare claims. Veterans reporting inpatient or outpatient visits but having no Medicare claims were classified as VHA-only users. Proportional hazards regression was used.

Results

897 (59%) of the men were veterans, of whom 134 (15%) were dual users. Among dual users, 60 (45%) met the criterion based on inpatient services, 54 (40%) based on outpatient services, and 20 (15%) based on both. 766 men (50%) died. Adjusting for covariates, the independent effect of any dual use was a 38% increased mortality risk (AHR = 1.38; p = .02). Dual use based on outpatient services marginally increased mortality risk by 45% (AHR = 1.45; p = .06), and dual use based on both inpatient and outpatient services increased the risk by 98% (AHR = 1.98; p = .02).

Conclusion

Indirect measures of dual use were associated with increased mortality risk. New strategies to better coordinate care, such as shared medical records, should be considered.
Rosiglitazone decreases postprandial production of acylation stimulating protein in type 2 diabetics
Authors: Tahiri Youssef , Karpe Fredrik , Tan Garry D , Cianflone Katherine
Published: May 2007

Background

We evaluated plasma ASP and its precursor C3 in type 2 diabetic men with/without rosiglitazone (ROSI) treatment compared to healthy non-obese men. We tested (1) whether plasma ASP or C3 are altered postprandially in subcutaneous adipose tissue or forearm muscle effluent assessed by arteriovenous (A-V) differences in healthy lean men and older obese diabetic men and (2) whether treatment with ROSI changes the arteriovenous gradient of ASP and/or C3.

Methods

In this ongoing placebo-controlled, crossover, double-blinded study, AV differences following a mixed meal were measured in diabetic men (n = 6) as compared to healthy men (n = 9).

Results

Postprandial arterial and adipose venous TG and venous NEFA were increased in diabetics vs. controls (p < 0.05–0.0001). ROSI treatment decreased postprandial arterial TG (p < 0.001), adipose venous NEFA (p < 0.005), reduced postprandial glucose (p < 0.0001) and insulin concentrations (p < 0.006). In healthy men, there was no change in postprandial C3, but an increase in adipose venous ASP vs. arterial ASP (p < 0.02), suggesting ASP production, with no change in forearm muscle. In older, obese diabetic subjects, arterial C3 was greater than in controls (p < 0.001). Arterial C3 was greater than venous C3 (p < 0.05), an effect that was lost with ROSI treatment. In diabetics, postprandial venous ASP was greater than arterial (p < 0.05), indicating ASP production, an effect that was lost with ROSI treatment (p < 0.01).

Conclusion

Increased postprandial venous production of ASP is specific for adipose tissue (absent in forearm muscle). Increased postprandial C3 and ASP in diabetic subjects is consistent with an ASP resistant state, this state is partially normalized by treatment with ROSI.
2D pore-scale simulation of wide-band electromagnetic dispersion of saturated rocks
Authors: Toumelin Emmanuel , Torres-Verdín Carlos
Published: May 2007

Effective medium theories (EMTs) are invoked routinely to interpret multifrequency dispersions of dielectric permittivity and electrical conductivity of saturated rocks. However, EMTs exhibit limitations that substantially restrict their validity for petrophysical interpretation. For instance, pore connectivity is of significant interest in the study of subsurface reservoirs, but no existing EMT includes it as an explicit property in the analysis of kilohertz- to gigahertz-range dielectric measurements. We introduce a new approach to quantify the effects of pore geometry and connectivity on the kilohertz-gigahertz frequency dispersion of dielectric permittivity and electrical conductivity of clay-free porous rocks. This approach is based on the numerical solution of the internal electric fields within submicron-resolution pore maps constructed with grain and rock pixels. The discrepancy between the internal fields and electrical currents calculated for ahomogeneous scatterer and those calculated for a given pore map is minimized to yield the effective electrical conductivity and dielectric constant for that pore map. This minimization is performed independently for each frequency and is verified to agree implicitly with Kramers-Kronig's causality relationships. We show that EMTs only predict an average dispersion for given microscopic geometrical parameters (e.g., porosity, pore eccentricity), whereas individual realizations honoring the same parameters are associated with dispersion about average values predicted by EMTs. Unlike any EMT prediction, we show that pore connectivity plays a major role in both the shape and amplitude of wide-band electromagnetic property dispersions. The simulation procedure introduced in this paper provides a systematic method to assess the sensitivity of a multitude of pore-scale properties on the macroscopic wide-band dielectric dispersion of saturated rocks.
Fluid substitution in shaley sediment using effective porosity
Authors: Dvorkin Jack , Mavko Gary , Gurevich Boris
Published: May 2007

The traditional method of fluid substitution in porous rock requires the total porosity and the elastic modulus of the mineral phase as input and assumes that the fluid reaches instantaneous hydraulic equilibrium throughout the pore space. This assumption may not be appropriate for shaley sediment because of the low permeability of shale and the resulting immobility of the water in it. To address this problem, we propose an alternative method that uses effective porosity instead of total porosity. Effective porosity is lower than total porosity if porous shale is present in the system. A new, composite mineral phase is introduced, which includes the porous water-saturated shale together with the nonporous minerals and whose elastic modulus is an average of those of its components, including the porous shale. This alternative method increases the sensitivity of the elastic properties of sediment-to-pore-fluid changes and therefore may be used as a physics-based theoretical tool to better explain and interpret seismic data during exploration as well as variations in seismic response as hydrocarbon production progresses.
Cooperative inversion of 2D geophysical data sets: A zonal approach based on fuzzy c-means cluster analysis
Authors: Paasche Hendrik , Tronicke Jens
Published: May 2007

In many near-surface geophysical applications, it is now common practice to use multiple geophysical methods to explore subsurface structures and parameters. Such multimethod-based exploration strategies can significantly reduce uncertainties and ambiguities in geophysical data analysis and interpretation. We propose a novel 2D approach based on fuzzy [Formula: see text]-means cluster analysis for the cooperative inversion of disparate data sets. We show that this approach results in a single zonal model of subsurface structures in which each zone is characterized by a set of different parameters. This finding implies that no further structural interpretation of geophysical parameter fields is needed, which is a major advantage compared with conventional inversions that rely on a single input data set and cooperative inversion approaches.
Detector coupling corrections for vector infidelity of multicomponent OBC data
Authors: Gaiser James E.
Published: May 2007

Differences in the frequency response of horizontal and vertical detectors (vector infidelity) in ocean bottom cable (OBC) surveys can cause problems for multicomponent processing, such as S-wave birefringence and amplitude variation with azimuth (AVA) analyses, and combining vertical and hydrophone data for water-born multiple suppression. One source of this problem is poor detector coupling with the seabed that produces resonances and phase distortions. Coupling and data quality are generally excellent for the inline component. However, the crossline component often exhibits low-frequency resonance compared to the inline. Also, OBCs are susceptible to rotational modes about the cable axis that produce spurious S-waves on the vertical component. I derive a method for correcting the crossline and vertical components based on a model of OBC detector coupling, and design vector operators in the frequency domain from shots over many offsets and azimuths. The crossline data are corrected,relative to the inline, assuming linear polarization of early, near-offset arrivals on the radial-horizontal component. Thus, the transverse-horizontal component provides a convenient error or objective function to be minimized for operator design. Using the corrected crossline, as a model of rotational modes, leads to an estimate of spurious S-waves on the vertical component, which are adaptively subtracted. Data examples from the Gulf of Mexico and offshore Nigeria are presented to illustrate improvements in crossline frequency content and match to inline data. Typically there is [Formula: see text] reduction in error using the rms ratio of transverse-to-radial component data computed in the time domain. Suppression of spurious S-waves from the vertical component without undesirable effects of low-cut or [Formula: see text] filters is shown for prestack and poststack data. Also, vector operators indicate they contain important information related to resonance modes of crossline coupling and rotational modes associated with seabed-deployed versus buried OBCs.
Kimberlite exploration at Serra da Canastra province, Brazil
Authors: Menezes Paulo T. , García Mauricio D.
Published: May 2007

Kimberlite and lamproite pipes are the only economically significant source rocks forming primary diamond deposits. Brazil, the world’s seventh largest diamond producer, has all of its production from alluvial deposits. The quest for a primary deposit has continued over several decades with very few positive results. To that end, airborne magnetic data from the Serra da Canastra diamondiferous province was used to identify kimberlite signatures. Serra da Canastra is located in the central portion of the Brazilian province in a low-magnetic-latitude region. The main tectonic feature of the area is a northwest-southeast major crustal fracture zone that extends for more than [Formula: see text] within the territory. The interpretation strategy was based on joint analysis of analytic signal and Euler deconvolution. A selected kimberlite target should typically have a roughly circular analytic signal anomaly coincident with a depth [Formula: see text] and structural [Formula: see text] constrained Euler solution. The proposed approach led to recognition of previously known pipes and generation of new targets. Ground geologic, geophysical, and geochemical follow-up surveys are necessary to test these selected targets.
Prestack Gaussian-beam depth migration in anisotropic media
Authors: Zhu Tianfei , Gray Samuel H. , Wang Daoliu
Published: May 2007

Gaussian-beam depth migration is a useful alternative to Kirchhoff and wave-equation migrations. It overcomes the limitations of Kirchhoff migration in imaging multipathing arrivals, while retaining its efficiency and its capability of imaging steep dips with turning waves. Extension of this migration method to anisotropic media has, however, been hampered by the difficulties in traditional kinematic and dynamic ray-tracing systems in inhomogeneous, anisotropic media. Formulated in terms of elastic parameters, the traditional anisotropic ray-tracing systems aredifficult to implement and inefficient for computation, especially for the dynamic ray-tracing system. They may also result inambiguity in specifying elastic parameters for a given medium.To overcome these difficulties, we have reformulated the ray-tracing systems in terms of phase velocity.These reformulated systems are simple and especially useful for general transversely isotropic and weak orthorhombic media, because the phase velocities for these two types of media can be computed with simple analytic expressions. These two types of media also represent the majority of anisotropy observed in sedimentary rocks. Based on these newly developed ray-tracing systems, we have extended prestack Gaussian-beam depth migration to general transversely isotropic media. Test results with synthetic data show that our anisotropic, prestack Gaussian-beam migration is accurate and efficient. It produces images superior to those generated by anisotropic, prestack Kirchhoff migration.
Amplitude analysis with an optimal model-based linear AVO approximation: Part II — Field data example
Authors: Causse E. , Riede M. , van Wijngaarden A. J. , Buland A. , Dutzer J. F. , Fillon R.
Published: May 2007

AVO analysis can be conducted by estimating amplitude variation with offset (AVO) attributes from seismic prestack data and by characterizing the measured amplitude responses by the position of their projection in the attribute space. The most common AVO attributes are the intercept (zero-offset reflectivity) and AVO gradient. We have constructed an optimized, model-based linear AVO equation that is more accurate than usual AVO approximations. The parameters of this equation represent new AVO attributes that are more directly related to the information contained in seismic reflection amplitudes. We use these new AVO attributes to classify reflector responses from field data. Five seismic facies are defined that are characterized by differentdistributions of seismic parameters. Nine reflector classes are formed by associating appropriate pairs of facies. The expected locations of the different reflector classes in the space of optimized attributes are found by modeling and are used to derive a classification scheme. This scheme is applied to sections of optimized attributes calculated from the prestack data, leading to a vertical section showing the distribution of most probable facies in an area containing a sand reservoir. We compare the new approach to classification with intercept and gradient. The new method is more robust and less sensitive to the number of attributes (two or three) used for classification. It offers an optimal, flexible, and robust way of extracting the information contained in reflection amplitudes by simple linear AVO equations.
Geometry of ophiolites in eastern Cuba from 3D inversion of aeromagnetic data, constrained by surface geology
Authors: Batista-Rodríguez José A. , Pérez-Flores Marco A. , Quiroga-Goode Gerardo , Gallardo Luis A.
Published: May 2007

This study combined geophysical, geologic, and topographic information to investigate the Mayarí-Baracoa ophiolitic belt in eastern Cuba. A recently developed interpretation technique for 3D inversion of magnetic data was employed to determine the geometry at depth of ophiolitic and other rocks. Based on measured susceptibilities, lithologies were divided into four groups. The geophysical data allowed 3D imaging of ophiolites (serpentinized peridotites and gabbros), as well as sedimentary and volcanic rocks. The study verified that both the Pinares de Mayari Plateau and the Sagua de Tánamo Basin have been strongly influenced by tectonic activity. The modeling showed evidence of more east-west structural deformation of the ophiolite belt than had been previously reported. The depth of the depocenter of the Sagua de Tánamo basin and its rate of subsidence were determined. We identified some areas with potential for economic deposits of chromium, cobalt, and nickel, as well as precious metals; these were related to the thickness of the peridotite layer. The modeling also corroborated the presence of previously mapped faults and revealed other previously unrecognized faults.
Detection of reservoir quality using Bayesian seismic inversion
Authors: Gunning James , Glinsky Michael E.
Published: May 2007

Sorting is a useful predictor for permeability. We show how to invert seismic data for a permeable rock sorting parameter by incorporating a probabilistic rock-physics model with floating grains into a Bayesian seismic inversion code that operates directly on rock-physics variables. The Bayesian prior embeds the coupling between elastic properties, porosity, and the floating-grain sorting parameter. The inversion uses likelihoods based on seismic amplitudes and a forward convolutional model to generate a posterior distribution containing refined estimates of the floating-grain parameter and its uncertainty. The posterior distribution is computed using Markov Chain Monte Carlo methods. The test cases we examine show that significant information about both sorting characteristics and porosity is available from this inversion, even in difficult cases where the contrasts with the bounding lithologies are not strong, provided the signal-to-noise ratio (S/N) of the data is favorable. These test cases show about 25% and 15% improvements in estimated standard deviations for porosity and floating-grain fraction, respectively, for peak S/N of [Formula: see text]. The full posterior distribution of floating-grain content is more informative, and shows enhanced separation into two clusters of clean and poorly sorted rocks. This holds true even in the more difficult test case we examine, where notably, the laminated reservoir net-to-gross is not significantly improved by the inversion process.
Gravity data as a tool for detecting faults: In-depth enhancement of subtle Almada’s basement faults, Brazil
Authors: Barbosa Valeria C. , Menezes Paulo T. , Silva João B.
Published: May 2007

We demonstrate the potential of gravity data to detect and to locate in-depth subtle normal faults in the basement relief of a sedimentary basin. This demonstration is accomplished by inverting the gravity data with the constraint that the estimated basement relief presents local abrupt faults and is smooth elsewhere. We inverted the gravity data from the onshore Almada Basin in northeastern Brazil, and we mapped several normal faults whose locations and plane geometries were already known from seismic imaging. The inversion method delineated well both the discontinuities with small or large slips and a sequence of step faults. Using synthetic data, we performed a systematic search of normal fault slips versus fault displacement depths to map the fault-detectable region in this space. This mapping helps to assess the ability of gravity inversion to detect normal faults. Mapping shows that normal faults with small [Formula: see text], medium (about [Formula: see text]), and large (about [Formula: see text]) vertical slips can be detected if the maximum midpoint depths of the fault planes are smaller than 1.8, 3.8, and [Formula: see text], respectively.
True-amplitude prestack depth migration
Authors: Deng Feng , McMechan George A.
Published: May 2007

Most current true-amplitude migrations correct only for geometric spreading. We present a new prestack depth-migration method that uses the framework of reverse-time migration to compensate for geometric spreading, intrinsic [Formula: see text] losses, and transmission losses. Geometric spreading is implicitly compensated by full two-way wave propagation. Intrinsic [Formula: see text] losses are handled by including a [Formula: see text]-dependent term in the wave equation. Transmission losses are compensated based on an estimation of angle-dependent reflectivity using a two-pass recursive reverse-time prestack migration. The image condition used is the ratio of receiver/source wavefield amplitudes. Two-dimensional tests using synthetic data for a dipping-layer model and a salt model show that loss-compensating prestack depth migration can produce reliable angle-dependent reflection coefficients at the target. The reflection coefficient curves are fitted to give least-squares estimates of the velocity ratio at the target. The main new result is a procedure for transmission compensation when extrapolating the receiver wavefield. There are still a number of limitations (e.g., we use only scalar extrapolation for illustration), but these limitations are now better defined.
A case of SI attenuation in 4D seismic data recorded with a permanently installed array
Authors: Kommedal Jan H. , Semb Per Helge , Manning Ted
Published: May 2007

For seismic monitoring of reservoirs, interference noise from other seismic operations can delay data acquisition because of time-sharing or necessitate additional efforts to attenuate the seismic interference (SI) during processing. We present a method that takes advantage of the different shot interval and flexible recording length of the monitoring system to allow efficient attenuation of the SI by adaptive subtraction. The method is applied successfully to multicomponent 4D data.
Redundant and useless seismic attributes
Authors: Barnes Arthur E.
Published: May 2007

Many seismic attributes are redundant or useless and confuse seismic interpretation more than they help. They are easily recognized given a few guidelines and tools. Discarding them leaves an attribute list that is both more manageable and more honest.
A comparison of streamer and OBC seismic data at Beryl Alpha field, U. K. North Sea
Authors: Stewart Jonathan , Shatilo Andrew , Jing Charlie , Rape Tommie , Duren Richard , Lewallen Kyle , Szurek Gary
Published: May 2007

Compressional P-wave ocean-bottom-cable (OBC) seismic data from the Beryl Alpha field in the U. K. North Sea provide a superior image of the subsurface compared to heritage streamer seismic data. To determine the reason for the superiority of OBC data, the results of a detailed comparison of these OBC and streamer data sets are compared. The streamer and OBC data sets are reprocessed using a strategy that attempts to isolate the roles of processing, fold, azimuth, PZ combination, and hydrophone and geophone data have on the improved OBC image. The vertical component of the geophone (OBC Z) provides the major contribution to the improved OBC image. The imaged OBC Z datacontain fewer multiples and have a higher signal-to-noise ratio than the streamer. The OBC data have a lower level of multiple contamination because of the contribution from the OBC Z component, together with an effective suppression of receiver-side water-column reverberations as a result of the combination of the OBC hydrophone and geophone traces (PZ combination). The increased fold and wider azimuths of OBC data improve the OBC image slightly. Wider azimuths improve fault imaging, especially for faults oriented obliquely to the inline and crossline directions. The particular conditions at Beryl Alpha field that make the OBC survey successful are the relatively hard water bottom and the presence of multiples that are difficult to remove from streamer data using standard demultiple techniques.
Vitamin D 1α-Hydroxylase Gene Mutations in Patients with 1α-Hydroxylase Deficiency
Authors: Kim Chan Jong , Kaplan Larry E. , Perwad Farzana , Huang Ningwu , Sharma Amita , Choi Yong , Miller Walter L. , Portale Anthony A.
Published: May 2007

Context: Vitamin D 1α-hydroxylase deficiency, also known as vitamin D-dependent rickets type 1, is an autosomal recessive disorder characterized by the early onset of rickets with hypocalcemia and is caused by mutations of the 25-hydroxyvitamin D 1α-hydroxylase (1α-hydroxylase, CYP27B1) gene. The human gene encoding the 1α-hydroxylase is 5 kb in length, located on chromosome 12, and comprises nine exons and eight introns. We previously isolated the human 1α-hydroxylase cDNA and gene and identified 19 different mutations in 25 patients with 1α-hydroxylase deficiency.

Objectives, Patients, and Methods: We analyzed the 1α-hydroxylase gene of 10 patients, five from Korea, two from the United States, and one each from Argentina, Denmark, and Morocco, all from nonconsanguineous families. Each had clinical and radiographic features of rickets, hypocalcemia, and low serum concentrations of 1,25-dihydroxyvitamin D3.

Results: Direct sequencing identified the responsible 1α-hydroxylase gene mutations in 19 of 20 alleles. Four novel and four known mutations were identified. The new mutations included a nonsense mutation in exon 6, substitution of adenine for guanine (2561G→A) creating a stop signal at codon 328; deletion of adenine in exon 9 (3922delA) causing a frameshift; substitution of thymine for cytosine in exon 2 (1031C→T) causing the amino acid change P112L; and a splice site mutation, substitution of adenine for guanine in the first nucleotide of intron 7 (IVS7+1 G→A) causing a frameshift.

Conclusions: Mutations in the 1α-hydroxylase gene previously were identified in 44 patients, to which we add 10 more. The studies show a strong correlation between 1α-hydroxylase mutations and the clinical findings of 1α-hydroxylase deficiency.
Hypertrophy and Increased Kisspeptin Gene Expression in the Hypothalamic Infundibular Nucleus of Postmenopausal Women and Ovariectomized Monkeys
Authors: Rometo Adonna M. , Krajewski Sally J. , Lou Voytko Mary , Rance Naomi E.
Published: May 2007

Context: Human menopause is characterized by ovarian failure, gonadotropin hypersecretion, and neuronal hypertrophy in the hypothalamic infundibular (arcuate) nucleus. Recent studies have demonstrated a critical role for kisspeptins in reproductive regulation, but it is not known whether menopause is accompanied by changes in hypothalamic kisspeptin neurons.

Objectives: Our objective was to map the location of neurons expressing kisspeptin gene (KiSS-1) transcripts in the human hypothalamus and determine whether menopause is associated with changes in the size and gene expression of kisspeptin neurons. In monkeys, our objective was to evaluate the effects of ovariectomy and hormone replacement on neurons expressing KiSS-1 mRNA in the infundibular nucleus.

Subjects: Hypothalamic tissues were collected at autopsy from eight premenopausal and nine postmenopausal women and from 42 young cynomolgus monkeys in various endocrine states.

Methods: We used hybridization histochemistry, quantitative autoradiography, and computer-assisted microscopy.

Results: Examination of human hypothalamic sections revealed that KiSS-1 neurons were located predominantly in the infundibular nucleus. In the infundibular nucleus of postmenopausal women, there was a significant increase in the size of neurons expressing KiSS-1 mRNA and the number of labeled cells and autoradiographic grains per neuron. Similar to postmenopausal women, ovariectomy induced neuronal hypertrophy and increased KiSS-1 gene expression in the monkey infundibular nucleus. Conversely, in ovariectomized monkeys, estrogen replacement markedly reduced KiSS-1 gene expression.

Conclusions: The cynomolgus monkey experiments provide strong evidence that the increase in KiSS-1 neuronal size and gene expression in postmenopausal women is secondary to ovarian failure. These studies suggest that kisspeptin neurons regulate estrogen negative feedback in the human.
The Molecular Mechanisms Underlying the Proinflammatory Actions of Thiazolidinediones in Human Macrophages
Authors: Hall Julie M. , McDonnell Donald P.
Published: May 2007

It is hypothesized that the antiinflammatory actions of peroxisome proliferator-activated receptors (PPARs) may explain the protective effect of these receptors in diabetes, atherosclerosis, cancer, and other inflammatory diseases. However, emerging evidence for proinflammatory activities of activated PPARs is concerning in light of new studies that associate PPAR modulators with an increased incidence of both cardiovascular events in humans and the sporadic formation of tumors in rodents. In an attempt to define the role of each PPAR subtype in inflammation, we made the unexpected observation that human PPARδ is a positive regulator of inflammatory responses in both monocytes and macrophages. Notably, TNFα-stimulated cells administered PPARδ agonists express and secrete elevated levels of inflammatory cytokines. Most surprising, however, was the finding that thiazolidinediones (TZDs) and other known PPARγ ligands display different degrees of proinflammatory activities in a PPARγ- and PPARα-independent manner via their ability to augment PPARδ signaling. A series of mechanistic studies revealed that TZDs, at clinically relevant concentrations, bind and activate the transcriptional activity of PPARδ. Collectively, these studies suggest that the observed proinflammatory and potentially deleterious effects of PPARγ ligands may be mediated through an off-target effect on PPARδ. These studies highlight the need for PPAR modulators with increased receptor subtype specificity. Furthermore, they suggest that differences in systemic exposure and consequently in the activation of PPARγ and PPARδ may explain why TZDs can exhibit both inflammatory and antiinflammatory activities in humans.
The Down syndrome critical region protein TTC3 inhibits neuronal differentiation via RhoA and Citron kinase
Authors: Berto Gaia , Camera Paola , Fusco Carlo , Imarisio Sara , Ambrogio Chiara , Chiarle Roberto , Silengo Lorenzo , Di Cunto Ferdinando
Published: May 2007

The Down syndrome critical region (DSCR) on Chromosome 21 contains many genes whose duplication may lead to the major phenotypic features of Down syndrome and especially the associated mental retardation. However, the functions of DSCR genes are mostly unknown and their possible involvement in key brain developmental events still largely unexplored. In this report we show that the protein TTC3, encoded by one of the main DSCR candidate genes, physically interacts with Citron kinase (CIT-K) and Citron N (CIT-N), two effectors of the RhoA small GTPase that have previously been involved in neuronal proliferation and differentiation. More importantly, we found that TTC3 levels can strongly affect the NGF-induced differentiation of PC12 cells, by a CIT-K-dependent mechanism. Indeed, TTC3 overexpression leads to strong inhibition of neurite extension, which can be reverted by CIT-K RNAi. Conversely, TTC3 knockdown stimulates neurite extension in the same cells. Finally, we find that Rho, but not Rho kinase, is required for TTC3 differentiation-inhibiting activity. Our results suggest that the TTC3–RhoA–CIT-K pathway could be a crucial determinant of in vivo neuronal development, whose hyperactivity may result in detrimental effects on the normal differentiation program.
Newly Designed Catalysts for the Enantioselective Borohydride Reduction: Prediction from the Theoretical Analysis
Authors: Ikeno Taketo , Iwakura Izumi , Shibahara Atsushi , Hatanaka Miho , Kokura Ai , Tanaka Saiko , Nagata Takushi , Yamada Tohru
Published: May 2007

For the catalytic enantioselective borohydride reduction, the theoretical simulation of various axial groups in Co complex catalysts predicted that the Co–carbene complexes could be employed as efficient catalysts. The newly designed complexes generated from the Co complex and methyl diazoacetate made it possible to catalyze the enantioselective borohydride reduction in a halogen-free solvent.
Evidence for the effectiveness of a chlamydia awareness campaign: increased population rates of chlamydia testing and detection
Authors: Chen Marcus Y , Karvelas Maria , Sundararajan Vijaya , Hocking Jane S , Fairley Christopher K
Published: May 2007

The objective of this study was to determine the effectiveness of a statewide campaign aimed at increasing chlamydia awareness and testing among younger people. In November 2002, a narrowcast media campaign targeting men and women aged 16–29 years was launched in Victoria, Australia. This was expanded in June 2003. Data on chlamydia testing via Medicare and chlamydia notifications, before and after the campaign, were compared to determine possible effects of the campaign on population rates of chlamydia testing and detection. During the campaign, chlamydia testing rates increased significantly for both women ( P=0.04) and men ( P=0.04), while testing rates before and after the campaign remained relatively stable. Although testing rates increased, only 4.3% of Victorian women and 1.9% of men aged 16–30 were tested through Medicare in 2003. The increase in chlamydia testing over the study period was closely paralleled by an increase in notification rates for chlamydia, with strong correlations between the two ( r=0.97, P<0.001). In conclusion, an estimated minimum of A$70 was spent on the campaign for each additional chlamydia test performed. Testing within the framework of a national chlamydia screening programme may be a more cost-effective way of increasing chlamydia testing.
Retrospective review of clinical practice in chronic pelvic pain syndrome i.e. category III chronic prostatitis at two hospital sites over five years 2000–2005 (an audit)
Authors: Evans D T P , Jaleel H , Keefe A
Published: May 2007

All category III chronic prostatitis cases in two hospital sites were retrospectively reviewed from the year 2000 until 2005. The mean age of the patients was 38.7 years. Of these, 56.6% were St Bartholomew's Genitourinary Medicine Department patients and 43.5% were Southend Genitourinary Medicine Clinic patients. We observed that 33.1% of these had at least one transrectal ultrasound of the prostate. The commonest abnormal findings in transrectal ultrasounds of the prostate of the series were focal calcification (16.2%), calculi (9.3%) and inflammatory changes (5.4%). Of this series, 35% were lost to follow-up. The vast majority of the remainder got better over periods ranging from approximately two weeks to approximately three years.
Behçet's disease
Authors: Yesudian P D , Edirisinghe D N , O'Mahony C
Published: May 2007

Behçet's disease (BD) is a chronic, relapsing multisystem vasculitis with predominant involvement of the oral and genital mucosa. It has a worldwide distribution, but the prevalence is highest in Central Asia and the Far East (along the ancient 'Silk Route'). Genetic, environmental, immunological and haemostatic factors play a role in the aetiopathogenesis. The International Study Group for BD proposed criteria for the diagnosis of this condition, the essential feature being recurrent oral ulceration. Genital ulcers and skin manifestations are common, while ocular changes are the most important cause of morbidity. Almost any organ in the body can be involved, and systemic involvement may portend a poorer prognosis. There is no pathognomonic test for BD and the diagnosis is made on clinical findings. Treatment of BD would require multidisciplinary cooperation, and early referral to an ophthalmologist is advisable to prevent ocular morbidity. Topical and systemic agents (colchicine, dapsone and thalidomide) are useful in controlling exacerbation of the oral and genital ulcers. Severe disease may require immunosuppressive agents and, more recently, biological agents have been used successfully. It tends to follow an unpredictable course, and the eventual prognosis depends on the systemic involvement.
Prevalence of primary HIV-1 drug resistance in pregnant women and in newly diagnosed adults at Tijuana General Hospital, Baja California, Mexico
Authors: Viani R M , Hsia K , Hubbard P , Ruiz-Calderon J , Lozada R , Alvelais J , Gallardo M , Spector S A
Published: May 2007

At Tijuana General Hospital, between March 2003 and June 2005, pregnant women and other adults, recently identified as HIV infected, antiretroviral naïve, were enrolled to examine the prevalence of primary HIV drug resistance. All subjects had the Calypte® HIV-1 BED Incidence enzyme immunoassay test to identify recent infection. Genotypic analysis of HIV-1 protease and reverse transcriptase regions in plasma was performed. Forty-six subjects participated, eight (17%) men, 38 (83%) women. Ten (22%) subjects were classified as having recent HIV infection. HIV genotype was performed in 41 subjects. One subject (2.5%) had a major mutation in the reverse transcriptase region (K219Q) conferring zidovudine resistance, one had a minor mutation at V118I (2.5%) and two subjects (5%) had minor mutation (V179D) associated with non-nucleoside reverse transcriptase inhibitor resistance. There were no major protease inhibitor-associated mutations but minor mutations were common. The prevalence of primary HIV drug resistance in Baja California is low.