Mining Clinical Notes for Physical Rehabilitation Exercise Information: Natural Language Processing Algorithm Development and Validation Study

BACKGROUND

The rehabilitation of a patient who had a stroke requires precise, personalized treatment plans. Natural language processing (NLP) offers the potential to extract valuable exercise information from clinical notes, aiding in the development of more effective rehabilitation strategies.

OBJECTIVE

This study aims to develop and evaluate a variety of NLP algorithms to extract and categorize physical rehabilitation exercise information from the clinical notes of patients who had a stroke treated at the University of Pittsburgh Medical Center.

METHODS

A cohort of 13,605 patients diagnosed with stroke was identified, and their clinical notes containing rehabilitation therapy notes were retrieved. A comprehensive clinical ontology was created to represent various aspects of physical rehabilitation exercises. State-of-the-art NLP algorithms were then developed and compared, including rule-based, machine learning-based algorithms (support vector machine, logistic regression, gradient boosting, and AdaBoost) and large language model (LLM)-based algorithms (ChatGPT [OpenAI]). The study focused on key performance metrics, particularly F1-scores, to evaluate algorithm effectiveness.

RESULTS

The analysis was conducted on a data set comprising 23,724 notes with detailed demographic and clinical characteristics. The rule-based NLP algorithm demonstrated superior performance in most areas, particularly in detecting the "Right Side" location with an F1-score of 0.975, outperforming gradient boosting by 0.063. Gradient boosting excelled in "Lower Extremity" location detection (F1-score: 0.978), surpassing rule-based NLP by 0.023. It also showed notable performance in the "Passive Range of Motion" detection with an F1-score of 0.970, a 0.032 improvement over rule-based NLP. The rule-based algorithm efficiently handled "Duration," "Sets," and "Reps" with F1-scores up to 0.65. LLM-based NLP, particularly ChatGPT with few-shot prompts, achieved high recall but generally lower precision and F1-scores. However, it notably excelled in "Backward Plane" motion detection, achieving an F1-score of 0.846, surpassing the rule-based algorithm's 0.720.

CONCLUSIONS

The study successfully developed and evaluated multiple NLP algorithms, revealing the strengths and weaknesses of each in extracting physical rehabilitation exercise information from clinical notes. The detailed ontology and the robust performance of the rule-based and gradient boosting algorithms demonstrate significant potential for enhancing precision rehabilitation. These findings contribute to the ongoing efforts to integrate advanced NLP techniques into health care, moving toward predictive models that can recommend personalized rehabilitation treatments for optimal patient outcomes.

Conventional oxygen therapy versus CPAP as a ceiling of care in ward-based patients with COVID-19: a multi-centre cohort evaluation

BACKGROUND

Continuous positive airway pressure (CPAP) therapy is commonly used for respiratory failure due to severe COVID-19 pneumonitis, including in patients deemed not likely to benefit from invasive mechanical ventilation (nIMV). Little evidence exists demonstrating superiority over conventional oxygen therapy, whilst ward-level delivery of CPAP presents practical challenges. We sought to compare clinical outcomes of oxygen therapy versus CPAP therapy in patients with COVID-19 who were nIMV.

METHODS

This retrospective multi-centre cohort evaluation included patients diagnosed with COVID-19 who were nIMV, had a treatment escalation plan of ward-level care and clinical frailty scale ≤ 6. Recruitment occurred during the first two waves of the UK COVID-19 pandemic in 2020; from 1^st March to May 31^st, and from 1^st September to 31^st December. Patients given CPAP were compared to patients receiving oxygen therapy that required FiO₂ ≥0_.4 for more than 12 hours at hospitals not providing ward-level CPAP. Logistic regression modelling was performed to compare 30-day mortality between treatment groups, accounting for important confounders and within-hospital clustering.

FINDINGS

Seven hospitals provided data for 479 patients during the UK COVID-19 pandemic in 2020. Overall 30-day mortality was 75.6% in the oxygen group (186/246 patients) and 77.7% in the CPAP group (181/233 patients). A lack of evidence for a treatment effect persisted in the adjusted model (adjusted odds ratio 0.84 95% CI 0.57-1.23, p=0.37). 49.8% of patients receiving CPAP-therapy (118/237) chose to discontinue it.

INTERPRETATION

No survival difference was found between using oxygen alone or CPAP to treat patients with severe COVID-19 who were nIMV. A high patient-initiated discontinuation rate for CPAP suggests a significant treatment burden. Further reflection is warranted on the current treatment guidance and widespread application of CPAP in this setting.

FUNDING

L Pearmain is supported by the MRC (MR/R00191X/1). TW Felton is supported by the NIHR Manchester Biomedical Research Centre.

Using the Gene Ontology to Annotate Key Players in Parkinson's Disease

The Gene Ontology (GO) is widely recognised as the gold standard bioinformatics resource for summarizing functional knowledge of gene products in a consistent and computable, information-rich language. GO describes cellular and organismal processes across all species, yet until now there has been a considerable gene annotation deficit within the neurological and immunological domains, both of which are relevant to Parkinson’s disease. Here we introduce the Parkinson’s disease GO Annotation Project, funded by Parkinson’s UK and supported by the GO Consortium, which is addressing this deficit by providing GO annotation to Parkinson’s-relevant human gene products, principally through expert literature curation. We discuss the steps taken to prioritise proteins, publications and cellular processes for annotation, examples of how GO annotations capture Parkinson’s-relevant information, and the advantages that a topic-focused annotation approach offers to users. Building on the existing GO resource, this project collates a vast amount of Parkinson’s-relevant literature into a set of high-quality annotations to be utilized by the research community.

The Oral Fluid MEMS/NEMS Chip (OFMNC): diagnostic and translational applications

The ability to monitor health status, disease onset and progression, and treatment outcome through non-invasive means is a most desirable goal in health-care promotion and delivery. There are three prerequisites for this goal to be realized: specific biomarkers associated with a health or disease state, a non-invasive approach to detect and monitor the biomarkers, and the technologies to discriminate between and among the biomarkers. We present a roadmap to achieve these goals using oral fluids as the diagnostic medium to scrutinize the health and/or disease status of individuals. This is an ideal opportunity to bridge state-of-the-art micro-/nano-electromechanical system (MEMS/NEMS) sensors to oral fluid for diagnostic applications. As the "mirror of body", oral fluid is a perfect medium to be explored for health and disease surveillance. The translational applications and opportunities are enormous.

Potential of a tropical subsurface constructed wetland to remove phenol from pre-treated pulp and papermill wastewater

The capacity of a pilot project subsurface flow constructed wetland in the tropics to remove phenol from pre-treated pulp and paper mill wastewater was studied under varying hydraulic retention times (HRT) with batch loading. Initial 15 months results indicate that removal efficiencies for phenol were variable but on average reached 60% at 5-day HRT and 77% at 3-day HRT. It was thought that the longer retention time might have caused oxygen and nutrient deficiencies, which may have reduced removal performance. Although phenol was sometimes not detectable in the wetland outflow, on average values over the experimental period did not meet set national guidelines. In the ongoing study, the impact of varying hydraulic retention time and/or loading rate on the removal of phenols will be evaluated and the main removal process established.

The effect of wastewater discharge on biomass production and nutrient content of Cyperus papyrus and Miscanthidium violaceum in the Nakivubo wetland, Kampala, Uganda

The nutrient content of representative plant parts and biomass production in the Nakivubo wetland, correlation of these with the wastewater flow patterns and determination of nutrient uptake, storage and biomass production of Cyperus papyrus (papyrus) and Miscanthidium violaceum was studied. On average papyrus vegetation under the influence of wastewater had higher nutrient content in the above ground biomass (1.6% N and 0.23% P on dry weight basis) than those not affected (0.98% N and 0.18% P). The biomass varied between 3,529-5,844 g/m2 and 883-1,156 g/m2 in the two respective sites. The juvenile plants of papyrus and Miscanthidium had higher concentrations of P and N in their organs compared to the mature ones. Considering the nutrients stored by the dominant vegetation and the current flow patterns of wastewater in the Nakivubo wetland, harvesting of the above ground biomass once a year, would remove 7.7% of the N input and 15.8% of the P input of the annual total load entering the wetland. However, if the wetland is bio-manipulated and the wastewater flow distributed over the whole wetland, up to 70% nitrogen and 76% phosphorus would be removed by harvesting above ground papyrus biomass.

[Jejunal volvulus secondary to torsion of a pedunculated subserosal lipoma: CT diagnosis of a rare cause of bowel obstruction]

The authors report a case of a bowel obstruction secondary to jejunal volvulus in relation with the torsion of a large pedunculated subserosal lipoma. To our knowledge, no such case has ever been reported. The differential diagnosis of intra-abdominal fatty tumors and differential diagnosis of such tumors in association with small bowel obstruction will be discussed. Small bowel volvulus secondary to torsion of a subserosal lipoma should be considered when CT shows a large encapsulated fatty tumor in a patient with suggestion of mechanical small bowel obstruction.

A radiation hybrid map of mouse genes

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, the Medical Research Council UK Mouse Genome Centre, and the National Center for Biotechnology Information. The map contains 11,109 genes, screened against the T31 RH panel and positioned relative to a reference map containing 2,280 mouse genetic markers. It includes 3,658 genes homologous to the human genome sequence and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome.

Genetic, physical, and phenotypic characterization of the Del(13)Svea36H mouse

The Del(13)Svea36H deletion was recovered from a radiation mutagenesis experiment and represents a valuable resource for investigating gene content and function at this region of mouse Chromosome (Chr) 13 and human Chr 6p21.3-23 and 6p25. In this paper we examine the physical extent of chromosome loss and construct an integrated genetic and radiation hybrid map of the deleted segment. We show that embryos which are homozygous for the deletion die at or before implantation and that heterozygotes are subviable, with a substantial proportion of carriers dying after mid-gestation but before weaning. The majority of viable carriers exhibit a variety of phenotypes including decreased size, eyes open at birth, corneal opacity, tail kinks, and craniofacial abnormalities. Both the heterozygous viability and the penetrance of the visible phenotypes vary with genetic background.

High-resolution quantitative trait locus mapping for body weight in mice by recombinant progeny testing

A major obstacle to the positional cloning of quantitative trait loci (QTLs) lies in resolving genetic factors whose allelic effects are blurred by environmental and background genetic variation. We investigate a fine-mapping approach that combines the use of an interval-specific congenic strain with progeny testing of recombinants for markers flanking a QTL. We apply the approach to map a murine QTL with an approximately 20% effect on growth rate by progeny testing 39 recombinants in a 12 cM region of the X chromosome. We use a likelihood analysis in an attempt to maximize the information on QTL map location and effect. The major X-linked effect is mapped to an approximately 2 cM region flanked by markers about 5 cM apart, outside which LOD support for the QTL drops extremely steeply by about 80. Nearly unambiguous assignment of the QTL genotypic state is obtained for each recombinant. The resolution of individual recombinants in the region is therefore sufficiently high to facilitate the positional cloning of the locus, although progress has been hampered because the genomic region containing the QTL shows an exceptionally low level of polymorphism in comparison with recent studies.

The impact of alum discharges on a natural tropical wetland in Uganda

Alum sludge discharge effects on a natural wetland on the shores of Lake Victoria at Gaba in Uganda has been investigated. The water quality in the swamp, the sediment chemistry and plant growth and productivity were monitored. The subsequent application of alum sludge discharges shows no immediate, noticeable, adverse overall effects on the water quality and sediment chemistry. A distinct effect on plant productivity was noted in Cyperus papyrus L. the dominant macrophyte in the Gaba swamp resulting in a low productivity rate of 5.1 g/m2 d and the apparent phasing out of this macrophyte in the swamp. Phragmites mauritianus (Kunth) exhibited better tolerance to alum sludge. Clear indications are cited of the ecosystem degrading and cumulative effects being marked over a longer time frame.

[Contrast-enhanced MRA of the carotid arteries using 0.5 Tesla: comparison with selective digital angiography]

PURPOSE

To assess the feasability, the imaging quality and the effectiveness of contrast-enhanced MRA (CE MRA) using a 0.5 Tesla MR unit in the evaluation of internal carotid artery (ICA) stenosis. Materials and Methods. 29 patients underwent CE MRA and selective digital substraction angiography (DSA). All data were reviewed in a blinded fashion by 2 independant observers. Imaging quality was graded as good, moderate but interpretable, and insufficient. Stenosis was graded according to the NASCET classification from grade 1 to 4, with the following thresholds:<30%,<70%,<99% and occlusion. Inter and intra- observer agreement was evaluated using the kappa index.

RESULTS

Imaging quality was good for 79 arteries, moderate for 24 and insufficient for 13 (k MRA=0.72 and 0.64 respectively for the right and left ICAs). Interobserver agreement was good with values for right/left ICA of 0.84/0.94, 0.72/0.74 respectively for CE-MRA and DSA. For the comparison between CE MRA and DSA, agreement was also good, with values of 0.74 and 0.64 for both readers. Sensitivity of CE MRA in the detection of hemodynamically significant stenosis (>70%) was of 0.95 and 0.94 and specifity of 0.91 and 0.89 respectively for reader n degrees 1 and reader n degrees 2.

CONCLUSION

CE MRA using a 0.5T MR unit is a valuable technique in the evaluation of ICA stenosis.

Role of genetic resistance in invasive pneumococcal infection: identification and study of susceptibility and resistance in inbred mouse strains

From a panel of nine inbred mice strains intranasally infected with Streptococcus pneumoniae type 2 strain, BALB/c mice were resistant and CBA/Ca and SJL mice were susceptible to infection. Further investigation revealed that BALB/c mice were able to prevent proliferation of pneumococci in the lungs and blood, whereas CBA/Ca mice showed no bacterial clearance. Rapidly increasing numbers of bacteria in the blood was a feature of CBA/Ca but not BALB/c mice. In the lungs, BALB/c mice recruited significantly more neutrophils than CBA/Ca mice at 12 and 24 h postinfection. Inflammatory lesions in BALB/c mice were visible much earlier than in CBA/Ca mice, and there was a greater cellular infiltration into the lung tissue of BALB/c mice at the earlier time points. Our data suggest that resistance or susceptibility to intranasal pneumococci may have an association with recruitment and/or function of neutrophils.

What use is the human genome for understanding the mouse?

Having a working draft of the human genome sequence is proving invaluable to mouse genetic and genomic studies, providing a useful stepping-stone towards the finished sequence of the mouse genome.

Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression

Higher-order chromatin has been implicated in epigenetic gene control and in the functional organization of chromosomes. We have recently discovered mouse (Suv39h1) and human (SUV39H1) histone H3 lysine 9-selective methyltransferases (Suv39h HMTases) and shown that they modulate chromatin dynamics in somatic cells. We describe here the isolation, chromosomal assignment, and characterization of a second murine gene, Suv39h2. Like Suv39h1, Suv39h2 encodes an H3 HMTase that shares 59% identity with Suv39h1 but which differs by the presence of a highly basic N terminus. Using fluorescent in situ hybridization and haplotype analysis, the Suv39h2 locus was mapped to the subcentromeric region of mouse chromosome 2, whereas the Suv39h1 locus resides at the tip of the mouse X chromosome. Notably, although both Suv39h loci display overlapping expression profiles during mouse embryogenesis, Suv39h2 transcripts remain specifically expressed in adult testes. Immunolocalization of Suv39h2 protein during spermatogenesis indicates enriched distribution at the heterochromatin from the leptotene to the round spermatid stage. Moreover, Suv39h2 specifically accumulates with chromatin of the sex chromosomes (XY body) which undergo transcriptional silencing during the first meiotic prophase. These data are consistent with redundant enzymatic roles for Suv39h1 and Suv39h2 during mouse development and suggest an additional function of the Suv39h2 HMTase in organizing meiotic heterochromatin that may even impart an epigenetic imprint to the male germ line.

The NOD Idd9 genetic interval influences the pathogenicity of insulitis and contains molecular variants of Cd30, Tnfr2, and Cd137

Previous analyses of NOD mice have shown that some genes control the development of both insulitis and diabetes, while other loci influence diabetes without reducing insulitis. Evidence for the existence of a gene only influencing diabetes, Idd9 on mouse chromosome 4, is provided here by the development of a novel congenic mouse strain, NOD.B10 Idd9. NOD.B10 Idd9 mice display profound resistance to diabetes even though nearly all develop insulitis. Subcongenic analysis has demonstrated that alleles of at least three B10 genes, Idd9.1, Idd9.2, and Idd9.3 are required to produce Idd9-mediated diabetes resistance. Candidate genes with amino acid differences between the NOD and B10 strains have been localized to the 5.6 cM Idd9.2 interval (Tnfr2, Cd30) and to the 2.0 cM Idd9.3 interval (Cd137).

Mouse as the measure of man?

The humble house mouse's cohabitation with humans has been noted since the birth of agriculture, about 10 000 years ago, in the fertile flood plains of the Middle East. In recent times, however, the mouse has been elevated from pest to model for the study of human health and disease. Recent genomics and genetics initiatives will ensure the continued growth of the house mouse as a disease model.

The effect of ageing on parenchymal cell populations in adult female mouse submandibular gland

The submandibular gland shows an array of responses that accompany ageing, which are usually modest. However, the submandibular acinar-cell mucin shows a substantial decline in total amount per gland. In the submandibular gland, there is also a loss of secretory parenchyma. A number of factors that could influence either parenchymal loss or a change in its cellular composition were examined in three ages of adult female mice. The goal was to see if there are ageing-related cellular changes that might have an effect on mucin production or secretion. The factors examined included DNA, protein, rates of cell division and apoptosis, cell volume and cellular composition of the parenchymal population. The parenchymal cell composition showed significant differences during ageing, with a substantial decrease in the percentage of acinar cells and increases in the percentage of both types of ductal cell components. This decline in the proportion of acinar cells in the parenchyma also reflected an overall reduction in the total number of acinar cells in the gland. Thus, the change in proportions of cells may potentially be a direct cause of the ageing-related decline in the submandibular acinar-cell mucin. The alteration in cellular composition was not attributable to changes in the cell-division indices; however, there was an increased rate of apoptosis for acinar cells that was significantly different between 3 and 28 months. The apoptotic rate doubled for acinar cells but showed no significant change in ductal cells. This selective change in the rate of apoptosis with ageing suggests that it is one of the main reasons for the decline in the proportion of acinar cells in the submandibular gland.

Comparative genome sequence analysis of the Bpa/Str region in mouse and Man

The progress of human and mouse genome sequencing programs presages the possibility of systematic cross-species comparison of the two genomes as a powerful tool for gene and regulatory element identification. As the opportunities to perform comparative sequence analysis emerge, it is important to develop parameters for such analyses and to examine the outcomes of cross-species comparison. Our analysis used gene prediction and a database search of 430 kb of genomic sequence covering the Bpa/Str region of the mouse X chromosome, and 745 kb of genomic sequence from the homologous human X chromosome region. We identified 11 genes in mouse and 13 genes and two pseudogenes in human. In addition, we compared the mouse and human sequences using pairwise alignment and searches for evolutionary conserved regions (ECRs) exceeding a defined threshold of sequence identity. This approach aided the identification of at least four further putative conserved genes in the region. Comparative sequencing revealed that this region is a mosaic in evolutionary terms, with considerably more rearrangement between the two species than realized previously from comparative mapping studies. Surprisingly, this region showed an extremely high LINE and low SINE content, low G+C content, and yet a relatively high gene density, in contrast to the low gene density usually associated with such regions.

Congenic mapping of the type 1 diabetes locus, Idd3, to a 780-kb region of mouse chromosome 3: identification of a candidate segment of ancestral DNA by haplotype mapping

Type 1 diabetes in the nonobese diabetic (NOD) mouse arises as a consequence of T cell-mediated destruction of the insulin-producing beta cells of the pancreas. Although little is known of the events that initiate and subsequently drive beta-cell destruction it is clear that the entire process is under complex genetic control. At present 19 loci have been mapped that influence the development of diabetes either at the level of initiation of insulitis or at the level of progression from insulitis to overt diabetes, or both. Previously, we have mapped one of these loci, Idd3, to a 0.35-cM interval on proximal mouse chromosome 3. In the present study we have narrowed the map position of this locus to an interval of 0.15 cM by a combination of novel congenic strains and an ancestral haplotype analysis approach. We have constructed a physical contig in bacterial artificial chromosome (BAC) clones across the minimal interval. Restriction mapping of the BAC contig placed the maximum size of the Idd3 interval at 780 kb between the markers D3Nds36 and D3Nds76. To refine further the Idd3 interval we developed a series of novel single nucleotide polymorphisms (SNPs) and carried out haplotype analysis on DNA from mouse strains known to carry either Idd3 susceptibility or protective alleles. This haplotype analysis identified a 145-kb segment of ancestral DNA between the microsatellite marker D3Nds6 and the SNP 81.3. One haplotype of this ancestral segment of DNA is found in mouse strains carrying an Idd3 susceptibility allele and another is found in mouse strains carrying an Idd3 protective allelle. Within the 780-kb congenically defined interval this 145-kb segment represents the most likely location for Idd3. The Il2 gene, which encodes the cytokine interleukin 2 (IL2), maps to this interval and is a strong candidate for Idd3. To investigate whether sequence variation exists in the promoter region of the Il2 gene, which might alter its expression, we sequenced the promoter region of the Il2 gene from mouse strains carrying either an Idd3 susceptibility or resistance allele. Two sequence variants were identified, neither of which fell in known regulatory elements within the Il2 promoter. In agreement with this observation steady-state Il2 mRNA levels showed no variation between susceptible and resistant mouse strains. These data suggest that the profound protection from diabetes seen in congenic mice carrying an Idd3 protective allele is unlikely to be due to differences in the level of expression of the Il2 gene. Instead, all of the current data support our hypothesis that Idd3 corresponds to amino acid variation at the amino terminus of Il2.

A YAC-based physical map of the mouse genome

A physical map of the mouse genome is an essential tool for both positional cloning and genomic sequencing in this key model system for biomedical research. Indeed, the construction of a mouse physical map with markers spaced at an average interval of 300 kb is one of the stated goals of the Human Genome Project. Here we report the results of a project at the Whitehead Institute/MIT Center for Genome Research to construct such a physical map of the mouse. We built the map by screening sequenced-tagged sites (STSs) against a large-insert yeast artificial chromosome (YAC) library and then integrating the STS-content information with a dense genetic map. The integrated map shows the location of 9,787 loci, providing landmarks with an average spacing of approximately 300 kb and affording YAC coverage of approximately 92% of the mouse genome. We also report the results of a project at the MRC UK Mouse Genome Centre targeted at chromosome X. The project produced a YAC-based map containing 619 loci (with 121 loci in common with the Whitehead map and 498 additional loci), providing especially dense coverage of this sex chromosome. The YAC-based physical map directly facilitates positional cloning of mouse mutations by providing ready access to most of the genome. More generally, use of this map in addition to a newly constructed radiation hybrid (RH) map provides a comprehensive framework for mouse genomic studies.

The gene mutated in bare patches and striated mice encodes a novel 3beta-hydroxysteroid dehydrogenase

X-linked dominant disorders that are exclusively lethal prenatally in hemizygous males have been described in human and mouse. None of the genes responsible has been isolated in either species. The bare patches (Bpa) and striated (Str) mouse mutations were originally identified in female offspring of X-irradiated males. Subsequently, additional independent alleles were described. We have previously mapped these X-linked dominant, male-lethal mutations to an overlapping region of 600 kb that is homologous to human Xq28 (ref. 4) and identified several candidate genes in this interval. Here we report mutations in one of these genes, Nsdhl, encoding an NAD(P)H steroid dehydrogenase-like protein, in two independent Bpa and three independent Str alleles. Quantitative analysis of sterols from tissues of affected Bpa mice support a role for Nsdhl in cholesterol biosynthesis. Our results demonstrate that Bpa and Str are allelic mutations and identify the first mammalian locus associated with an X-linked dominant, male-lethal phenotype. They also expand the spectrum of phenotypes associated with abnormalities of cholesterol metabolism.

[Radiologic aspects of infarction of the appendix epiploica]

Clinical, US, CT and MR findings were reviewed in 5 patients with primary epiploic appendagitis (3 men, 2 women, mean age 38 years, age range 29-62 years) seen between December 1994 and December 1997. Diagnosis was reached in all cases with CT, with US in 3 and with MR in 1. Follow-up CT was performed in 2 cases and clinical follow-up in 4. One patient underwent surgery. Initial US, CT or MR examinations revealed a fatty oval-shaped nodule located anteriorly or anterolaterally to the left colon. The greater diameter ranged from 20 to 30 mm. Perinodular lesions with strands of periappendicular fat and thickened parietal peritoneum were visualized in all cases without any other inflammatory process in the abdomen. Symptoms resolved within 4 days in all patients. Signs of fatty inflammatory processes resolved in the 2 patients who had follow-up CTs. Primary epiploic appendagitis has characteristic US, CT and MR features which help guide medical treatment.

[Diagnostic imaging of idiopathic segmental infarct of the greater omentum. Diagnostic and physiopathologic considerations]

Primary infarction of the greater omentum is a rare cause of acute abdominal syndrome. Rate of occurrence may nevertheless be underestimated. We report a series of six cases observed over a 30-month period with US and CT imaging. We assessed early signs and their course. CT-scans depicted fatty oval-shaped masses below the right anterior or anterolateral parietal wall, associated with a thickening of the anterior parietal peritoneum, explaining symptom pathogenesis. Torsion can be identified, but has no specific impact on prognosis. Follow-up CT scan may evidence spontaneous, but sometimes slow, resolution.

Localization of two insulin-dependent diabetes (Idd) genes to the Idd10 region on mouse chromosome 3

Multiple genes control the development of autoimmune diabetes both in humans and in the nonobese diabetic (NOD) strain of mouse. Previously, three insulin-dependent diabetes (Idd) genes, Idd3, Idd10, and Idd17, were localized to mouse Chromosome (Chr) 3. The B10- or B6-derived resistance alleles at Idd10 and Idd3 together provide the NOD mouse with nearly complete protection from diabetes. In the present study, the 10.2-cM region encoding Idd10 was defined further with newly developed congenic strains. A locus, located in the centromeric 2.1 cM of the 10.2 cM region, contributed to the Idd10 trait. However, this locus did not account for the full effect of Idd10, suggesting the presence of a second gene in the distal portion of the 10.2-cM region. This second gene is designated as Idd18 and is localized to a 5.1-cM region. The resolution of the originally defined Idd3 locus into at least four separate loci, Idd3, Idd10, Idd17, and Idd18, illustrates the complex polygenic nature of diabetes.

[MRI aspect of hepatic adenomatosis]

We report a case of hepatic adenomatosis demonstrated with MR imaging. The diagnosis can be suspected when this technique shows multiple hepatic lesions which present an iso-signal intensity on T1-wi, a hyperintense signal on T2-wi and rapid wash-in and wash-out of gadolinium. Injection of superparamagnetic iron oxide mag be useful in the characterization of the lesion: a decreased signal intensity after injection rules out the diagnosis of metastasis. Because of the unknown course of hepatic adenomatosis, histological proof and radiological follow-up are recommended.

Congenic mapping of the insulin-dependent diabetes (Idd) gene, Idd10, localizes two genes mediating the Idd10 effect and eliminates the candidate Fcgr1

The development of autoimmune diabetes in the nonobese diabetic (NOD) mouse is under the control of multiple insulin-dependent diabetes (Idd) genes. The Idd3 gene, originally defined as a broad peak of linkage on mouse chromosome 3, was subsequently identified as two genes, Idd3 and Idd10, separated by at least 20 cM. The resistance alleles of Idd3 and Idd10 individually confer only partial protection from diabetes but, in combination, result in profound resistance to disease due to an epistatic genetic interaction. In this study, we used newly developed congenic strains to further localize Idd10. Surprisingly, we found that Idd10 itself comprises at least two linked loci: Idd10 and the newly designated Idd17. Idd17 was localized to a 1.1-cM region between D3Mit26 and D3Mit40, proximal to Fcgr1, a candidate gene encoding the high affinity Fc receptor for IgG. Idd10 was localized to a 10-cM region between D3Mit213 and D3Mit106, distal to Fcgr1. Thus, Fcgr1 was excluded as a candidate for either Idd10 or Idd17, despite the fact that the NOD strain expresses a mutant form of the receptor. Interestingly, although Idd10 and Idd17 participate in a genetic interaction with each other, Idd10 but not Idd17 participates in the genetic interaction with Idd3. Our study on chromosome 3 begins to reveal the extent of the polygenic nature of autoimmune diabetes, and demonstrates that the use of congenic strains is an effective mapping strategy, even in the dissection of multiple, linked genes with subtle effects.

Congenic mapping of the insulin-dependent diabetes (Idd) gene, Idd10, localizes two genes mediating the Idd10 effect and eliminates the candidate Fcgr1

The development of autoimmune diabetes in the nonobese diabetic (NOD) mouse is under the control of multiple insulin-dependent diabetes (Idd) genes. The Idd3 gene, originally defined as a broad peak of linkage on mouse chromosome 3, was subsequently identified as two genes, Idd3 and Idd10, separated by at least 20 cM. The resistance alleles of Idd3 and Idd10 individually confer only partial protection from diabetes but, in combination, result in profound resistance to disease due to an epistatic genetic interaction. In this study, we used newly developed congenic strains to further localize Idd10. Surprisingly, we found that Idd10 itself comprises at least two linked loci: Idd10 and the newly designated Idd17. Idd17 was localized to a 1.1-cM region between D3Mit26 and D3Mit40, proximal to Fcgr1, a candidate gene encoding the high affinity Fc receptor for IgG. Idd10 was localized to a 10-cM region between D3Mit213 and D3Mit106, distal to Fcgr1. Thus, Fcgr1 was excluded as a candidate for either Idd10 or Idd17, despite the fact that the NOD strain expresses a mutant form of the receptor. Interestingly, although Idd10 and Idd17 participate in a genetic interaction with each other, Idd10 but not Idd17 participates in the genetic interaction with Idd3. Our study on chromosome 3 begins to reveal the extent of the polygenic nature of autoimmune diabetes, and demonstrates that the use of congenic strains is an effective mapping strategy, even in the dissection of multiple, linked genes with subtle effects.

HOSEpipe--a WWW-hosted data management and analysis system for STS content mapping projects

We have developed a data management system, 'HOSEpipe' (High Output STS Evaluation pipeline) to aid sample tracking and data analysis in STS content mapping projects. The system is based around a World Wide Web (WWW) server that provides a number of pages including forms for sample processing and data entry accessible via a standard WWW browser application. The system is split into two main modules: firstly, a sequence evaluation and annotation module that takes de novo sequence for a potential STS, screens it against existing STSs and DNA sequence databases, followed by appropriate primer sequence design; secondly, a module that handles YAC library STS screening and includes facilities for both sample tracking and experimental data analysis. We present the design and rationale of the HOSEpipe system and its development to support a whole chromosomal physical mapping project. This software and design approach is potentially applicable to physical mapping projects of varying sizes and resolution and to similar projects, such as sample sequencing and the construction of sequence-ready maps.

Thiostrepton binds to malarial plastid rRNA

Binding of the thiazolyl peptide antibiotic thiostrepton to the GTPase domain of 23S rRNA involves a few crucial nucleotides, notably A1067 (E. coli). Small RNA transcripts were prepared corresponding to the GTPase domain of the plastid 23S rRNA and the two forms of cytosolic 28S rRNAs found in the human malaria parasite Plasmodium falciparum, as well as the plastid form of rRNA of the AIDS-related pathogen Toxoplasma gondii. Binding affinities of the wild type and mutated RNA sequences were as predicted; the malarial plastid sequence had by far the highest affinity, whereas that from toxoplasma did not bind thiostrepton.

Mapping of the IDDM locus Idd3 to a 0.35-cM interval containing the interleukin-2 gene

Currently, 16 loci that contribute to the development of IDDM in the NOD mouse have been mapped by linkage analysis. To fine map these loci, we used congenic mapping. Using this approach, we localized the Idd3 locus to a 0.35-cM interval on chromosome 3 containing the Il2 gene. Segregation analysis of the known variations within this interval indicated that only one variant, a serine-to-proline substitution at position 6 of the mature interleukin-2 (IL-2) protein, consistently segregates with IDDM in crosses between NOD and a series of nondiabetic mouse strains. These data, taken together with the immunomodulatory role of IL-2, provide circumstantial evidence in support of the hypothesis that Idd3 is an allelic variation of the Il2 gene, or a variant in strong linkage disequilibrium.

The Sry-related HMG box-containing gene Sox6 is expressed in the adult testis and developing nervous system of the mouse

We have cloned and sequenced a full-length cDNA for the HMG box-containing, SRY-related gene Sox6 from mouse. The deduced protein sequence of Sox6 has considerable homology with that of the previously determined Sox5 sequence. It seems likely that these genes have diverged more recently than other members of the SOX gene family, although the two genes map to different chromosomes in the mouse. In common with Sox5, Sox6 is highly expressed in the adult mouse testis and the HMG domains of both proteins bind to the sequence 5'-AACAAT-3'. This suggests that the two genes may have overlapping functions in the regulation of gene expression during spermatogenesis in the adult mouse. However, Sox6 may have an additional role in the mouse embryo, where it is specifically expressed in the developing nervous system.

DNA binding and bending properties of the post-meiotically expressed Sry-related protein Sox-5

Sox-5 is one of a family of genes which show homology to the HMG box region of the testis determining gene SRY. We have used indirect immunofluorescence to show that Sox-5 protein is localized to the nucleus of post-meiotic round spermatids in the mouse testis. In vitro footprinting and gel retardation assays demonstrate that Sox-5 binds specifically to the sequence AACAAT with moderately high affinity (Kd of approximately 10(-9) M). Moreover, interaction of Sox-5 with its target DNA induces a significant bend in the DNA, characteristic of HMG box proteins. Circular dichroism spectroscopy of the Sox-5 HMG box and its specific complex with DNA shows an alteration in the DNA spectrum, perhaps as a consequence of DNA bending, but none in the protein spectrum on complex formation. The dependence of the change in the CD spectrum with protein to DNA ratio demonstrates the formation of a 1:1 complex. Analysis of the structure of the Sox-5 HMG box by 2D NMR suggests that both the location of helical secondary structure as well as the tertiary structure is similar to that of HMG1 box 2.

An SRY-related gene expressed during spermatogenesis in the mouse encodes a sequence-specific DNA-binding protein

SRY, the testis determining gene, encodes a member of a family of DNA binding proteins characterized by an amino acid sequence motif known as the HMG box. Using degenerate primers and the polymerase chain reaction, we have isolated SRY-related cDNAs from adult murine testis RNA. One of these, Sox-5, encodes a 43 kDa HMG-box protein with similarities to transcription activating proteins. Anti-Sox-5 antibody was used to analyse expression of Sox-5 in pre-pubertal testis and in fractionated spermatogenic cells. Sox-5 is restricted to post-meiotic germ cells, being found at highest levels in round spermatids. Sox-5 is a DNA binding protein and binding site selection assays suggest that it can bind specifically to oligonucleotides containing the consensus motif AACAAT. Sry can also bind to this motif, indicating that the Sry family may have overlapping sequence specificities.

A zinc finger protein-encoding gene expressed in the post-meiotic phase of spermatogenesis

Spermatogenesis is the complex series of physiological and morphological changes that occur when spermatogonial stem cells differentiate into mature spermatozoa. Some of these changes are likely to be regulated at the level of transcription. To approach this problem, we have cloned a cDNA from mouse testis, encoding a protein (Zfp-29) with 14 copies of the zinc finger (Zf) motif commonly found in transcriptional regulatory proteins. The expression of this gene, Zfp-29, is restricted to the testis in adult mice, but also occurs during embryonic development. Within the testis, Zfp-29 mRNA is enriched in round spermatids, the earliest post-meiotic cells. Thus, the putative Zfp-29-encoded protein may have a role in regulating the class of genes that are expressed in post-meiotic germ cells.

Expression of tachykinins by ileal and lung carcinoid tumors assessed by combined in situ hybridization, immunocytochemistry, and radioimmunoassay

Mid-gut carcinoid tumors have been shown to produce substance P, a tachykinin. A recent addition to this family of peptides is neurokinin A which is cleaved from the same precursor as substance P; beta-pre-pro-tachykinin. The authors have examined mid-gut and pulmonary carcinoid tumors for the presence of the two tachykinins, using immunocytochemical study and radioimmunoassay, and have applied the techniques of in situ hybridization and Northern blot analysis to investigate the expression of mRNA for beta-pre-pro-tachykinin. All gut tumors (n = 8) and three of the six lung tumors examined were found by immunocytochemical study to contain both tachykinins or neurokinin A alone. Chromatographic analysis of tumor extracts suggests that this peptide is being detected as a separate molecule and/or as the C-terminal portion of a larger, uncleaved form. Three of the cases positive for tachykinins showed no detectable serotonin immunoreactivity. Strong hybridization signals for beta-pre-pro-tachykinin mRNA were seen in all but one of the cases studied which contained tachykinin immunoreactivity. Intact mRNA and positive hybridization was found by Northern blot analysis in two mid-gut tumors. Concentrations of tachykinins were found by radioimmunoassay to be higher in mid-gut tumors (substance P 27.2 +/- 19.7 pmol/g; neurokinin A 31.8 +/- 24.2 pmol/g; mean +/- SEM, n = 5) than in lung cases (substance P mean 0.8, range 0.5-1.0 pmol/g; neurokinin A mean 11.0, range 10.0-12.0 pmol/g; n = 3). These results show that mid-gut and pulmonary carcinoid tumors produce tachykinins, which are detected, in some cases, where no serotonin immunoreactivity can be found, possibly because of a high rate of amine secretion. Screening for tachykinins may prove to be a useful diagnostic adjunct for these tumors.

Detection of human probombesin mRNA in neuroendocrine (small cell) carcinoma of the lung. In situ hybridization with cRNA probe

The production of human bombesin (gastrin-releasing peptide), a peptide with mitogenic action, is a recognized feature of neuroendocrine (small cell) carcinoma of the lung. However, immunostaining of bombesin is not always possible in these tumors, probably because of poor storage mechanisms or rapid release of hormone. Molecular biological analysis of the gene encoding human bombesin has revealed the DNA sequence of human pro-bombesin. We have used in situ hybridization to study the expression of the human bombesin gene at the cellular level in small cell carcinoma of the lung. Probombesin cDNA was subcloned in pSP64 vector, linearized with Bam HI and transcribed in the presence of phosphorus 32(32P)-cytosine triphosphate (CTP) and SP6 polymerase. The cRNA probe was applied to tissue sections (from six cases of small cell carcinoma of the lung, freshly fixed in 4% paraformaldehyde), cell culture preparations (two different cell lines of small cell carcinoma), and cytologic specimens (smears of cells from three different cases of small cell carcinoma). Hybridization of probombesin mRNA was detected in tumor cells in all samples. Specificity of the signal was determined by control experiments, including the use of a probe which has a sequence identical to probombesin mRNA. Our results provide evidence for the expression of the bombesin gene in small cell carcinoma of the lung at a cellular level and show that probombesin mRNA is highly expressed in these tumors.

Generation of DNA probes for peptides with highly degenerate codons using mixed primer PCR

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Calcitonin gene-related peptide messenger RNA is expressed in sensory neurones of the dorsal root ganglia and also in spinal motoneurones in man and rat

Calcitonin gene-related peptide (CGRP) mRNA was localised to neurones of the dorsal root ganglia and motoneurones of the ventral horn in man and rat. Presence of alpha- and beta-CGRP mRNA was confirmed by Northern blot analysis of rat tissues which showed alpha-CGRP was the predominant gene. The distribution of CGRP gene transcripts corresponded with neurones displaying CGRP immunoreactivity in the ganglia of both species and in the rat ventral horn. In man few motoneurones were immunoreactive despite many expressing CGRP mRNA. In situ hybridisation revealed not only sensory but also motor neurones are sites of CGRP manufacture. Thus in conjunction with other evidence the present study reinforces the proposed muscle trophic role for this peptide.