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PubMed1990

On the measurement and interpretation of birth defect associations in epidemiologic studies.

The extent of clustering of 2 or more defects in the same infant can be expressed as the ratio of the observed number of infants with the defects (O) over the expected number of such infants (E). The expected is usually derived from the product of population rates of individual defects. Because large O/E ratios are obtained for many defect combinations, it has been suggested that clustering of defects is generalized and nonspecific. To control for the tendency of nonspecific clustering of defects, an alternative method is to perform the same calculations among multimalformed infants only. A main limitation of this method is that it adjusts for the clustering tendency of all defects rather than the ones of interest, often resulting in spuriously low O/E ratios. We present a new method to adjust for the tendency for nonspecific clustering between defects that overcomes this limitation. With this method, adjusted O/E ratios are inversely related to the proportion of infants who are multimalformed and have one or more of the defects being examined. Using data from the Metropolitan Atlanta Congenital Defects Program, we apply this method to the previously described associations among VACTERL defects and midline or "schisis" defects. We show that adjusted O/E ratios obtained are greater than those obtained by using multimalformed infants. For midline defects, many of the adjusted ratios were close to one, indicating nonspecific clustering of these defects. Finally, using the example of isotretinoin embryopathy, we show that O/E ratios depend highly on the frequency of exposure in the population, and thus, they should be interpreted with caution.

Abnormalities, Drug-Induced↗
PubMed1993

Cancer clusters: the importance of monitoring multiple geographic scales.

Analysis of cancer incidence data at a variety of geographic scales provides surveillance information that can allay fears of the general public, prevent costly and unwarranted epidemiologic studies driven by political pressures, and target appropriate cases for further investigation. We systematically examined New Jersey Cancer Registry data (1979-1985) for childhood and young adult (0-24 years) cancers at multiple geographic scales--at the state level, then by degree of urbanization, county boundaries, and minor civil divisions. The state had increased rates for some cancers when compared to four other SEER (Surveillance, Epidemiology and End Results) states. No meaningful patterns at either the most urban/suburban/most rural scales or at the county level of analysis were found. At the minor civil division level, the Ederer, Myers and Mantel method found evidence of clustering of pediatric and young adult cases statewide. Stratification of cases by race yielded even stronger findings and indicated that whites had clustering of cases for several cancer types. In-depth analysis of individual cases yielded hypotheses for investigating identified clusters.

Adolescent↗
PubMed2005

Metabolic syndrome amplifies the LDL-cholesterol associated increases in carotid atherosclerosis.

OBJECTIVE: Carotid intima-media thickness (IMT) is a useful surrogate marker of cardiovascular disease. In addition to low-density lipoprotein cholesterol (LDL-C), metabolic syndrome has been linked to the pathogenesis of atherosclerosis. The present study investigated whether the clustering of multiple components of metabolic syndrome has a greater impact on vascular parameters than individual components of metabolic syndrome, and assessed the association between carotid IMT and LDL-C and metabolic syndrome. METHODS: Carotid IMT was evaluated on B-mode ultrasonography in 760 patients (340 men aged 64+/-16 years and 420 women aged 69+/-13 years) in the Medical Department of Seiyo Municipal Nomura Hospital. The subjects did not demonstrate any clinical signs of cardiovascular disease. We investigated the association between carotid IMT and confounding risk factors including LDL-C and metabolic syndrome using the 2005 Japanese criteria. RESULTS: Carotid IMT increased with increasing numbers of metabolic syndrome components (p for trend<0.001). Multiple regression models, including age, sex, body mass index, smoking status, LDL-C, diabetes mellitus as well as each individual component of metabolic syndrome as continuous variables, showed that both metabolic syndrome (beta=0.100; p=0.029) and LDL-C (beta=0.210, p<0.001) were independent determinants of carotid IMT. Metabolic syndrome amplified the LDL-C associated increases in carotid atherosclerosis. CONCLUSIONS: Even after taking into account each individual component of MS, the clustering of visceral obesity with at least 2 of the 3 components, and LDL-C are independently associated with increased carotid IMT. This suggests that the components of metabolic syndrome interact to synergistically impact vascular thickness.

Aged↗
PubMed2006

[The index and secondary patients in tuberculosis transmission--a retrospective epidemiological study of 3783 patients newly registered in recent 15 years in Aichi, Japan].

OBJECTIVES: To elucidate the characteristics of the index and secondary patients in clusters containing multiple TB patients who were examined epidemiologically. SUBJECTS AND METHODS: The subjects of this retrospective study were 3783 TB patients registered in Aichi between 1989 and 2003. All recorded files were reviewed to identify multiple TB patients in the same transmission group. When multiple patients with a registration interval of less than 10 years were found in the same transmission group, the first patient was considered as the index case, and the other patients were regarded as secondary cases. RESULTS: A total of 106 index patients and 132 secondary patients were found. The index patients occupied 2.8% of the total 3783 registered patients, or 0.9 per 100,000 population. Secondary patients occupied 3.5% and 1.2 per 100,000. Of the 106 clusters, 77.4% consisted of two patients, 15.1% three patients, and 7.5% four or more patients. Smear-positive patients were found in 66.0% of the index patients, 27.3% of the secondary patients, and 30.3% of the 3783 overall patients, and the differences were highly significant between the index and secondary patients, as well as between the index and overall registered patients (p < 0.001). The proportion of the index patients to all registered patients was 6.1% for smear-positive patients, 1.8% for culture-positive patients, and 1.1% for bacilli-negative patients. The differences were highly significant between smear-positive and culture-positive patients, as well as between smear-positive and bacilli-negative patients (p < 0.001). CONCLUSION: The findings of this retrospective study suggest that 2.8% of the total registered patients, 6.1% of smear-positive patients, and 0.9 per 100,000 population was the index patients.

Cluster Analysis↗
PubMed2005

Profile of major congenital malformations at Nizwa Hospital, Oman: 10-year review.

OBJECTIVE: The objective of this study was to establish the profile of major congenital malformations at Nizwa Hospital, which is a major hospital in the Al-Dakhliya region of Oman. METHODS: All births with birthweight more than 500 g were prospectively studied from January 1993 through December 2002 for a period of 10 years. A congenital anomaly register was maintained in the special care baby unit (SCBU) and details of each case were recorded after parents' interviews, clinical evaluation and relevant radiological and laboratory investigations. The major malformations were classified as multiple or single-system abnormalities as well as genetic or non-genetic disorders. RESULTS: Of the 21 988 births during the study period, 541 babies (24.6 per 1000 births) had major malformations. Of the 541 babies, 158 (29.2%) had multiple malformations and 335 (61.9%) had involvement of a single system. In 48 (8.9%) babies a complete evaluation was not possible. Of the cases with multiple abnormalities, 57 had recognized syndromes, of which 28 (49.1%) were autosomal recessive disorders. Seventy (12.9%) cases had chromosomal abnormalities. The most common systems involved in neonates with single-system malformations were the gastrointestinal system (100 cases), the central nervous system (79 cases) and the cardiovascular system (63 cases). Although the consanguinity rate of 53.1% among Omani births almost matched with the regional average of 52.7%, it was 76% among those with major malformations. Also, there was an increased clustering of multiple abnormalities and rare recessive disorders in cases with closely related parents and grandparents. The birth prevalence of major malformations was 14.6 per 1000 in non-Omani births as compared to 25.2 in Omani births (P < 0.05). Genetic factors could be implicated in 343 (63.4%) cases and 130 (37.9%) of these were potentially preventable. CONCLUSION: Genetic disorders account for a significant proportion of congenital malformations in Oman.

Congenital Abnormalities↗
PubMed2000

Computational and experimental characterization of physically clustered simple sequence repeats in plants.

The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.

Arabidopsis↗
PubMed1995

Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions.

Fundamental chemical transformations for biogeochemical cycling of sulfur and nitrogen are catalyzed by sulfite and nitrite reductases. The crystallographic structure of Escherichia coli sulfite reductase hemoprotein (SiRHP), which catalyzes the concerted six-electron reductions of sulfite to sulfide and nitrite to ammonia, was solved with multiwavelength anomalous diffraction (MAD) of the native siroheme and Fe4S4 cluster cofactors, multiple isomorphous replacement, and selenomethionine sequence markers. Twofold symmetry within the 64-kilodalton polypeptide generates a distinctive three-domain alpha/beta fold that controls cofactor assembly and reactivity. Homology regions conserved between the symmetry-related halves of SiRHP and among other sulfite and nitrite reductases revealed key residues for stability and function, and identified a sulfite or nitrite reductase repeat (SNiRR) common to a redox-enzyme superfamily. The saddle-shaped siroheme shares a cysteine thiolate ligand with the Fe4S4 cluster and ligates an unexpected phosphate anion. In the substrate complex, sulfite displaces phosphate and binds to siroheme iron through sulfur. An extensive hydrogen-bonding network of positive side chains, water molecules, and siroheme carboxylates activates S-O bonds for reductive cleavage.

Amino Acid Sequence↗
PubMed2001

A Light Scattering Study of the Transition Region between Diffusion- and Reaction-Limited Cluster Aggregation.

Two limiting regimes for colloidal particle aggregation are well described in the literature: diffusion-limited cluster aggregation and reaction-limited cluster aggregation. Between these two limiting regimes, a vast transition region is expected. In this paper, the transition region is studied by means of static and dynamic light scattering. Therefore, a system of latex particles is aggregated at different electrolyte concentrations. The time dependence of the average diffusion coefficient is fitted considering the Brownian kernel and the kernel proposed by Schmitt et al. [Phys. Rev. E 62, 8335 (2000)]. The first fits the experimental data only at high electrolyte concentrations while the latter, which considers multiple cluster-cluster contacts, is found to fit the complete set of experimental data. Copyright 2001 Academic Press.

Journal Article↗
PubMed2000

Multiple founder effects and geographical clustering of BRCA1 and BRCA2 families in Finland.

In the Finnish breast and ovarian cancer families six BRCA1 and five BRCA2 mutations have been found recurrently. Some of these recurrent mutations have also been seen elsewhere in the world, while others are exclusively of Finnish origin. A haplotype analysis of 26 Finnish families carrying a BRCA1 mutation and 20 families with a BRCA2 mutation indicated that the carriers of each recurrent mutation have common ancestors. The common ancestors were estimated to trace back to 7-36 generations (150-800 years). The time estimates and the geographical clustering of these founder mutations in Finland are in concordance with the population history of this country. Analysis of the cancer phenotypes showed differential ovarian cancer expression in families carrying mutations in the 5' and 3' ends of the BRCA1 gene, and earlier age of ovarian cancer onset in families with BRCA1 mutations compared with families with BRCA2 mutations. The identification of prominent and regional BRCA1 and BRCA2 founder mutations in Finland will have significant impact on diagnostics in Finnish breast and ovarian cancer families. An isolated population with known history and multiple local founder effects in multigenic disease may offer distinct advantages also for mapping novel predisposing genes.

Adult↗
PubMed2004

Electrophysiology and plasticity in isolated postsynaptic densities.

The organization and regulation of excitatory synapses in the mammalian CNS entails complex molecular and cellular processes. In the postsynaptic membrane, scaffolding proteins bring together glutamate receptors with multiple regulatory proteins involved in signal transduction. This gives rise to an elaborate postsynaptic structure known as the postsynaptic density (PSD). This protein network plays a critical role in the regulation of glutamate receptor function and thus in synaptic plasticity. To study this regulation, we have developed a system in which ionotropic glutamate receptors (iGluRs) can be recorded, in the steady state, by the patch clamp technique in isolated PSDs incorporated into giant liposomes. In this preparation, ionotropic glutamate receptors maintain their characteristic physiological and pharmacological properties. The recordings reflect the presence of channel clusters, as multiple conductance and subconductance states are observed. Each of the receptor subtypes is activated by a specific set of kinases that are activated differentially by Ca(2+): the "kainate receptor kinases" are active even in the presence of EGTA, i.e. they are not calcium-dependent; the "N-methyl-D-aspartate receptor (NMDAR) channel kinases" are active in the presence of submicromolar calcium concentrations, whereas the "alpha-amino-3- hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptor kinases" need microM calcium for activation. The NMDA receptor showed its characteristic voltage-dependent Mg(2+) blockade, and activation by phosphorylation was in part a consequence of a relief of Mg(2+) blockade. These results allow us to propose a model in which phosphorylation of NMDA receptors can contribute to a long-lasting and self-maintained change in synaptic function. The experimental approach we present will allow us to test the functional consequence of activation of the multiple signal transduction pathways thought to regulate excitatory neurotransmission in the adult CNS.

Animals↗
PubMed1991

The inheritance of conotruncal malformations: a review and report of two siblings with tetralogy of Fallot with pulmonary atresia.

Congenital heart defects (CHD) are a group of structural abnormalities that in humans have a combined incidence of approximately 1%. It is estimated that 4-5% of CHD are associated with chromosome abnormalities, 1-2% are associated with single gene syndromes, 1-2% are due to known teratogens, with the rest presumably determined multifactorially. We report on a brother and sister with tetralogy of Fallot with pulmonary atresia, and review the inheritance of familial conotruncal anomalies. We feel the small number of family clusters and the rare instances of consanguinity in non-syndromal conotruncal defects are consistent with multifactorial determination. While it is prudent in counseling families with 2 or more individuals with conotruncal CHD to raise the possibility of single gene inheritance, we believe that current empiric recurrence risk estimates most accurately reflect their risks.

Abnormalities, Multiple↗
PubMed2001

Ferric dicitrate transport system (Fec) of Shigella flexneri 2a YSH6000 is encoded on a novel pathogenicity island carrying multiple antibiotic resistance genes.

Iron uptake systems which are critical for bacterial survival and which may play important roles in bacterial virulence are often carried on mobile elements, such as plasmids and pathogenicity islands (PAIs). In the present study, we identified and characterized a ferric dicitrate uptake system (Fec) in Shigella flexneri serotype 2a that is encoded by a novel PAI termed the Shigella resistance locus (SRL) PAI. The fec genes are transcribed in S. flexneri, and complementation of a fec deletion in Escherichia coli demonstrated that they are functional. However, insertional inactivation of fecI, leading to a loss in fec gene expression, did not impair the growth of the parent strain of S. flexneri in iron-limited culture media, suggesting that S. flexneri carries additional iron uptake systems capable of compensating for the loss of Fec-mediated iron uptake. DNA sequence analysis showed that the fec genes are linked to a cluster of multiple antibiotic resistance determinants, designated the SRL, on the chromosome of S. flexneri 2a. Both the SRL and fec loci are carried on the 66,257-bp SRL PAI, which has integrated into the serX tRNA gene and which carries at least 22 prophage-related open reading frames, including one for a P4-like integrase. This is the first example of a PAI that carries genes encoding antibiotic resistance and the first report of a ferric dicitrate uptake system in Shigella.

Bacterial Proteins↗
PubMed1995

The role of insulin in clustering of serum lipids and blood pressure in children and adolescents. The Cardiovascular Risk in Young Finns Study.

In adults hyperinsulinaemia is associated with an atherogenic risk profile including obesity, low levels of HDL-cholesterol, high levels of triglycerides and elevated blood pressure. To examine these associations in the young we studied the cross-sectional relationships of insulin with obesity indices (body mass index, subscapular skinfold thickness), serum lipids and blood pressure in 1,865 children, adolescents and young adults aged 6-24 years. We also used longitudinal data to study the value of a single insulin measurement to predict high risk factor levels and clustering of multiple risk factors after a 6-year follow-up. In cross-sectional analyses the levels of triglycerides, HDL-cholesterol, systolic blood pressure and obesity indices were usually significantly different across the quartiles of fasting insulin in both sexes among children, adolescents and young adults. In general, no associations were seen with total cholesterol or LDL-cholesterol. In prospective analysis elevated baseline insulin was related to the incidence of hypertriglyceridaemia (> or = 95th percentile) at the follow-up. This relationship persisted even after adjustments for baseline obesity or 6-year change in obesity status. Moreover, baseline insulin concentration was higher in subjects who subsequently showed clustering of high triglycerides, low HDL-cholesterol and high systolic blood pressure levels at the follow-up. We conclude that high fasting insulin levels measured in children and adolescents predict the development of hypertriglyceridaemia years later. In addition, high insulin levels seem to precede the development of a potentially atherogenic risk factor profile including low HDL-cholesterol, high triglycerides and high systolic blood pressure.

Adolescent↗
PubMed2001

Interaction of fission yeast ORC with essential adenine/thymine stretches in replication origins.

BACKGROUND: Eukaryotic DNA replication is initiated from distinct regions on the chromosome. However, the mechanism for recognition of replication origins is not known for most eukaryotes. In fission yeast, replication origins are isolated as autonomously replicating sequences (ARSs). Multiple adenine/thymine clusters are essential for replication, but no short consensus sequences are found. In this paper, we examined the interaction of adenine/thymine clusters with the replication initiation factor ORC. RESULTS: The SpOrc1 or SpOrc2 immunoprecipitates (IPs) containing at least four subunits of SpORC, interacted with the ars2004 fragment, which is derived from a predominant replication origin on the chromosome. SpORC-IPs preferentially interacted with two regions of the ars2004, which consist of consecutive adenines and AAAAT repeats and are essential for ARS activity. The nucleotide sequences required for the interaction with SpORC-IPs correspond closely to those necessary for in vivo ARS activity. CONCLUSION: Our results suggest that the SpORC interacts with adenine/thymine stretches, which have been shown to be the most important component in the fission yeast replication origin. The presence of multiple SpORC-binding sites, with certain sequence variations, is characteristic for the fission yeast replication origins.

Adenine↗
PubMed2006

The comparison of clinical imaging devices with respect to parallel readings in both devices.

OBJECTIVE: Many proposals for the comparison of diagnostic devices refer to the computation of ROC curves or sensitivity / specificity-based parameters, thereby strictly assuming the presence of a reliably parameterized clinical reference method. When none of the devices under consideration can be regarded as a reference, Cohen's kappa coefficient for assessing the methods' relative agreement becomes increasingly popular. If, however, not only the agreement between two diagnostic devices, but also the devices' reliability must be taken into account (for example, if multiple parallel readings are obtained from one or both of the devices), no corresponding coefficients can be obtained from standard software. Bearing the recent modifications in the German Medicinal Devices Law (Medizinproduktegesetz) in mind, such methods will soon become necessary and strongly demanded for the sake of immediate re-evaluation of previously certified medicinal devices. METHODS: Generalizations of Cohen's kappa (kappa) for complex multi reader designs can be found by estimating weighted averages of the observed and expected agreement among subsets of parallel readings. A flexible, although instructive, strategy for designing kappa coefficients in the context of method comparison trials is proposed, which measures the two methods' overall agreement while correcting for each method's underlying inter / intra observer reliability. Cluster algorithms will be outlined, which allow to identify (in)compatible clusters of readings. Their application will be illustrated by means of the intraindividual comparison of two different strategies in radiographical imaging, where none of the underlying imaging methods can be regarded as a reference. RESULTS: The algorithms are illustrated by the comparison of two radiological imaging devices R and F, where none of these imaging methods could be considered as a valid reference, i.e. replicate readings by three independent radiologists were taken from each device, respectively. The setting allowed for intraindividual comparison of the imaging methods, since each of the three involved radiologists took one reading from both devices on each of 120 individuals. The algorithm identifies a subset of compatible reading patterns with an overall agreement of kappa = 0.83 (95% confidence interval 0.78 - 0.88) despite the fact, that the underlying readings arose from two different imaging devices. An obvious interpretation suggests, that the gradient in experience between the readers was more relevant to their reading patterns' outcome than any difference between the imaging devices. CONCLUSIONS: The generalized kappa coefficients can be modified according to the study design at hand to instructively identify (in)compatible clusters of multiple parallel reading patterns; the relative agreement of imaging methods can be estimated as well as each imaging method's internal reliability as assessed by parallel readings from the respective methods.

Algorithms↗
PubMed2005

Tandem mobility mass spectrometry study of electrosprayed tetraheptyl ammonium bromide clusters.

Multiply charged electrospray ions from concentrated solutions of Heptyl4N+Br- (designated A+B- hereafter) in formamide are analyzed mass spectrometrically (MS) following mobility selection in ambient air in a differential mobility analyzer (DMA). Most of the sharp mobility peaks seen are identified as (AB)(n)A+ clusters, with 0 < or = n < ot = 5. One anomalously abundant and mobile ion is identified as NH4+(AB)4. Six ions in the (AB)n(A+)2 series are also identified, completing and correcting earlier mobility data for singly and doubly charged ions up to masses of almost 9000 Da. The more mobile of two broad humps seen in the mobility spectrum includes m/z values approximately from 2500 up to 12,000 Da. It is formed primarily by multiply charged (AB)n(A+)z clusters with multiple ammonium bromide adducts. Because of overlapping of many peaks of different m/z and charge state z, only a few individual species can be identified by MS alone in this highly congested region. However, the spectral simplification brought about by mobility selection upstream of the MS reveals a series of broad modulations in m/z space, with all ions resolved in the second, third, ...sixth modulation being in charge states z = 2, 3, ...6, respectively. Extrapolation of this trend beyond the sixth wave fixes the ion charge state (in some cases up to z = 15) and mass (beyond m = 175,000 u). This wavy structure had been previously observed and explained in terms of ion evaporation kinetics from volatile drops, though without mass identification. All observations indicate that the clusters are formed as charged residues, but their charge state is fixed by the Iribarne-Thomson ion evaporation mechanism. Consequently, the measured curve of cluster diameter versus z yields the two parameters governing ion evaporation kinetics. Clusters with z > 1 and electrical mobility Z > 0.495 cm2/V/s are metastable and evaporate a singly charged cluster, probably (AB)2A+, between the DMA and the MS. Plotting the electrical mobilities Z of the clusters in the form (z/Z)1/2 versus m(1/3) (both proportional to cluster diameter) collapse the data for all cluster sizes and charge states into one single straight line for Z below 0.495 cm2/V/s. This linear relation reveals a uniform apparent cluster density of 0.935 g/cm3 and an effective hard-sphere diameter of the air molecules of 0.44 nm. An anomalous mobility increase is observed at diameters below 3 nm.

Bromides↗
PubMed1988

A family study of multiple mutations of alpha and delta glycophorins (glycophorins A and B).

Glycophorins alpha and delta are the carriers of the antigens of the MNSs blood system; this report documents the presence of three glycophorin mutations in two individuals of a 16 member family. Erythrocytes were examined by serology, sodium dodecyl sulfate electrophoresis, and immunoblotting. The inheritance pattern and immunoblot profile revealed: (1) A variant Dantu glycophorin showed properties consistent with a delta-alpha glycophorin hybrid structure, previously noted in other individuals. The gene responsible for the Dantu glycophorin in this family is linked to a gene coding for an M-specific alpha glycophorin. (2) Another variant glycophorin, Mi-III glycophorin, was first revealed by immunoblotting and subsequently confirmed by erythrocyte antigen typing. This autosomal dominant trait is associated with N blood group activity and the inheritance pattern indicates that it could be a variant of delta glycophorin. (3) In the individuals with both Dantu and Mi-III glycophorins a delta glycophorin deficiency was observed suggesting that a deletion or alteration of delta gene may exist cis to the Dantu gene. Our findings that document clustering of multiple mutations in MNSs gene loci in the propositus family are very unusual as such variants are relatively rare.

Female↗
PubMed2000

Simulating the oxygen K-edge spectrum from grain boundaries in ceramic oxides using the multiple scattering methodology

In this paper we demonstrate the use of the multiple scattering methodology to interpret oxygen K-edge spectra from both the bulk and grain boundaries in a variety of ceramic oxides. The experimental electron energy loss spectra (EELS) used in this study, were obtained from a dedicated scanning transmission electron microscope (STEM). Using the STEM to obtain the spectra has the advantage that each spectrum can be acquired with atomic spatial resolution. While the energy resolution is limited to approximately 0.8 eV, and the angular integration in the microscope apertures precludes momentum resolved spectroscopy, this unprecedented spatial resolution allows the electronic structure at individual defect sites to be determined. Additionally, as the microscope can also provide an atomic resolution image of the defect, the relationship between the atomic structure of the defect and its local electronic structure can be determined. In practice, this is achieved by using the structure observed in the image to build the real space atomic cluster for multiple scattering simulations. Detailed interpretation of the simulations of oxygen K-edge spectra from bulk MgO, CaO, SrTiO3, TiO2, MnO2, Mn3O4, Mn2O3 and MnO are presented. In addition, the simulations from grain boundaries in TiO2 (undoped) and SrTiO3 (undoped and Mn doped) are discussed in relation to quantifying the changes in the local electronic structure that are a direct consequence of the defect structure. The simulations are used to make interpretations of the structure-property relationships at these grain boundaries.

Journal Article↗