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At least 55 records · Page 3Linked to original sources
PubMed2004

Routine dose estimates for the removal of soil from a basin to the burial ground at the Savannah River Site.

Worker dose estimates have been made for various exposure scenarios resulting from the relocation of soil from the H Area Retention Basin to the Old Radioactive Waste Burial Ground at the Savannah River Site. Estimates were performed by hand calculations and using RESRAD and MAXDOSE-SR. Doses were estimated for the following pathways: (1) shine and inhalation as a result of standing on contaminated soil at the H Area Retention Basin and the Old Radioactive Waste Burial Ground; (2) exposure to off-unit receptors due to soil disturbances from excavation type activities at the H Area Retention Basin and the Old Radioactive Waste Burial Ground; (3) exposure to off-unit receptors due to soil disturbances from dumping of soil from bucket and from roll-off pan; and (4) exposure to off-unit receptors from wind driven dust from contaminated area. The highest dose estimates (0.25 mSv h(-1)) resulted from the receptor standing on the H Area Retention Basin.

Air Pollutants, Radioactive↗
PubMed2005

Asymmetry in the burial of hydrophobic residues along the histone chains of eukarya, archaea and a transcription factor.

BACKGROUND: The histone fold is a common structural motif of proteins involved in the chromatin packaging of DNA and in transcription regulation. This single chain fold is stabilized by either homo- or hetero-dimer formation in archaea and eukarya. X-ray structures at atomic resolution have shown the eukaryotic nucleosome core particle to consist of a central tetramer of two bound H3-H4 dimers flanked by two H2A-H2B dimers. The c-terminal region of the H3 histone fold involved in coupling the two eukaryotic dimers of the tetramer, through a four-fold helical bundle, had previously been shown to be a region of reduced burial of hydrophobic residues within the dimers, and thereby provide a rationale for the observed reduced stability of the H3-H4 dimer compared with that of the H2A-H2B dimer. Furthermore, comparison between eukaryal and archaeal histones had suggested that this asymmetry in the distribution of hydrophobic residues along the H3 histone chains could be due to selective evolution that enhanced the coupling between the eukaryotic dimers of the tetramer. RESULTS AND DISCUSSION: The present work describes calculations utilizing the X-ray structures at atomic resolution of a hyperthermophile from Methanopyrus kandleri (HMk) and a eukaryotic transcription factor from Drosophila melanogaster (DRm), that are structurally homologous to the eukaryotic (H3-H4)2 tetramer. The results for several other related structures are also described. Reduced burial of hydrophobic residues, at the homologous H3 c-terminal regions of these structures, is found to parallel the burial at the c-terminal regions of the H3 histones and is, thereby, expected to affect dimer stability and the processes involving histone structural rearrangement. Significantly different sequence homology between the two histones of the HMk doublet with other archaeal sequences is observed, and how this might have occurred during selection to enhance tetramer stability is described.

Animals↗
PubMed2006

Raman spectroscopic analysis of human remains from a seventh century cist burial on Anglesey, UK.

Specimens from human remains exhibiting unusual preservation excavated from a seventh century stone cist burial at Towyn y Capel in Anglesey, UK, have been analysed using Raman spectroscopy with near-infrared laser excitation at 1,064 and 785 nm. Specimens of hair and bone provided evidence for severe degradation and microbial colonisation. The deposits within the stone cist showed that some microbially mediated compounds had been formed. Analysis of crystals found at the interface between the hair and the skeletal neck vertebrae revealed a mixture of newberyite and haematite, associated with decomposition products of the hair and bone. An interesting differential degradation was noted in the specimens analysed which could be related to the air-void and the presence of plant root inclusions into the stone cist. This is the first time that Raman spectroscopy has been used in the forensic archaeological evaluation of burial remains in complex and dynamic environments.

Archaeology↗
PubMed2004

Evidence of adipocere in a burial pit from the foot and mouth epidemic of 1967 using gas chromatography-mass spectrometry.

Gas-chromatography-mass spectrometry was used to characterise the fatty acids from soils and associated tissues excavated from a 1967 Foot and Mouth burial pit. Subcutaneous fats were mainly comprised of 55-75% palmitic acid, 17-22% stearic acid and 3-16% oleic acid as well as 5-7% myristic acid. The distribution of fatty acids confirmed that the tissues were decayed to adipocere. The loss of oleic acid to <3% in two of the decayed fats suggested advanced stages of adipocere. However, adipocere formation was limited in a third tissue sample recovered from greater depth. Inductively coupled plasma atomic emission spectrometry of the pore waters revealed a decrease in Ca concentration and concurrent increase in Na concentrations this suggested that insoluble calcium salt had formed through displacement of sodium. The use of fatty acid profiles from soils and soil interstitial pore waters provide complementary evidence of adipocere formation in foot and mouth burial pits.

Adipose Tissue↗
PubMed2003

Burial at Srebrenica: linking place and trauma.

Five years after the massacre at Srebrenica in Bosnia-Herzegovina, survivors were faced with the decision: where did they want their loved ones buried? This report explores the reasons for their choice in qualitative interviews with 37 survivors of the massacre and 22 key informants performed over the summer 2000. Survivors wanted the loved ones buried at Potocari, a site just outside of Srebrenica, because it represented the site of ultimate horror, was connected to their sense of home, and underscored the various power relationships. The data points to the importance of place for health. Trauma, as it occurs in particular locations, breaks the sense of attachment to a particular place. Restoring the physical and social environment through burial and memorials mitigates the consequences of the trauma. The burial at Potocari provides a window into the mourning, politics, and recovery after mass violence.

Bereavement↗
PubMed2006

Upper Palaeolithic infant burials.

Decorations on the bodies of newborns indicate that they were probably important in their community. Several adult graves from the Stone Age (Upper Palaeolithic period) have been found but child burials seem to be rare, which has prompted discussion about whether this apparently different treatment of infants could be significant. Here we describe two recently discovered infant burials from this period at Krems-Wachtberg in Lower Austria, in which the bodies were covered with red ochre and decorated with ornaments and were therefore probably ritually buried. These findings indicate that even newborns were considered to be full members of these hunter-gatherer communities about 27,000 years ago.

Austria↗
PubMed2005

Stability of ferruginous bodies in human lung tissue following death, embalmment, and burial.

The identification of asbestos bodies in tissue sections is an indicator of past exposure to longer asbestos fibers. These structures are formed in lung tissue as a consequence of interactions with pulmonary macrophages resulting in the deposition of a ferroprotein (ferruginous) coating on the fiber. While the process of ferruginous body formation is known to take months in animal tissue, there is no published information on the stability of ferruginous bodies in tissue following death. The material assessed in the present study was obtained from lung material collected from an exhumed body approximately 8(1/2) mo after death, embalmment, and burial. Tissue sections were reviewed for the presence of asbestos bodies. Additional pieces of lung tissue were digested, with the digestate being evaluated by light microscopy for ferruginous bodies and by electron microscopy for uncoated asbestos fibers and core analysis of asbestos bodies. Classical ferruginous (asbestos) bodies were found in abundance in the tissue sections including in areas with fibrosis. The levels of uncoated asbestos fibers and classical appearing ferruginous bodies (asbestos bodies) were consistent with occupational levels of tissue burden. The data from this study indicate that ferruginous bodies remain morphologically stable within the tissue for months following death, embalmment, and burial. Thus the lung tissue from this exhumed individual was usable not only to pathologically confirm asbestosis but also to provide quantitative data of occupational exposure to asbestos.

Aged, 80 and over↗
PubMedDate not supplied

[Discrimination between functions of an expert bureau and a burial firm (topic for discussion)].

The authors suggest measures aimed at discrimination of the functions performed by forensic medical experts and the services rendered by burial firms. The responsibilities of pathology departments of hospitals and bureaus of forensic medical expert evaluations, which should be reflected in official documents, should be confined to manipulations needed to solve the professional problems and removal of sections. Cases when utilization of certain chemicals or manipulations aimed at restoration of the body are prohibited should be listed in detail. The order of transfer of the body from pathology department or forensic medical bureau to the burial firm and to relatives should be regulated with consideration for the results of autopsy. The moment of the end of autopsy studies is to be determined.

Burial↗
PubMedDate not supplied

[The forensic medical assessment of the bone damages to skeletons from a group burial in the environs of Yekaterinburg].

Results of comprehensive expert evaluation of bone remains found at the place of burial made 80 years ago are presented. Injuries inflicted by gunshots, mechanical, chemical, and other factors are classified. Diagnostic criteria for reconstruction of circumstances of death and burial of the Romanov family and subjects in their attendance are defined.

Autopsy↗
PubMedDate not supplied

[The results of the expert studies on the bone remains from the site of the burial of the family of the former Emperor Nicholas II].

Results of expert studies of bone remains found at the site of burial of the family of late Emperor Nicholas II and subjects in their attendance are presented. All expert evaluations and identification studies (forensic biological, microosteological, forensic dental, medical anthropological, molecular genetic analysis, computer photoblending of the skull and life-time photographs, plastic reconstruction, etc.) are listed. Gunshot and other injuries on bone rudiments are described. Signs of long stay of bone remains in soil are detected. Signs of exposure of some remains to aggressive chemical medium (probably inorganic acid) at the site where they were found are noted. The remains of 9 subjects from group burial near Ekaterinburg are identified as Russian Emperor Nicholas II and his family members (N. A. Romanov, A. F. Romanova, O. N. Romanova, T. N. Romanova, and A. N. Romanova) and persons in their attendance Ye. S. Botkin, A. S. Demidova, A. Ye. Troupp, and I. M. Kharitonov. Official documents of the State Commission are offered.

Bone and Bones↗
PubMed1975

Otosclerotic stapedial footplate fixation in an 18th century burial.

Fixation of the footplate of the stapes by otosclerosis had been found in the left ear of a probable Spaniard who died about 200 years ago and was buried in the Tuscon Presidio. Previous studies on North and South Dakota American Indian crania of about the same time period did not demonstrate any stapedial fixation in 2,600 burials (4,064 temporal bones), 1,416 of which were over 16 years of age at death. The Tucson burial would indicate that this abnormality can be demonstrated in old interred skeletal material. Our other studies suggest that this disease process was not common in the prehistoric and historic Indian populations of the Dakotas.

Adolescent↗
PubMed2004

Evaluation of local structure alphabets based on residue burial.

Residue burial, which describes a protein residue's exposure to solvent and neighboring atoms, is key to protein structure prediction, modeling, and analysis. We assessed 21 alphabets representing residue burial, according to their predictability from amino acid sequence, conservation in structural alignments, and utility in one fold-recognition scenario. This follows upon our previous work in assessing nine representations of backbone geometry.1 The alphabet found to be most effective overall has seven states and is based on a count of C(beta) atoms within a 14 A-radius sphere centered at the C(beta) of a residue of interest. When incorporated into a hidden Markov model (HMM), this alphabet gave us a 38% performance boost in fold recognition and 23% in alignment quality.

Amino Acids↗
PubMed2006

Beach morphodynamics forcements in oiled shorelines: Coupled physical and chemical processes during and after fuel burial.

In November 2002, the sinking of the Prestige oil tanker off the Galician coast (N.W. Spain) caused the largest ecological catastrophe in the history of Spain, affecting the coast called the 'Costa da Morte' (Galicia, N.W. Spain). This work is focused on the study of the oil contamination of the intertidal area of two beaches located on this stretch of coast. The study of twenty cores extracted from both beaches has identified fuel embedded in the sedimentary column up to a depth of 2.38 m (this being the maximum depth of extraction). This, along with the presence of oil below the groundwater indicates the existence of a new factor which determines the burial of oil: the morphodynamic behaviour of the beach. Furthermore, this morphodynamic variation conditions the physical appearance of the buried oil. Four different types have been identified: tar-balls (cm), particles (mm), oil coatings on sediment grains and on emulsion, with distribution patterns conditioned by the degree of wave exposure. The analysis of the information obtained have permitted the development of a conceptual model of the burial and oil evolution in the sedimentary column in relation to wave exposure, and thus to the morphodynamic variability of the beach.

Accidents, Occupational↗
PubMed2005

The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation.

The hydrophobic effect is a major driving force in all chemical and biological events involving chain collapse in aqueous solution. Here, we show that the burial of nonpolar solvent-accessible surface area (NSASA) is a powerful criterion to predict the folding and misfolding behavior of small single-domain proteins as a function of chain elongation. This bears fundamental implications for co- and post-translational protein folding in the cell and for understanding the interplay between noncovalent interactions and formation of native-like structure and topology. Comparison between the fraction of NSASA in fully unfolded and folded elongating chains shows that efficient burial of nonpolar surface area is preferentially achieved only when the polypeptide chain is almost complete. This effect has no preferential vectorial character in that it is present upon elongation from both the N and C termini. For incomplete chains that do not have the ability to fold and bury nonpolar surface intramolecularly, the overall hydrophobic nature of the polypeptide chain (expressed as FBA, i.e., fractional buried surface area per residue) dictates the tendency toward misfolding and self-association. N-terminal chains characterized by FBA exceeding 0.73 are likely to misfold and aggregate, if unable to fold intramolecularly.

Amino Acids↗
PubMed2003

The contribution of polar group burial to protein stability is strongly context-dependent.

We previously suggested that proteins gain more stability from the burial and hydrogen bonding of polar groups than from the burial of nonpolar groups (Pace, C. N. (2001) Biochemistry 40, 310-313). To study this further, we prepared eight Thr-to-Val mutants of RNase Sa, four in which the Thr side chain is hydrogen-bonded and four in which it is not. We measured the stability of these mutants by analyzing their thermal denaturation curves. The four hydrogen-bonded Thr side chains contribute 1.3 +/- 0.9 kcal/mol to the stability; those that are not still contribute 0.4 +/- 0.9 kcal/mol to the stability. For 40 Thr-to-Val mutants of 11 proteins, the average decrease in stability is 1.0 +/- 1.0 kcal/mol when the Thr side chain is hydrogen-bonded and 0.0 +/- 0.5 kcal/mol when it is not. This is clear evidence that hydrogen bonds contribute favorably to protein stability. In addition, we prepared four Val-to-Thr mutants of RNase Sa, measured their stability, and determined their crystal structures. In all cases, the mutants are less stable than the wild-type protein, with the decreases in stability ranging from 0.5 to 4.4 kcal/mol. For 41 Val-to-Thr mutants of 11 proteins, the average decrease in stability is 1.8 +/- 1.3 kcal/mol and is unfavorable for 40 of 41 mutants. This shows that placing an [bond]OH group at a site designed for a [bond]CH3 group is very unfavorable. So, [bond]OH groups can contribute favorably to protein stability, even if they are not hydrogen-bonded, if the site was selected for an [bond]OH group, but they will make an unfavorable contribution to stability, even if they are hydrogen-bonded, when they are placed at a site selected for a [bond]CH3 group. The contribution that polar groups make to protein stability depends strongly on their environment.

Crystallography, X-Ray↗
PubMed1997

Burial and seed survival in Brassica napus subsp. oleifera and Sinapis arvensis including a comparison of transgenic and non-transgenic lines of the crop.

The creation of transgenic plants through genetic engineering has focused interest on how the fitness of a plant species may be altered by small changes in its genome. This study concentrates on a key component of fitness: persistence of seeds overwinter. Seeds of three lines of oilseed rape (Brassica napus subsp. oleifera DC Metzger) and of charlock (Sinapis arvensis L.) were buried in nylon mesh bags at two depths in four habitats in each of three geographically separated sites: Cornwall, Berkshire and Sutherland. Seeds were recovered after 12 and 24 months. Charlock exhibited much greater seed survival (average 60% surviving the first year and 32.5% surviving the second year) than oilseed rape (1.5% surviving the first year and 0.2% surviving the second) at all sites. Charlock showed higher survival at 15 cm burial than 2 cm burial at certain sites, but oilseed rape showed no depth effect. Different genetic lines of oilseed rape displayed different rates of seed survival; non-transgenic rape showed greater survival (2%) than the two transgenic lines, one developed for tolerance to the antibiotic kanamycin (0.3%) and one for tolerance to both kanamycin and the herbicide glufosinate (0.25%). The absolute and relative performances of the different genetic lines of oilseed rape were context specific, illustrating the need to test hypotheses in a wide range of ecological settings.

Brassica↗
PubMed2003

Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method.

Helices in membrane spanning regions are more tightly packed than the helices in soluble proteins. Thus, we introduce a method that uses a simple scale of burial propensity and a new algorithm to predict transmembrane helical (TMH) segments and a positive-inside rule to predict amino-terminal orientation. The method (the topology predictor of transmembrane helical proteins using mean burial propensity [THUMBUP]) correctly predicted the topology of 55 of 73 proteins (or 75%) with known three-dimensional structures (the 3D helix database). This level of accuracy can be reached by MEMSAT 1.8 (a 200-parameter model-recognition method) and a new HMM-based method (a 111-parameter hidden Markov model, UMDHMM(TMHP)) if they were retrained with the 73-protein database. Thus, a method based on a physiochemical property can provide topology prediction as accurate as those methods based on more complicated statistical models and learning algorithms for the proteins with accurately known structures. Commonly used HMM-based methods and MEMSAT 1.8 were trained with a combination of the partial 3D helix database and a 1D helix database of TMH proteins in which topology information were obtained by gene fusion and other experimental techniques. These methods provide a significantly poorer prediction for the topology of TMH proteins in the 3D helix database. This suggests that the 1D helix database, because of its inaccuracy, should be avoided as either a training or testing database. A Web server of THUMBUP and UMDHMM(TMHP) is established for academic users at http://www.smbs.buffalo.edu/phys_bio/service.htm. The 3D helix database is also available from the same Web site.

Algorithms↗
PubMed2001

Heat capacity changes upon burial of polar and nonpolar groups in proteins.

In this paper we address the question of whether the burial of polar and nonpolar groups in the protein locale is indeed accompanied by the heat capacity changes, DeltaC(p), that have an opposite sign, negative for nonpolar groups and positive for polar groups. To accomplish this, we introduced amino acid substitutions at four fully buried positions of the ubiquitin molecule (Val5, Val17, Leu67, and Gln41). We substituted Val at positions 5 and 17 and Leu at position 67 with a polar residue, Asn. As a control, Ala was introduced at the same three positions. We also replaced the buried polar Gln41 with Val and Leu, nonpolar residues that have similar size and shape as Gln. As a control, Asn was introduced at Gln41 as well. The effects of these amino acid substitutions on the stability, and in particular, on the heat capacity change upon unfolding were measured using differential scanning calorimetry. The effect of the amino acid substitutions on the structure was also evaluated by comparing the (1)H-(15)N HSQC spectra of the ubiquitin variants. It was found that the Ala substitutions did not have a considerable effect on the heat capacity change upon unfolding. However, the substitutions of aliphatic side chains (Val or Leu) with a polar residue (Asn) lead to a significant (> 30%) decrease in the heat capacity change upon unfolding. The decrease in heat capacity changes does not appear to be the result of significant structural perturbations as seen from the HSQC spectra of the variants. The substitution of a buried polar residue (Gln41) to a nonpolar residue (Leu or Val) leads to a significant (> 25%) increase in heat capacity change upon unfolding. These results indicate that indeed the heat capacity change of burial of polar and nonpolar groups has an opposite sign. However, the observed changes in DeltaC(p) are several times larger than those predicted, based on the changes in water accessible surface area upon substitution.

Amino Acid Substitution↗