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Biomedical subjects

D C Richardson

Publications and source records attributed to D C Richardson.

At least 19 recordsLinked to original sources
PubMed2002

Biological variability in serum and urinary indices of bone formation and resorption in dogs.

Serum and urinary assays of bone markers provide a noninvasive alternative to bone biopsy in the study of bone metabolism in humans. Many of the commercial assays that were originally developed for use in humans have been shown to cross-react in dogs, and it should therefore be possible to use these assays to study bone remodeling in dogs. The interpretation of bone marker data in humans is hampered by extensive inter- and intra-subject variability. The specific aim of this study was therefore to determine the extent of biological variability in bone markers in dogs. Serum and urine samples were collected every 4 hours over a 24-hour period (short-term study), and every week over a 12-week period (long-term study). Serum bone-specific alkaline phosphatase (BALP) and urinary deoxypyridinoline (Dpd) and N-terminal telopeptide of collagen (NTx) were measured with commercial enzyme immunoassays. Serum osteocalcin (OC) and carboxyterminal crosslinked telopeptide of type I collagen (ICTP) were measured with commercial radioimmunoassays. In the short-term study, statistically significant diurnal rhythms were identified for OC, BALP, ICTP, and Dpd. No clear rhythm was evident for NTx. There was no evidence of statistically significant long-term variability in marker excretion over the 12 weeks. Our findings confirm the utility of these assays in dogs. However, as in humans, care must be taken to ensure that specimens are collected at a consistent time of day. Moreover, given the inherent variability in marker excretion in individual animals, the most appropriate use for these assays is as a screening tool for cohort studies, rather than as a diagnostic or prognostic tool in the individual animal.

Alkaline Phosphatase↗
PubMed2001

Collisions and gravitational reaccumulation: forming asteroid families and satellites.

Numerical simulations of the collisional disruption of large asteroids show that although the parent body is totally shattered, subsequent gravitational reaccumulation leads to the formation of an entire family of large and small objects with dynamical properties similar to those of the parent body. Simulations were performed in two different collisional regimes representative of asteroid families such as Eunomia and Koronis. Our results indicate that all large family members must be made of gravitationally reaccumulated fragments; that the post-collision member size distribution and the orbital dispersion are steeper and smaller, respectively, than for the evolved families observed today; and that satellites form frequently around family members.

Journal Article↗
PubMed2001

Evaluation of susceptibility testing to detect fluoroquinolone resistance mechanisms in Streptococcus pneumoniae.

To determine if susceptibility testing of Streptococcus pneumoniae could detect those isolates that had one of the recognized mechanisms of fluoroquinolone resistance, 101 isolates were selected; the levofloxacin MIC for 28 of these isolates was > or =4 microg/ml. Only isolates with both parC and gyrA mutations or with no recognized resistance mechanisms were reliably identified by using these results. Isolates with only a parC mutation could not be detected reliably using any susceptibility testing method.

Anti-Infective Agents↗
PubMed2001

Trimethoprim-sulfamethoxazole induced aseptic meningitis in a renal transplant patient.

A 45-year-old man underwent renal transplant for end-stage renal disease complicating systemic lupus erythematosis. Within 24 hours of initiating Pneumocystis carinii pneumonia (PCP) prophylaxis with trimethoprim-sulfamethoxazole (TMP-SMX) he developed fever and confusion. Cerebrospinal fluid examination revealed a pleocytosis but cultures were negative. The patient improved within three days after cessation of the TMP-SMX but symptoms recurred rapidly upon drug rechallenge. Drug-induced aseptic meningitis is an uncommon but well described clinical entity. This is the first case described in a patient following renal transplantation. The literature is reviewed and the clinical features, diagnostic challenges and possible mechanisms of TMP-SMX-induced aseptic meningitis are discussed. This problem may be more common in the transplant population than is recognized given the difficulty of diagnosis combined with the widespread use of TMP-SMX as PCP prophylaxis.

Anti-Infective Agents↗
PubMed2000

Representation, space and Hollywood Squares: looking at things that aren't there anymore.

It has been argued that the human cognitive system is capable of using spatial indexes or oculomotor coordinates to relieve working memory load (Ballard, D. H., Hayhoe, M. M., Pook, P. K., & Rao, R. P. N. (1997). Behavioral and Brain Sciences, 20(4), 723), track multiple moving items through occlusion (Scholl, D. J., & Pylyshyn, Z. W. (1999). Cognitive Psychology, 38, 259) or link incompatible cognitive and sensorimotor codes (Bridgeman, B., & Huemer, V. (1998). Consciousness and Cognition, 7, 454). Here we examine the use of such spatial information in memory for semantic information. Previous research has often focused on the role of task demands and the level of automaticity in the encoding of spatial location in memory tasks. We present five experiments where location is irrelevant to the task, and participants' encoding of spatial information is measured implicitly by their looking behavior during recall. In a paradigm developed from Spivey and Geng (Spivey, M. J., & Geng, J. (2000). submitted for publication), participants were presented with pieces of auditory, semantic information as part of an event occurring in one of four regions of a computer screen. In front of a blank grid, they were asked a question relating to one of those facts. Under certain conditions it was found that during the question period participants made significantly more saccades to the empty region of space where the semantic information had been previously presented. Our findings are discussed in relation to previous research on memory and spatial location, the dorsal and ventral streams of the visual system, and the notion of a cognitive-perceptual system using spatial indexes to exploit the stability of the external world.

Adult↗
PubMed2000

The penultimate rotamer library.

All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar terminal groups when required by atomic overlaps or H-bonding. Sensitivity to skew and to the boundaries of chi angle bins is avoided by using modes rather than traditional mean values. Rotamer definitions are listed both as the modal values and in a preferred version that maximizes common atoms between related rotamers. The resulting library shows significant differences from previous ones, differences validated by considering the likelihood of systematic misfitting of models to electron density maps and by plotting changes in rotamer frequency with B-factor. Few rotamers now show atomic overlaps in ideal geometry; those overlaps are relatively small and can be understood in terms of bond angle distortions compensated by favorable interactions. The new library covers 94.5% of examples in the highest quality protein data with 153 rotamers and can make a significant contribution to improving the accuracy of new structures. Proteins 2000;40:389-408.

Amino Acids↗
PubMed2000

SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics.

Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical short helices, we here proceed by an extensive redesign of the ROP protein. A fully symmetrical SymROP sequence derived from ROP was chosen by modeling ideal-geometry side chains, including hydrogens, while maintaining the "goodness-of-fit" of side-chain packing by calculating all-atom contact surfaces with the Reduce and Probe programs. To estimate the probable extent of backbone movement and side-chain mobility, restrained molecular dynamics simulations were compared for candidate sequences and controls, including substitution of Abu for all or half the core Ala residues. The resulting 17-residue designed sequence is 41% identical to the relevant regions in ROP. SymROP is intended for construction by the Template Assembled Synthetic Proteins approach, to control the bundle topology, to use short helices, and to allow blocked termini and unnatural amino acids. ROP protein has been a valuable system for studying helical protein structure because of its simplicity and regularity within a structure large enough to have a real hydrophobic core. The SymROP design carries that simplicity and regularity even further.

Amino Acid Sequence↗
PubMed2000

A comparison of two techniques for the determination of serum bone-specific alkaline phosphatase activity in dogs.

Bone-specific alkaline phosphatase (BALP) shows potential as a marker of bone formation in the dog. Recent studies have indicated that serum BALP may provide a useful, non-invasive indicator of skeletal health in dogs, and as a diagnostic and prognostic marker in the management of dogs with musculoskeletal or metabolic disorders. Two assay techniques (one based on wheatgerm lectin precipitation followed by a simple enzymatic reaction, the second on a specific enzyme-linked immunoassay) were used to measure serum levels of BALP in 35 dogs of different ages. As expected, BALP concentrations decreased with age. For the enzymatic assay, mean (+/-SD) serum concentrations of BALP activities were 100.3 (+/-11.6) U/liter in dogs under 1 year of age, 25.3 (+/-6.8) U/L in dogs 1 to 2 years of age, 16.5 (+/-7.3) U/L in dogs 2 to 3 years of age, 14.3 (+/-5.6) U/L in dogs 3 to 7 years of age, and 12.3 (+/-4.8) U/L in dogs aged 8 years and older. Corresponding results from the immunoassay were 56.3 (+/-9.8) U/L, 10.7 (+/-4.5) U/L, 7.0 (+/-2.5) U/L, 6.7 (+/-3.6) U/L and 7.0 (+/-2.9) U/L. There was excellent correlation between the results from the two assay techniques (r = 0. 96; P < 0.0001). The correlation between BALP and total ALP activities was poor (r = 0.20 for enzymatic BALP, r = 0.31 for immunoreactive BALP), indicating that total ALP should be considered unreliable as an indicator of BALP activity in canine serum. The immunoassay demonstrated acceptable (13 per cent) cross-reactivity with the liver isoform of ALP. The commercial immunoassay kit is simple and provides fast results. Although the wheatgerm lectin/enzymatic technique is preferred in situations where the activities of all three isoforms of ALP are required, the immunoassay should be considered whenever the activity of BALP is the focus of interest.

Alkaline Phosphatase↗
PubMed2000

Urinary markers of type I collagen degradation in the dog.

Urinary assays for type I collagen metabolites provide a non invasive index of bone resorption in humans, and are widely used in the management of patients with metabolic bone diseases. The specific aims of this study were to investigate the feasibility of using commercial human assay kits for quantifying the urinary excretion of type I collagen metabolites in dogs of different ages. Urine and serum samples were collected from 35 beagle dogs in five age groups (0 to 1 years; 1 to 2 years; 2 to 3 years; 3 to 7 years; > 8 years old). Urinary concentrations of pyridinoline (Pyd), deoxypyridinoline (Dpd), and the carboxy- and amino-terminal cross-linked telopeptides of type I collagen (CTx and NTx, respectively) were measured with commercial enzyme-linked immunoassay kits. Serum concentrations of another type I collagen metabolite, the carboxy-terminal cross-linked teloptide of type I collagen (ICTP), were measured with a commercial radioimmunoassay. Dilutional studies indicated that the four urinary assays show specific cross-reactivity with canine urine. Age-related differences in urinary marker excretion were identified, with young dogs excreting the highest concentrations of Pyd, Dpd, NTx and CTx. The correlation between the individual urinary markers was excellent (r = 0.87 to 0.98), while the correlation between serum ICTP and individual urinary markers was weaker (r = 0.52 to 0.64). These results validate the usefulness of the commercial assay kits in monitoring type I collagen metabolism in dogs. Histomorphometric studies have confirmed the relationship between collagen degradation and bone resorption in humans, and similar studies are now needed in dogs.

Age Factors↗
PubMed2000

Exploring steric constraints on protein mutations using MAGE/PROBE.

When planning a mutation to test some hypothesis, one crucial question is whether the new side chain is compatible with the existing structure; only if it is compatible can the interpretation of mutational results be straightforward. This paper presents a simple way of using the sensitive geometry of all-atom contacts (including hydrogens) to answer that question. The interactive MAGE/PROBE system lets the biologist explore conformational space for the mutant side chain, with an interactively updated kinemage display of its all-atom contacts to the original structure. The Autobondrot function in PROBE systematically explores that same conformational space, outputting contact scores at each point, which are then contoured and displayed. These procedures are applied here in two types of test cases, with known mutant structures. In ricin A chain, the ability of a neighboring glutamate to rescue activity of an active-site mutant is modeled successfully. In T4 lysozyme, six mutations to Leu are analyzed within the wild-type background structure, and their Autobondrot score maps correctly predict whether or not their surroundings must shift significantly in the actual mutant structures; interactive examination of contacts for the conformations involved explains which clashes are relieved by the motions. These programs are easy to use, are available free for UNIX or Microsoft Windows operating systems, and should be of significant help in choosing good mutation experiments or in understanding puzzling results.

Bacteriophage T4↗
PubMed1999

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

The technique of small-probe contact dot surfaces is described as a method for calculating and displaying the detailed atomic contacts inside or between molecules. It allows one both to measure and to visualize directly the goodness-of-fit of packing interactions. It requires both highly accurate structures and also the explicit inclusion of all hydrogen atoms and their van der Waals interactions. A reference dataset of 100 protein structures was chosen on the basis of resolution (1.7 A or better), crystallographic R-value, non-homology, and the absence of any unusual problems. Hydrogen atoms were added in standard geometry and, where needed, with rotational optimization of OH, SH, and NH+3 positions. Side-chain amide orientations were corrected where required by NH van der Waals clashes, as described in the accompanying paper. It was determined that, in general, methyl groups pack well in the default staggered conformation, except for the terminal methyl groups of methionine residues, which required rotational optimization. The distribution of serious clashes (i.e. non-H-bond overlap of >/=0.4 A) was studied as a function of resolution, alternate conformations, and temperature factor (B), leading to the decision that packing and other structural features would not be analyzed for residues in 'b' alternate conformations or with B-factors of 40 or above. At the level of the fine details analyzed here, structural accuracy improves quite significantly over the range from 1.7 to 1.0 A resolution. These high-resolution structures show impressively well-fitted packing interactions, with some regions thoroughly interdigitated and other regions somewhat sparser. Lower-resolution structures or model structures could undoubtedly be improved in accuracy by the incorporation of this additional information: for example, nucleic acid structures in non-canonical conformations are often very accurate for the bases and much less reliable for the backbone, whose conformation could be specified better by including explicit H atom geometry and contacts. The contact dots are an extremely sensitive method of finding problem areas, and often they can suggest how to make improvements. They can also provide explanations for structural features that have been described only as empirical regularities, which is illustrated by showing that the commonest rotamer of methionine (a left-handed spiral, with all chi values near -60 degrees) is preferred because it provides up to five good H atom van der Waals contacts. This methodology is thus applicable in two different ways: (1) for finding and correcting errors in structure models (either experimental or theoretical); and (2) for analyzing interaction patterns in the molecules themselves.

Crystallography, X-Ray↗
PubMed1999

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.

Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide groups in a dataset of 100 unrelated, high-quality protein crystal structures at 0.9 to 1.7 A resolution. For the movable-H groups, each connected, closed set of local H-bonds was optimized for both H-bonds and van der Waals overlaps. In addition to the Asn/Gln "flips", this process included rotation of OH, SH, NH3+, and methionine methyl H atoms, flip and protonation state of histidine rings, interaction with bound ligands, and a simple model of water interactions. However, except for switching N and O identity for amide flips (or N and C identity for His flips), no non-H atoms were shifted. Even in these very high-quality structures, about 20 % of the Asn/Gln side-chains required a 180 degrees flip to optimize H-bonding and/or to avoid NH2 clashes with neighboring atoms (incorporating a conservative score penalty which, for marginal cases, favors the assignment in the original coordinate file). The programs Reduce, Probe, and Mage provide not only a suggested amide orientation, but also a numerical score comparison, a categorization of the marginal cases, and a direct visualization of all relevant interactions in both orientations. Visual examination allowed confirmation of the raw score assignment for about 40 % of those Asn/Gln flips placed within the "marginal" penalty range by the automated algorithm, while uncovering only a small number of cases whose automated assignment was incorrect because of special circumstances not yet handled by the algorithm. It seems that the H-bond and the atomic-clash criteria independently look at the same structural realities: when both criteria gave a clear answer they agreed every time. But consideration of van der Waals clashes settled many additional cases for which H-bonding was either absent or approximately equivalent for the two main alternatives. With this extra information, 86 % of all side-chain amide groups could be oriented quite unambiguously. In the absence of further experimental data, it would probably be inappropriate to assign many more than this. Some of the remaining 14 % are ambiguous because of coordinate error or inadequacy of the theoretical model, but the great majority of ambiguous cases probably occur as a dynamic mix of both flip states in the actual protein molecule. The software and the 100 coordinate files with all H atoms added and optimized and with amide flips corrected are publicly available.

Algorithms↗
PubMed1999

Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.

Previous rotamer libraries showed little significant clustering for asparagine chi2 or glutamine chi3 values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at </=1.7 A resolution with <50% homology and <30 clashes per thousand atoms (atomic overlap >/=0.4 A). All H atoms were added and optimized, and amide orientation was flipped by 180 degrees if required by H bonding or atomic clashes. A side chain was included only if its amide orientation was clearly determined and if no atom had a B factor >/=40, alternate conformation, or severe clash; that selection process yielded 1,490 Asn and 863 Gln side chains. Clear clustering was observed for Asn chi2 and Gln chi3 (except when Gln chi2 is trans). For Gln, five major and four minor rotamers cover 87% of examples. For Asn, there are seven backbone-independent rotamers covering 94% of examples plus rotamers specified for strictly alpha-helical, beta, and left-handed (+phi) Asn. Although the strongest influence on chi angles is avoidance of atomic clashes (especially with the NH2 hydrogens), some Asn or Gln rotamers are influenced by favorable van der Waals contacts and others by specific local H-bond patterns.

Asparagine↗
PubMed1998

Nutrition and osteochondrosis.

Developmental orthopedic disease is a group of musculoskeletal disorders that occur in growing animals (most commonly fast growing, large breed dogs). Osteochondritis dissecans and canine hip dysplasia are the overwhelming majority of the diagnoses in those musculoskeletal problems with a possible nutritional-related etiology. Nutritional management alone will not completely control osteochondrosis or any of the developmental bone diseases. However, osteochondrosis and other developmental orthopedic diseases can be influenced during growth by feeding technique and nutrient profile. Dietary deficiencies are of minimal concern in this age of commercial foods specifically prepared for young, growing dogs. The potential for harm is in overnutrition from excess consumption and over supplementation.

Animal Nutritional Physiological Phenomena↗
PubMed1998

Serum markers of bone metabolism in dogs.

OBJECTIVE: To establish reference values for a panel of serum markers of bone turnover in dogs of various ages. ANIMALS: Dogs in 4 age groups (0 to 1 year; 1 to 2 years; 3 to 7 years; > 8 years). PROCEDURE: Serum concentrations of the carboxyterminal propeptide of type-I procollagen (PICP) and the aminoterminal propeptide of type-I procollagen (PINP), both markers of type-I collagen synthesis (hence, bone formation), were measured by use of commercial human radioimmunoassay kits. Serum concentrations of the carboxyterminal cross-linked telopeptide of type-I collagen (ICTP), a marker for type-I collagen breakdown (hence, bone resorption), also were measured by use of a commercial human radioimmunoassay kit. Serum osteocalcin (OC) concentrations and alkaline phosphatase (ALP) isoenzyme activities were measured by use of techniques developed specifically for dogs. RESULTS: As expected, the highest values for all of the markers were found in young dogs (< 12 months old). Concentrations of OC and ICTP decreased with age, and were lowest in dogs > 8 years old. Total ALP and bone-specific ALP activities initially decreased with age, then increased in dogs > 8 years old. CONCLUSIONS AND CLINICAL RELEVANCE: Serum markers of bone turnover may be useful diagnostic and prognostic tools for management of dogs with musculoskeletal disorders.

Aging↗
PubMed1997

Nutritional management of osteoarthritis.

Nutrition can influence developmental orthopedic diseases and the inflammatory process of arthritis. Developmental skeletal disease is a group of skeletal abnormalities that primarily affect fast-growing, large-breed dogs. Nutrient excesses (calcium and energy) and rapid growth (overfeeding and excess energy) are known risk factors. Inflammation can be directly or indirectly affected by nutritional influences. A direct effect can be achieved by modulating the immune response and inflammatory process with fatty acids. Weight control can indirectly influence the degenerative joint disease process by reducing the stresses on the joint.

Animal Nutritional Physiological Phenomena↗
PubMed1997

Interval breast cancers in the NHS Breast Screening Programme: does the current definition exclude too many?

OBJECTIVES: To examine the impact of the definition of interval breast cancers on interval cancer rates arising from the prevalent (first) screening round. DESIGN: Interval breast cancers arising from the prevalent (first) screening round at the Warwickshire, Solihull and Coventry Breast Screening Unit (17 April 1989 to 31 March 1992) were identified by comparison of data held at the unit with records at the West Midlands Cancer Intelligence Unit. Exclusion criteria used in National statistics were applied to this sample to quantify their impact on achieved interval cancer rates. The round lengths experienced by individual women at the unit were determined from the prevalent and incident invitation dates for 155 women with incident (re-screen) breast cancers detected in the second round. SETTING: Warwickshire, Solihull and Coventry Breast Screening Unit. SUBJECTS: 59,017 women screened between 17 April 1989 and 31 March 1992 with a negative screening result and 155 women with incident screen detected cancers. RESULTS: A total of 278 interval cancers were identified, giving an overall rate from the prevalent screening round of 47.1/10,000 women screened. Of these, 213 met the criteria used in the definition of interval cancers for National statistics and were termed "core" interval cancers. The overall "core" interval rate was 36.1/ 10,000 women screened, similar to interval cancer rates found in the north west of United Kingdom. Thus applying commonly used exclusion criteria produced a 23.4% reduction in the apparent interval cancer rate, with the largest decrease resulting from the exclusion of cancers arising at 36 months or more from the last screen. CONCLUSIONS: The exclusion criteria used in the definition of interval cancers have a significant impact on observed interval cancer rates. Of particular concern is the exclusion in the current National definitions of cancers arising at 36 months or more from the last screen, which may mask a problem with significant implications for the success of the NHSBSP.

Breast Neoplasms↗