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Biomedical subjects

J Bohr

Publications and source records attributed to J Bohr.

At least 37 records · Page 2Linked to original sources
PubMed1996

Relationship between protein structure and geometrical constraints.

We evaluate to what extent the structure of proteins can be deduced from incomplete knowledge of disulfide bridges, surface assignments, secondary structure assignments, and additional distance constraints. A cost function taking such constraints into account was used to obtain protein structures using a simple minimization algorithm. For small proteins, the approximate structure could be obtained using one additional distance constraint for each amino acid in the protein. We also studied the effect of using predicted secondary structure and surface assignments. The constraints used in this approach typically may be obtained from low-resolution experimental data. When using a cost function based on distances, half of the resulting structures will be mirrored, because the resulting structure and its mirror image will have the same cost. The secondary structure assignments were therefore divided into chirality constraints and distance constraints. Here we report that the problem of mirrored structures, in some cases, can be solved by using a chirality term in the cost function.

Protein Structure, Secondary↗
PubMed1996

Distance distributions in proteins: a six-parameter representation.

We present a statistical analysis of protein structures based on interatomic C alpha distances. The overall distance distributions reflect in detail the contents of sequence-specific substructures maintained by local interactions (such as alpha-helixes) and longer range interactions (such as disulfide bridges and beta-sheets). We also show that a volume scaling of the distances makes distance distributions for protein chains of different length superimposable. Distance distributions were also calculated specifically for amino acids separated by a given number of residues. Specific features in these distributions are visible for sequence separations of up to 20 amino acid residues. A simple representation, which preserves most of the information in the distance distributions, was obtained using six parameters only. The parameters give rise to canonical distance intervals and when predicting coarse-grained distance constraints by methods such as data-driven artificial neural networks, these should preferably be selected from these intervals. We discuss the use of the six parameters for determining or reconstructing 3-D protein structures.

Amino Acid Sequence↗
PubMed1996

Autoantibodies and immunoglobulins in collagenous colitis.

BACKGROUND: The aetiology and pathogenesis of collagenous colitis are unknown. Autoimmunity has been suggested, but no serological findings have supported such a theory. AIMS AND METHODS: Serum from 38 collagenous colitis patients and 38 matched healthy controls was analysed for autoantibodies--that is, antinuclear antibodies, antineutrophil cytoplasmic antibodies, smooth muscle and mitochondrial antibodies, rheumatoid factor and antibodies to thyroglobulin and microsomal antigen, together with antibodies to endomysium, gliadin, and cardiolipin. The serum values of IgA, IgG, IgM, and IgG-subclasses, and complement factors C3 and C4 were also determined. RESULTS: In patients with collagenous colitis the mean value of IgM was significantly increased 2.5 g/l (95% CI; 1.9, 3.2) compared with 1.4 g/l (95% CI; 1.2, 1.7) in controls (p = 0.002). Antinuclear antibodies occurred in nine of 38 patients compared with three of 38 controls, this difference was not statistically significant (p = 0.11). The results of all other immunoglobulins, complement factors, and specific antibodies showed no statistical difference between patients and controls. CONCLUSIONS: No firm evidence for an autoimmune genesis in collagenous colitis is found in this study, although the findings of a positive ANA-titre in some patients and an increased IgM level might give some support for this hypothesis.

Adult↗
PubMed1996

Collagenous colitis: a retrospective study of clinical presentation and treatment in 163 patients.

BACKGROUND: Data on collagenous colitis have been based on a limited number of patients. AIMS: To obtain more information on this disease from a register set up at Orebro Medical Center Hospital. PATIENTS AND METHODS: Twenty five Swedish hospitals have contributed to this patient register, which comprises 163 histopathologically verified cases. Clinical data were retrospectively analysed. RESULTS: Collagenous colitis followed a chronic intermittent course in most cases (85%) with a sudden onset in 42%. Symptoms were chronic watery diarrhoea, often nocturnal (27%), abdominal pain (41%), and weight loss (42%). Sixty six patients (40%) had one or more associated diseases. Routine laboratory data were mostly normal. The median age at diagnosis was 55 (range 16-86) years, but 25% of the patients were younger than 45 years. Seven patients died of unrelated diseases. The response rate for sulphasalazine was 59%, and 50% and 40% for mesalazine and olsalazine. Prednisolone was most effective with a response rate of 82%, but the required dose was often high and the effect was not sustained after withdrawal. Antibiotics were efficient in 63%. Cholestyramine and loperamide had response rates of 59% and 71% respectively. CONCLUSIONS: Collagenous colitis follows a chronic continuous course. Symptoms can be socially disabling, but the disease does not seem to have a malignant potential. A plan for the treatment of a newly diagnosed patient with collagenous colitis is proposed.

Adolescent↗
PubMed1995

[The clinical consequence of blood culture results].

The effect of blood culture results on patient management in a department of internal medicine was analyzed retrospectively. In a series of 300 patients 538 blood cultures were taken. Fifty-four (10%) of blood cultures from 44 of the 300 patients were positive, but in 16 patients cultures yielded organisms considered to be contaminants. Only 28 (9.3%) patients' cultures showed growth of clinically significant pathogenic bacteria. Antimicrobial chemotherapy was instituted in 234 (78%) patients before culture results were available. For only 21 (7%) patients did the result of the blood culture have any therapeutic consequences. The high frequency and lack of impact of negative blood cultures demands a more appropriate protocol for blood culturing, and guidelines are suggested.

Adult↗
PubMed1995

Collagenous colitis and fecal stream diversion.

BACKGROUND & AIMS: The cause of collagenous colitis is unknown. Data on treatment are sparse, and surgical therapy has not been reported. This study reports results of surgical therapy for collagenous colitis. METHODS: Nine women with unresponsive collagenous colitis underwent surgery. An ileostomy was performed as the first procedure in 8 patients, and a sigmoidostomy using the Hartmann procedure was performed in 1 patient. RESULTS: Preoperatively, all patients had severe diarrhea, and the median thickness of the subepithelial collagenous layer was 20 microns (range, 10-40 microns). Postoperatively, diarrhea ceased in all patients, and the collagen layer was reduced to 2 microns (range, 0-10 microns). Clinical symptoms and the abnormal collagen layer recurred after restoration of intestinal continuity. After the Hartmann procedure, the collagen layer remained abnormally thickened up to 30 microns in the proximal colon but was normalized in the excluded rectosigmoid colon. One year later, the sigmoidostomy was replaced by a split ileostomy; at follow-up, the collagen layer was normal in the whole colon. CONCLUSIONS: Fecal stream diversion induced clinical and histopathologic remission in collagenous colitis. After closure of the ostomy, clinical symptoms and the abnormal collagen layer recurred. The findings strongly indicate that a noxious luminal factor is of pathogenetic importance. In older patients with medically resistant disease, a split ileostomy may be the therapeutic procedure of choice.

Adult↗
PubMed1995

Collagenous colitis in Orebro, Sweden, an epidemiological study 1984-1993.

The incidence and prevalence of collagenous colitis are unknown. An epidemiological study was undertaken between 1984-93. All patients living in the immediate catchment area of Orebro Medical Center Hospital with the diagnosis collagenous colitis were identified. Biopsy specimens classified as unspecific intestinal fibrosis were re-examined to identify cases not correctly diagnosed at first. Medical records were scrutinised and colorectal biopsy specimens re-evaluated. Thirty patients with collagenous colitis were diagnosed during the study period. The female:male ratio was 9:1. The median age at diagnosis was 64 (28-78) years. The prevalence at 31 December 1993, was 15.7/10(5) inhabitants (95% CI; 9.8 to 21.6/10(5)). The mean annual incidence during the period 1984-93 was 1.8/10(5) inhabitants (95% CI; 1.2 to 2.4/10(5)). A peak incidence was found in women 70-79 years old. Collagenous colitis occurs mainly in middle aged women, and the frequency is higher than earlier anticipated. The prevalence and incidence is similar to primary biliary cirrhosis. In women 70-79 years of age, the incidence for collagenous colitis approaches the incidence for ulcerative colitis.

Adult↗
PubMed1993

Protein structures from distance inequalities.

A computer method for folding protein backbones from distance inequalities is presented. It involves an algorithm that uses a novel approach for handling inequalities through the minimization of a continuous energy function. Tests of the folding algorithm have been carried out on a small protein, the 6PTI (bovine pancreatic trypsin inhibitor) with 56 amino acid residues, and on a medium-size protein, the 1TRM (rat trypsin) with 223 amino acid residues. Reconstructions based on a real-valued distance matrix led to folded three-dimensional structures with root-mean-square values of 0.04 A when compared with the crystallographic data. The obtained root-mean-square measures were of the order of 1 A, when distance inequalities were used for the reconstruction. Subsequently, the folding approach has been applied to distance inequalities predicted by neural network techniques that use the amino acid sequence as the only input. The inaccuracy in the inequalities predicted by the neural network was the reason for the root-mean-square value of 5.2 A. An error analysis of the method for reconstruction was performed and showed that no more than 3% inaccurate distance inequalities could be corrected for. Finally, a simple technique for root-mean-square comparisons of different protein structures is discussed.

Algorithms↗