Evaluation of in silico pathogenicity prediction tools for the classification of small in-frame indels

BACKGROUND

The use of in silico pathogenicity predictions as evidence when interpreting genetic variants is widely accepted as part of standard variant classification guidelines. Although numerous algorithms have been developed and evaluated for classifying missense variants, in-frame insertions/deletions (indels) have been much less well studied.

METHODS

We created a dataset of 3964 small (< 100 bp) indels predicted to result in in-frame amino acid insertions or deletions using data from gnomAD v3.1 (minor allele frequency of 1-5%), ClinVar and the Deciphering Developmental Disorders (DDD) study. We used this dataset to evaluate the performance of nine pathogenicity predictor tools: CADD, CAPICE, FATHMM-indel, MutPred-Indel, MutationTaster2021, PROVEAN, SIFT-indel, VEST-indel and VVP.

RESULTS

Our dataset consisted of 2224 benign/likely benign and 1740 pathogenic/likely pathogenic variants from gnomAD (n = 809), ClinVar (n = 2882) and, DDD (n = 273). We were able to generate scores across all tools for 91% of the variants, with areas under the ROC curve (AUC) of 0.81-0.96 based on the published recommended thresholds. To avoid biases caused by inclusion of our dataset in the tools' training data, we also evaluated just DDD variants not present in either gnomAD or ClinVar (70 pathogenic and 81 benign). Using this subset, the AUC of all tools decreased substantially to 0.64-0.87. Several of the tools performed similarly however, VEST-indel had the highest AUCs of 0.93 (full dataset) and 0.87 (DDD subset).

CONCLUSIONS

Algorithms designed for predicting the pathogenicity of in-frame indels perform well enough to aid clinical variant classification in a similar manner to missense prediction tools.

Dissecting the Root Phenotypic and Genotypic Variability of the Iowa Mung Bean Diversity Panel

Mung bean [Vigna radiata (L.) Wilczek] is a drought-tolerant, short-duration crop, and a rich source of protein and other valuable minerals, vitamins, and antioxidants. The main objectives of this research were (1) to study the root traits related with the phenotypic and genetic diversity of 375 mung bean genotypes of the Iowa (IA) diversity panel and (2) to conduct genome-wide association studies of root-related traits using the Automated Root Image Analysis (ARIA) software. We collected over 9,000 digital images at three-time points (days 12, 15, and 18 after germination). A broad sense heritability for days 15 (0.22-0.73) and 18 (0.23-0.87) was higher than that for day 12 (0.24-0.51). We also reported root ideotype classification, i.e., PI425425 (India), PI425045 (Philippines), PI425551 (Korea), PI264686 (Philippines), and PI425085 (Sri Lanka) that emerged as the top five in the topsoil foraging category, while PI425594 (unknown origin), PI425599 (Thailand), PI425610 (Afghanistan), PI425485 (India), and AVMU0201 (Taiwan) were top five in the drought-tolerant and nutrient uptake "steep, cheap, and deep" ideotype. We identified promising genotypes that can help diversify the gene pool of mung bean breeding stocks and will be useful for further field testing. Using association studies, we identified markers showing significant associations with the lateral root angle (LRA) on chromosomes 2, 6, 7, and 11, length distribution (LED) on chromosome 8, and total root length-growth rate (TRL_GR), volume (VOL), and total dry weight (TDW) on chromosomes 3 and 5. We discussed genes that are potential candidates from these regions. We reported beta-galactosidase 3 associated with the LRA, which has previously been implicated in the adventitious root development via transcriptomic studies in mung bean. Results from this work on the phenotypic characterization, root-based ideotype categories, and significant molecular markers associated with important traits will be useful for the marker-assisted selection and mung bean improvement through breeding.

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution

Lupins are important grain legume crops that form a critical part of sustainable farming systems, reducing fertilizer use and providing disease breaks. It has a basal phylogenetic position relative to other crop and model legumes and a high speciation rate. Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten-free. We report the draft genome assembly (609 Mb) of NLL cultivar Tanjil, which has captured >98% of the gene content, sequences of additional lines and a dense genetic map. Lupins are unique among legumes and differ from most other land plants in that they do not form mycorrhizal associations. Remarkably, we find that NLL has lost all mycorrhiza-specific genes, but has retained genes commonly required for mycorrhization and nodulation. In addition, the genome also provided candidate genes for key disease resistance and domestication traits. We also find evidence of a whole-genome triplication at around 25 million years ago in the genistoid lineage leading to Lupinus. Our results will support detailed studies of legume evolution and accelerate lupin breeding programmes.

Occurrence and Characterization of Bean common mosaic virus Strain NL1 in Iowa

A legume survey in Story County was conducted to characterize legume viruses present in Iowa and potentially problematic to soybeans. Symptomatic (chlorosis, leaf curl, or vein banding) and non-symptomic leaves were selected from Apios americana, Cyamopsis tetragonolobus, Desmodium spp., Glycine max, Lablab purpureus, Lotus japonicus, Phaseolus coccineus, Phaseolus vulgaris, Vicia faba, Vigna ungulculata, and Chenopodium quinoa (an indicator species), and sent to Agdia Inc. for their Crop Screen: "Bean (Soybean)" tests. Cowpea mosaic virus (in L. purpureus), Southern bean mosaic virus (in A. americana), Soybean dwarf virus (in L. purpureus), and Tobacco streak virus (in Desmodium spp.) were identified. In addition, P. vulgaris was found positive in the serological Potyvirus group test, and was further characterized using reverse transcription (RT)-PCR using total RNA (Qiagen RNeasy extraction kit) from symptomatic leaves. A ~1-kb fragment of virus genome was amplified using degenerate primers, forward: 5' TGYGTNGAYGAYYTYAAYAA 3' (3) and reverse: 5' TCRTARAARTCRAAIGCRTAICKIG 3' (2). The closest GenBank BLAST hits for the sequence were BCMV strain NL1 (GenBank Accession No. AY112735) and BCMV MS1 (EU761198), both at 97% identity. RNA sequencing using an Illumina HiSeq 2500 (100 base paired ends) allowed construction of a nearly complete viral sequence from positions 38 to 10,037 nt (KM023744). This showed 99% similarity to BCMV-NL1 (AY112735) and 98% similarity to BCMV MS1 (EU761198). The BCMV isolate was recovered on the P. vulgaris cv. Taos Red and tested against a panel of Phaseolus, Glycine, and other hosts. Symptomatic hosts (vein-banding, mosaic, stunting, and leaf curl) were P. vulgaris cvs. Starlight, Tohono O'odham vaya Amarillo, Black Valentine Stringless, Sutter Pink, Hidatsa red, Stringless Green Refugee, Burpees Stringless Improved Bush, Princess d'Artois, Princess Double de Holland, and Dubelle Witte. Asymptomatic hosts included P. vulgaris cvs. Sierra, Great Northern Tara, Tara, and Vigna radiata. Non-host plants were P. vulgaris cvs. Michelite 62, Great Northern UI 31, Great Northern UI 123, Pure Gold Wax, Top Crop, Redlands Greanleaf B, Red Mexican UI 34, Imuna, Monroe, Pinto UI 114, Widusa, Othello, Sacramento, Red Kidney, Provider, Black Turtle Soup, Victor, and Witte boon, G. max cv. Williams, Cucumis sativus cv. Straight 8, Solanum lycopericum cv. Reine des Hatives, Vicia faba, Pisum sativum var. macrocarpon, V. unguiculata, and A. americana. The host range of the BCMV isolate on common bean differential species concurred with pathogenicity group I (1) and agreed with assignment as strain NL1. To our knowledge, this is the first complete characterization of a pathotype I strain NL1 of BCMV in the United States, combining biological typing and whole genome sequencing. References: (1) R. E. Klein et al. Plant Dis. 76:1263, 1992. (2) H. Yamamoto et al. J. Gen. Plant Pathol. 74:97, 2008. (3) L. Zheng et al. PLoS One 3:e1586, 2008.

Limb hypoplasia resulting from intrauterine infection with herpes simplex virus: a case report

Intrauterine infection with herpes simplex virus, although very rare, has devastating effects on multiple organ systems in the fetus and can lead to in utero fetal demise. Neonates born following intrauterine herpes simplex virus infection commonly manifest with cutaneous lesions, ocular damage and/or brain abnormalities. We describe the case of a dichorionic, diamniotic twin gestation complicated by intrauterine herpes simplex virus infection. This infection led to the fetal demise of twin A and a very uncommon presentation of limb hypoplasia in twin B.

Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine

We used a comparative genomics approach to investigate the evolution of a complex nucleotide-binding (NB)-leucine-rich repeat (LRR) gene cluster found in soybean (Glycine max) and common bean (Phaseolus vulgaris) that is associated with several disease resistance (R) genes of known function, including Rpg1b (for Resistance to Pseudomonas glycinea1b), an R gene effective against specific races of bacterial blight. Analysis of domains revealed that the amino-terminal coiled-coil (CC) domain, central nucleotide-binding domain (NB-ARC [for APAF1, Resistance genes, and CED4]), and carboxyl-terminal LRR domain have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare. In contrast, interparalogue exchanges involving the CC and LRR domains were common, consistent with both of these regions coevolving with pathogens. Residues under positive selection were overrepresented within the predicted solvent-exposed face of the LRR domain, although several also were detected within the CC and NB-ARC domains. Superimposition of these latter residues onto predicted tertiary structures revealed that the majority are located on the surface, suggestive of a role in interactions with other domains or proteins. Following polyploidy in the Glycine lineage, NB-LRR genes have been preferentially lost from one of the duplicated chromosomes (homeologues found in soybean), and there has been partitioning of NB-LRR clades between the two homeologues. The single orthologous region in common bean contains approximately the same number of paralogues as found in the two soybean homeologues combined. We conclude that while polyploidization in Glycine has not driven a stable increase in family size for NB-LRR genes, it has generated two recombinationally isolated clusters, one of which appears to be in the process of decay.

Proximal humeral replacement using a fixed-fulcrum endoprosthesis

Between 1997 and 2007, 68 consecutive patients underwent replacement of the proximal humerus for tumour using a fixed-fulcrum massive endoprosthesis. Their mean age was 46 years (7 to 87). Ten patients were lost to follow-up and 16 patients died. The 42 surviving patients were assessed using the Musculoskeletal Tumor Society (MSTS) Score and the Toronto Extremity Salvage Score (TESS) at a mean follow-up of five years and 11 months (one year to ten years and nine months). The mean MSTS score was 72.3% (53.3% to 100%) and the mean TESS was 77.2% (58.6% to 100%). Four of 42 patients received a new constrained humeral liner to reduce the risk of dislocation. This subgroup had a mean MSTS score of 77.7% and a mean TESS of 80.0%. The dislocation rate for the original prosthesis was 25.9; none of the patients with the new liner had a dislocation at a mean of 14.5 months (12 to 18). Endoprosthetic replacement for tumours of the proximal humerus using this prosthesis is a reliable operation yielding good results without the documented problems of unconstrained prostheses. The performance of this prosthesis is expected to improve further with a new constrained humeral liner, which reduces the risk of dislocation.

The clinical significance of the FUS-CREB3L2 translocation in low-grade fibromyxoid sarcoma

Background

Low-grade fibromyxoid sarcoma (LGFMS) is a rare soft-tissue neoplasm with a deceptively benign histological appearance. Local recurrences and metastases can manifest many years following excision. The FUS-CREB3L2 gene translocation, which occurs commonly in LGFMS, may be detected by reverse-transcriptase polymerase chain reaction (RT-PCR) and fluorescence in situ hybridisation (FISH). We assessed the relationship between clinical outcome and translocation test result by both methods.

Methods

We report genetic analysis of 23 LGFMS cases and clinical outcomes of 18 patients with mean age of 40.6 years. During follow-up (mean 24.8 months), there were no cases of local recurrence or metastasis. One case was referred with a third recurrence of a para-spinal tumour previously incorrectly diagnosed as a neurofibroma.

Results

Results showed 50% of cases tested positive for the FUS-CREB3L2 translocation by RT-PCR and 81.8% by FISH, suggesting FISH is more sensitive than RT-PCR for confirming LGFMS diagnosis. Patients testing positive by both methods tended to be younger and had larger tumours. Despite this, there was no difference in clinical outcome seen during short and medium-term follow-up.

Conclusions

RT-PCR and FISH for the FUS-CREB3L2 fusion transcript are useful tools for confirming LGFMS diagnosis, but have no role in predicting medium-term clinical outcome. Due to the propensity for late recurrence or metastasis, wide excision is essential, and longer-term follow-up is required. This may identify a difference in long-term clinical outcome between translocation-positive and negative patients.

A fluorescence in situ hybridization system for karyotyping soybean

The development of a universal soybean (Glycine max [L.] Merr.) cytogenetic map that associates classical genetic linkage groups, molecular linkage groups, and a sequence-based physical map with the karyotype has been impeded due to the soybean chromosomes themselves, which are small and morphologically homogeneous. To overcome this obstacle, we screened soybean repetitive DNA to develop a cocktail of fluorescent in situ hybridization (FISH) probes that could differentially label mitotic chromosomes in root tip preparations. We used genetically anchored BAC clones both to identify individual chromosomes in metaphase spreads and to complete a FISH-based karyotyping cocktail that permitted simultaneous identification of all 20 chromosome pairs. We applied these karyotyping tools to wild soybean, G. soja Sieb. and Zucc., which represents a large gene pool of potentially agronomically valuable traits. These studies led to the identification and characterization of a reciprocal chromosome translocation between chromosomes 11 and 13 in two accessions of wild soybean. The data confirm that this translocation is widespread in G. soja accessions and likely accounts for the semi-sterility found in some G. soja by G. max crosses.

Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

BACKGROUND

Soybeans grown in the upper Midwestern United States often suffer from iron deficiency chlorosis, which results in yield loss at the end of the season. To better understand the effect of iron availability on soybean yield, we identified genes in two near isogenic lines with changes in expression patterns when plants were grown in iron sufficient and iron deficient conditions.

RESULTS

Transcriptional profiles of soybean (Glycine max, L. Merr) near isogenic lines Clark (PI548553, iron efficient) and IsoClark (PI547430, iron inefficient) grown under Fe-sufficient and Fe-limited conditions were analyzed and compared using the Affymetrix GeneChip Soybean Genome Array. There were 835 candidate genes in the Clark (PI548553) genotype and 200 candidate genes in the IsoClark (PI547430) genotype putatively involved in soybean's iron stress response. Of these candidate genes, fifty-eight genes in the Clark genotype were identified with a genetic location within known iron efficiency QTL and 21 in the IsoClark genotype. The arrays also identified 170 single feature polymorphisms (SFPs) specific to either Clark or IsoClark. A sliding window analysis of the microarray data and the 7X genome assembly coupled with an iterative model of the data showed the candidate genes are clustered in the genome. An analysis of 5' untranslated regions in the promoter of candidate genes identified 11 conserved motifs in 248 differentially expressed genes, all from the Clark genotype, representing 129 clusters identified earlier, confirming the cluster analysis results.

CONCLUSION

These analyses have identified the first genes with expression patterns that are affected by iron stress and are located within QTL specific to iron deficiency stress. The genetic location and promoter motif analysis results support the hypothesis that the differentially expressed genes are co-regulated. The combined results of all analyses lead us to postulate iron inefficiency in soybean is a result of a mutation in a transcription factor(s), which controls the expression of genes required in inducing an iron stress response.

Local recurrence of osteosarcoma after 17 years

The recurrence of osteosarcoma is rare. Local recurrence occurs in 4-10% of patients following effective treatment. So far, recurrences as late as 15 years have been reported in the literature. We report a unique case of local recurrence of intramedullary osteosarcoma 17 years from initial diagnosis and treatment. Regular long-term follow-up of patients with this diagnosis is crucial to ensure early detection and treatment of potential recurrences.

Peri-acetabular resection and endoprosthetic reconstruction for tumours of the acetabulum

We treated 98 patients with peri-acetabular tumours by resection and reconstruction with a custom-made pelvic endoprosthesis. The overall survival of the patients was 67% at five years, 54% at ten years and 51% at 30 years. One or more complications occurred in 58.1% of patients (54), of which infection was the most common, affecting 30% (28 patients). The rate of local recurrence was 31% (29 patients) after a mean follow-up of 71 months (11 to 147). Dislocation occurred in 20% of patients (19). Before 1996 the rate was 40.5% (17 patients) but this was reduced to 3.9% (two patients) with the introduction of a larger femoral head. There were six cases of palsy of the femoral nerve with recovery in only two. Revision or excision arthroplasty was performed in 23.7% of patients (22), principally for uncontrolled infection or aseptic loosening. Higher rates of death, infection and revision occurred in men.

This method of treatment is still associated with high morbidity. Patients should be carefully selected and informed of this pre-operatively.

Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps

Whole-genome sequencing of the soybean (Glycine max (L.) Merr. 'Williams 82') has made it important to integrate its physical and genetic maps. To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the 'Williams 82' physical map. SSRs were screened against 3 mapping populations. We found the AAT and ACT motifs produced the greatest frequency of length polymorphisms, ranging from 17.2% to 32.3% and from 11.8% to 33.3%, respectively. Other useful motifs include the dinucleotide repeats AG, AT, and AG, with frequency of length polymorphisms ranging from 11.2% to 18.4% (AT), 12.4% to 20.6% (AG), and 11.3% to 16.4% (GT). Repeat lengths less than 16 bp were generally less useful than repeat lengths of 40-60 bp. Two hundred and sixty-five SSRs were genetically mapped in at least one population. Of the 265 mapped SSRs, 60 came from BAC singletons not yet placed into contigs of the physical map. One hundred and ten originated in BACs located in contigs for which no genetic map location was previously known. Ninety-five SSRs came from BACs within contigs for which one or more other BACs had already been mapped. For these fingerprinted contigs (FPC) a high percentage of the mapped markers showed inconsistent map locations. A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4x assembly of the whole genome sequence of soybean.

Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps

Whole-genome sequencing of the soybean (Glycine max (L.) Merr. 'Williams 82') has made it important to integrate its physical and genetic maps. To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the 'Williams 82' physical map. SSRs were screened against 3 mapping populations. We found the AAT and ACT motifs produced the greatest frequency of length polymorphisms, ranging from 17.2% to 32.3% and from 11.8% to 33.3%, respectively. Other useful motifs include the dinucleotide repeats AG, AT, and AG, with frequency of length polymorphisms ranging from 11.2% to 18.4% (AT), 12.4% to 20.6% (AG), and 11.3% to 16.4% (GT). Repeat lengths less than 16 bp were generally less useful than repeat lengths of 40-60 bp. Two hundred and sixty-five SSRs were genetically mapped in at least one population. Of the 265 mapped SSRs, 60 came from BAC singletons not yet placed into contigs of the physical map. One hundred and ten originated in BACs located in contigs for which no genetic map location was previously known. Ninety-five SSRs came from BACs within contigs for which one or more other BACs had already been mapped. For these fingerprinted contigs (FPC) a high percentage of the mapped markers showed inconsistent map locations. A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4x assembly of the whole genome sequence of soybean.

Effect of leg exercises on popliteal venous blood flow during prolonged immobility of seated subjects: implications for prevention of travel-related deep vein thrombosis

BACKGROUND

Venous stasis is an important contributing factor in the development of travel-related deep vein thrombosis. This study examined factors affecting popliteal venous blood flow in order to determine the most effective exercise regimen to prevent venous stasis.

METHODS

Twenty-one healthy subjects were randomly assigned to various activities over a 9-week period. Subjects remained seated throughout the investigation and 3660 duplex ultrasound examinations were performed by a single examiner using a SonoSite 180 Plus handheld ultrasound. Baseline popliteal vein blood flow velocity, cross-sectional area and volume flow in subjects sitting motionless were assessed in the first 3 weeks.The remaining 6 weeks involved subjects performing airline-recommended activities, foot exercises, foot exercises against moderate resistance and foot exercises against increased resistance in order to determine the most beneficial method for enhancing popliteal venous flow. Sitting with feet not touching the floor and the effect of sleeping were also assessed.

RESULTS

The median age of the subjects was 22 years (range: 18-25.5 years), height 171 cm (162.5-180.5 cm) and body mass index 25.3 kg m(-2) (23.2-26.3 kg m(-2)). Blood volume flow in the popliteal vein was reduced by almost 40% with immobility of seated subjects and by almost 2-fold when sitting motionless with feet not touching the floor. Foot exercises against increased resistance positively enhanced volume flow (P < 0.0001).

CONCLUSION

Leg exercise regimens enhanced popliteal venous flow during prolonged immobility of seated subjects, reinforcing the importance of regular leg movement to prevent venous stasis during prolonged sitting, such as in long-distance travel.

Kystes anévrismaux des phalanges et des métacarpiens. À propos de six cas et revue de la littérature

Aneurysmal bone cysts arising from tubular bones of the hand occur very rarely and require particular diagnostic and therapeutic management techniques. The authors report the diagnostic and surgical management of a monocentric case series of six aneurysmal bone cysts involving the phalangeal and metacarpal bones. In addition to hightlighting the use of diagnostic MRI and biopsy prior to surgical intervention, the authors describe the favourable outcome of curetage with and without the use of bone graft. An aggressive treatment approach such as cryotherapy or resection with reconstruction should only be used in cases when the articular surface is involved, when full bone invasion of the phalanx or metacarpal has occurred, or in case of more than one recurrence.

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.

Doxorubicin and cisplatin chemotherapy in high-grade spindle cell sarcomas of the bone, other than osteosarcoma or malignant fibrous histiocytoma: a European Osteosarcoma Intergroup Study

There are limited data that define the role of chemotherapy in the treatment of high-grade spindle cell sarcomas of bone, other than osteosarcoma or malignant fibrous histiocytoma (MFH-B). This prospective study evaluates the effect of doxorubicin and cisplatin on these tumours. Thirty-seven patients, age 65 years, with spindle cell sarcoma of bone, except osteosarcoma or MFH-B, were included. Chemotherapy consisted of doxorubicin and cisplatin every 3 weeks for six cycles. Resection was performed after three cycles. In 15 patients with metastases, response assessment showed three complete responses (CR), four stable disease (SD), five progression; three were not evaluable. Median time to progression was 30 months (95% Confidence Interval (CI), 8-51 months) for the operable non-metastatic patients; median survival 41 months (95% CI, 16-82 months). Median time to progression in the metastatic group was 10 months (95% CI, 0-18 months) and median survival was 14 months (95% CI, 4-45 months). This study suggests a limited role for doxorubicin and cisplatin in metastatic high-grade spindle cell sarcoma of bone, other than osteosarcoma or MFH-B cases.

Genome-Level Evolution of Resistance Genes in Arabidopsis thaliana

Pathogen resistance genes represent some of the most abundant and diverse gene families found within plant genomes. However, evolutionary mechanisms generating resistance gene diversity at the genome level are not well understood. We used the complete Arabidopsis thaliana genome sequence to show that most duplication of individual NBS-LRR sequences occurs at close physical proximity to the parent sequence and generates clusters of closely related NBS-LRR sequences. Deploying the statistical strength of phylogeographic approaches and using chromosomal location as a proxy for spatial location, we show that apparent duplication of NBS-LRR genes to ectopic chromosomal locations is largely the consequence of segmental chromosome duplication and rearrangement, rather than the independent duplication of individual sequences. Although accounting for a smaller fraction of NBS-LRR gene duplications, segmental chromosome duplication and rearrangement events have a large impact on the evolution of this multi-gene family. Intergenic exchange is dramatically lower between NBS-LRR sequences located in different chromosome regions as compared to exchange between sequences within the same chromosome region. Consequently, once translocated to new chromosome locations, NBS-LRR gene copies have a greater likelihood of escaping intergenic exchange and adopting new functions than do gene copies located within the same chromosomal region. We propose an evolutionary model that relates processes of genome evolution to mechanisms of evolution for the large, diverse, NBS-LRR gene family.

Single center experience of a new intensive induction therapy for ewing's family of tumors: feasibility, toxicity, and stem cell mobilization properties

PURPOSE

To examine the feasibility, tolerability, and toxicity of an intensified induction regimen (vincristine, ifosfamide, doxorubicin, and etoposide [VIDE]) in patients with newly diagnosed Ewing's family of tumors (EFT); to assess ability to maintain dose-intensity, and predictability of peripheral-blood stem cell mobilization.

PATIENTS AND METHODS

Thirty patients were treated with vincristine 1.4 mg/m2 (maximum 2 mg) on day 1, doxorubicin 20 mg/m2, ifosfamide 3 g/m2 plus mesna and etoposide 150 mg/m2 on days 1 to 3. Cycles were given every 21 days for up to six cycles.

RESULTS

One-hundred and seventy cycles of VIDE were given. The median treatment interval was 21 days (21 to 42) and nadir count: hemoglobin 8.3 (6.3 to 11.9), neutrophils 0.045 (0.0 to 2.1), and platelets 45 (3 to 343). There were 96 episodes of infection requiring hospitalization (56%). Growth factor support reduced infectious complications by 34%. Etoposide dose was reduced, or omitted, in 24% of cycles. Four patients did not complete six cycles due to unacceptable toxicity and one patient progressed on treatment. Twenty patients underwent peripheral-blood stem cell harvesting, 15 after cycle 3, and five after cycle 4. Median CD34+ yield was 4.6 x 106/kg per patient (1.8 to 14.5). Overall response to treatment, measured in 24 patients, was 88%. Seven of 11 patients undergoing surgery achieved greater than 90% necrosis of tumor (64%).

CONCLUSION

VIDE is an effective induction regimen with substantial but acceptable toxicity that allows predictable mobilization of stem cells. Maintenance of dose-intensity is feasible in the majority of patients. Growth factors play a role in maintaining dose-intensity and reduce infectious complications.

Posture-related tachycardia in older patients with hyponatremia

Hyponatremia (HN) is the commonest electrolyte abnormality in elderly patients. Its etiology in this setting is poorly understood. In this study, the authors aim to compare the hemodynamic and hormonal responses of a group of older patients with a predisposition to HN with a group of age-matched controls. We assessed hemodynamic and hormonal responses to postural challenge in 15 patients over age 65 with serum sodium concentrations of less than 130 mM (mean 128.7 mM) and 15 age-matched controls with normal sodium concentrations. Patients remained recumbent for 1 h and stood for the second. Blood was drawn at baseline and at 15 min intervals. Blood pressure (BP) and pulse rates (PR) were monitored electronically. Plasma arginine vasopressin (AVP), atrial natriuretic peptide (ANP), renin and aldosterone were determined periodically during the study period. No difference in BP between groups was noted. PR increased significantly in the HN group only within 3 min of standing (from 71 +/- 4 to 86 +/- 5, P<0.01) and remained significantly higher than controls until 90 min (87 +/- 5 vs. 69 +/- 4, P<0.01). While plasma AVP levels increased significantly following 30 min standing and remained elevated for both HN and control groups, it did not differ significantly between the two. Baseline plasma ANP levels were significantly higher in HN patients compared with controls and remained significantly higher (P<0.05) throughout the study. There was no significant difference in plasma renin or aldosterone levels between groups during the study period. We have demonstrated differing autonomic and hormonal responses to orthostatic challenge between HN patients and age-matched controls. Water retention due to the syndrome of inappropriate anti-diuretic hormone secretion (with reset osmostat) may lead to raised ANP levels in this older cohort of patients. Further physiological studies are required to clarify the precise mechanism of these varying responses.

Plasma P-selectin is elevated in the first trimester in women who subsequently develop pre-eclampsia

OBJECTIVE

To report plasma concentrations of the adhesion cell molecule P-selectin during pregnancy to determine the effect of subsequent development of hypertension and pre-eclampsia.

DESIGN

A longitudinal study.

METHODS

A longitudinal study involving 70 women followed up from early pregnancy; 20 who subsequently developed pre-eclampsia were compared with 24 who developed gestational hypertension and 26 normotensive women with normal obstetric outcome. The determination of citrate plasma soluble P-selectin levels throughout pregnancy was performed using a commercial quantitative sandwich immunoassay kit. The temporal course of plasma P-selectin in the three groups of subjects was analysed.

RESULTS

There was no significant difference in mean plasma P-selectin concentration between normotensive and gestational hypertensive subjects at any stage of pregnancy. Using a cutoff level of 60 ng/mL, P-selectin concentration at 10-14 weeks had a negative predictive value for pre-eclampsia of almost 99%. Mean plasma P-selectin concentrations were significantly elevated by 10-14 weeks in women who later developed pre-eclampsia (P < 0.001).

CONCLUSIONS

Our data support an inflammatory model for pre-eclampsia whereby endothelial cell activation may be secondary to a primary inflammatory response. Plasma P-selectin has significant potential as a first trimester clinical marker of pre-eclampsia.

Plasma P-selectin is elevated in the first trimester in women who subsequently develop pre-eclampsia

OBJECTIVE

To report plasma concentrations of the adhesion cell molecule P-selectin during pregnancy to determine the effect of subsequent development of hypertension and pre-eclampsia.

DESIGN

A longitudinal study.

METHODS

A longitudinal study involving 70 women followed up from early pregnancy; 20 who subsequently developed pre-eclampsia were compared with 24 who developed gestational hypertension and 26 normotensive women with normal obstetric outcome. The determination of citrate plasma soluble P-selectin levels throughout pregnancy was performed using a commercial quantitative sandwich immunoassay kit. The temporal course of plasma P-selectin in the three groups of subjects was analysed.

RESULTS

There was no significant difference in mean plasma P-selectin concentration between normotensive and gestational hypertensive subjects at any stage of pregnancy. Using a cutoff level of 60 ng/mL, P-selectin concentration at 10-14 weeks had a negative predictive value for pre-eclampsia of almost 99%. Mean plasma P-selectin concentrations were significantly elevated by 10-14 weeks in women who later developed pre-eclampsia (P < 0.001).

CONCLUSIONS

Our data support an inflammatory model for pre-eclampsia whereby endothelial cell activation may be secondary to a primary inflammatory response. Plasma P-selectin has significant potential as a first trimester clinical marker of pre-eclampsia.

Evaluating the self-assessed support needs of women with breast cancer

AIMS OF THE STUDY

The first aim of the study was to identify the self-assessed support needs of women with breast cancer at various points of illness and, secondly, to establish if these needs formed clusters which could provide the basis for developing a standardized scale of needs for use by breast care teams in the evaluation of care.

BACKGROUND

It has been found that support given to women with breast cancer has a positive effect upon their reactions to the illness and may even prolong their survival. Given that breast cancer affects a large number of women it is obviously important that those affected receive, in addition to the best available medical treatment, the type of support that best meets their needs. This study aimed to provide information on the impact of breast cancer and the need for various types of support by examining women's own assessment of their needs at different stages of their illness.

DESIGN AND METHODS

A purposive sample of 12 women with a diagnosis of breast cancer was selected in one health authority in England, United Kingdom (UK). Women selected represented a wide age range (between 26 and 58), were married or in long-term cohabiting relationships and were at different points on the illness trajectory. Women were invited to take part in a semi-structured interview about their experiences of breast cancer. The data from these interviews were analysed using the software package Qualitative Solutions and Research, Nonnumerical Data Indexing, Searching and Theorizing (QSR*NUDIST). Following this content analysis, a questionnaire was formulated which divided statements into seven categories: diagnosis, treatment, support, femininity and body image, family and friends, information and after care, to be rated on a Likert scale ranging from "of no importance" to "extremely important". Questionnaire data were analysed by means of a one-way analysis of variance (for three independent variables) or t-test for two independent variables. Results. The questionnaire was sent to 971 women and achieved a response rate of 50.4%. The mean score for statements of need reached the level of point 4 on the Likert scale (important) with three exceptions: having professional help with family problems and domestic upheaval, coping with feelings of anger and dealing with the question "why me?"

CONCLUSION

With the above three exceptions, women experienced a high level of need associated with a diagnosis of breast cancer. Studies of this kind should enable resources to be targeted to areas of highest need.

Experiences of women with a diagnosis of breast cancer: a clinical pathway approach

The study presented in this paper formed the first part of a large survey of breast cancer patients in one health authority in England, UK looking at individual needs expressed by women with a diagnosis of breast cancer. The paper provides an account of the experiences of 12 women with a diagnosis of breast cancer. The women represent a wide age range and different stages of illness. The transcribed accounts of the women were analysed by means of Qualitative Solutions and Research, Non-Numerical Unstructured Data Indexing Searching and Theorising (QSR*NUDIST). The study examined the individual experiences of women with a diagnosis of breast cancer and its aftermath as they passed through different stages related to it. The women's experiences are presented within the conceptual framework of the clinical pathway and their accounts represent their journey along the pathway. Various significant points in this journey are portrayed representing the women's reactions to diagnosis, treatment, femininity and body image, support, family and friends, information and after care.

Can we predict who will return to a genitourinary clinic?

One hundred and eighty-eight first-time attenders at a genitourinary (GU) clinic were monitored to establish who returned following discharge after treatment. Thirty-six (19%) returned within 2 years with a new infection. The re-attenders did not differ significantly from the rest of the cohort by age, gender or occupation, nor did they differ in their sexual history and psychological variables. Re-attenders were significantly more likely to have consulted their general practitioner (GP) in the 6 months prior to their first clinic attendance.

Factors influencing delay in treatment seeking by first-time attenders at a genitourinary clinic

We examined treatment-seeking behaviours amongst a consecutive sample of 188 first-time attenders at a busy genitourinary (GU) clinic in a general hospital. Participants were interviewed and completed a battery of questionnaires prior to receiving diagnosis or treatment. Delay in treatment seeking was measured in 3 ways: utilization delay, illness behaviour delay and appraisal delay. Appraisal delay and illness behaviour were significantly related, but were unrelated to utilization delay. Substantial delays were reported before seeking treatment, with a median of 30 days elapsing between first noticing symptoms and attending the clinic. Analysis of age groups indicated that the oldest groups--45 and above were likely to delay longest, on all 3 measures of delay.

Multiregional evaluation of the SimPlate heterotrophic plate count method compared to the standard plate count agar pour plate method in water

A new SimPlate heterotrophic plate count (HPC) method (IDEXX Laboratories, Westbrook, Maine) was compared with the pour plate method at 35 degrees C for 48 h. Six laboratories tested a total of 632 water samples. The SimPlate HPC method was found to be equivalent to the pour plate method by regression analysis (r = 0. 95; y = 0.99X + 0.06).

Chondromyxoid fibroma of the sacrum

A 30-year-old man with a 7-month history of mild sacral pain and intermittant left sciatica was found to have an expansile lesion in the sacrum on a plain radiograph. Biopsy confirmed a chondromyxoid fibroma which was removed surgically. A 1-year follow-up showed no recurrence. The case is the fifth to be reported. Plain film and MRI appearances, histology and treatment are described. The previously reported cases are reviewed and the current literature is discussed.

Local therapy and other factors influencing site of relapse in patients with localised Ewing's sarcoma. United Kingdom Children's Cancer Study Group (UKCCSG)

Relapse patterns have been documented in 191 children with localised Ewing's sarcoma treated with the United Kingdom Children's Cancer Group (UKCCSG) Ewing's Tumour regimen ET2. All received chemotherapy comprising ifosfamide, vincristine, doxorubicin and actinomycin D. Local treatment modality was excision and or radiotherapy depending on tumour site and response to primary chemotherapy. Although not strictly comparable, due to the clinical indications used for each modality, local relapse rates were very low and were similar, irrespective of the type of local treatment modality: radiotherapy (3/56), surgery (7/114) or a combination (0/20). Combined relapse (local + distant) rates were similarly low irrespective of the type of local therapy: radiotherapy (4/56), surgery (4/114) or a combination (0/20). Overall survival was lower in females (P = < 0.04), older children (P = < 0.002) and those with primaries at sites other than long bones (P = < 0.02). It is concluded that with effective intensive chemotherapy combined with either radiotherapy or surgery, local control in this study was excellent at sites other than the pelvis. Preventing distant relapse, predominantly to lung and bone, remains the major challenge.

Suppression subtractive hybridization identifies high glucose levels as a stimulus for expression of connective tissue growth factor and other genes in human mesangial cells

Accumulation of mesangial matrix is a pivotal event in the pathophysiology of diabetic nephropathy. The molecular triggers for matrix production are still being defined. Here, suppression subtractive hybridization identified 15 genes differentially induced when primary human mesangial cells are exposed to high glucose (30 mM versus 5 mM) in vitro. These genes included (a) known regulators of mesangial cell activation in diabetic nephropathy (fibronectin, caldesmon, thrombospondin, and plasminogen activator inhibitor-1), (b) novel genes, and (c) known genes whose induction by high glucose has not been reported. Prominent among the latter were genes encoding cytoskeleton-associated proteins and connective tissue growth factor (CTGF), a modulator of fibroblast matrix production. In parallel experiments, elevated CTGF mRNA levels were demonstrated in glomeruli of rats with streptozotocin-induced diabetic nephropathy. Mannitol provoked less mesangial cell CTGF expression in vitro than high glucose, excluding hyperosmolality as the key stimulus. The addition of recombinant CTGF to cultured mesangial cells enhanced expression of extracellular matrix proteins. High glucose stimulated expression of transforming growth factor beta1 (TGF-beta1), and addition of TGF-beta1 to mesangial cells triggered CTGF expression. CTGF expression induced by high glucose was partially suppressed by anti-TGF-beta1 antibody and by the protein kinase C inhibitor GF 109203X. Together, these data suggest that 1) high glucose stimulates mesangial CTGF expression by TGFbeta1-dependent and protein kinase C dependent pathways, and 2) CTGF may be a mediator of TGFbeta1-driven matrix production within a diabetic milieu.

Differential effects of protein kinase A on Ras effector pathways

Ras mutants with the ability to interact with different effectors have played a critical role in the identification of Ras-dependent signaling pathways. We used two mutants, RasS35 and RasG37, which differ in their ability to bind Raf-1, to examine Ras-dependent signaling in thyroid epithelial cells. Wistar rat thyroid cells are dependent upon thyrotropin (TSH) for growth. Although TSH-stimulated mitogenesis requires Ras, TSH activates protein kinase A (PKA) and downregulates signaling through Raf and the mitogen-activated protein kinase (MAPK) cascade. Cells expressing RasS35, a mutant which binds Raf, or RasG37, a mutant which binds RalGDS, exhibited TSH-independent proliferation. RasS35 stimulated morphological transformation and anchorage-independent growth. RasG37 stimulated proliferation but not transformation as measured by these indices. TSH exerted markedly different effects on the Ras mutants and transiently repressed MAPK phosphorylation in RasS35-expressing cells. In contrast, TSH stimulated MAPK phosphorylation and growth in cells expressing RasG37. The Ras mutants, in turn, exerted differential effects on TSH signaling. RasS35 abolished TSH-stimulated changes in cell morphology and thyroglobulin expression, while RasG37 had no effect on these activities. Together, the data indicate that cross talk between Ras and PKA discriminates between distinct Ras effector pathways.

Training staff to prevent aggressive behavior of cognitively impaired elderly patients during bathing and grooming

1. Cognitively impaired elderly patients often become aggressive toward caregivers who are providing assistance with bathing and grooming, but caregivers can learn methods to prevent or reduce some of the aggression. 2. The R.E.S.P.E.C.T. model describes key practices caregivers can use to better meet patient needs and reduce aggression, increasing their understanding and skill. 3. In addition to training, observation of performance and consultation are important steps in enabling caregivers to apply and maintain their skills.

Predictive value of objective esophageal insufflation testing for acquisition of tracheoesophageal speech

This prospective study was undertaken to assess the predictive value of esophageal insufflation on the acquisition of tracheoesophageal (TE) speech. Fourteen total laryngectomy patients were evaluated prior to tracheoesophageal puncture (TEP) using objective esophageal pressure measurements. These patients then were followed prospectively for 6 to 13 months. Speech was assessed at the time of prosthesis fitting, at 1 month, at less than 6 months, and at greater than 6 months post-TEP. No patient underwent pharyngeal myotomy. Pre-TEP esophageal insufflation pressure was associated (P = .065) with successful TE speech at the time of prosthesis fitting, but was not associated with successful TE speech acquisition after 6 months. This study's results suggest that patients with poor pre-TEP esophageal insufflation test results will usually obtain successful TE speech given adequate time and training, even without pharyngeal myotomy.

Clinical oncology: case presentations from oncology centres. 1. Ewing's sarcoma. The London Bone Tumour Service

The management of a case of Ewing's sarcoma of the left proximal humerus in a 15-year-old girl is presented, and the radiological and pathological findings are described. The chemotherapeutic, radiotherapeutic and surgical management of Ewing's sarcoma are discussed with reference to the case.

Thermogenic synergism between ephedrine and caffeine in healthy volunteers: a double-blind, placebo-controlled study

Animal and human studies have suggested a thermogenic synergism between ephedrine (E), a beta-agonist, and caffeine (C), an adenosine antagonist, which may be suitable for the treatment of obesity. To study this phenomenon, the thermogenic effect of single doses of oral placebo, E 10 mg, E 20 mg, C 100 mg, and C 200 mg were compared with the effects of three different combinations of E + C, 10 mg/200 mg, 20 mg/100 mg, and 20 mg/200 mg, measured by indirect calorimetry in six healthy, lean subjects. The thermogenic effect after E + C 20 mg/200 mg was larger than that of any of the other combinations. In this dose ratio, ephedrine and caffeine exerted a supra-additive synergism, whereas the thermogenic effects of the other two combinations were only additive. The 3-hour postintake increase in systolic blood pressure after all three combinations averaged 5 to 7 mm Hg more than placebo (P less than .01), which exceeded the predicted additive effect fivefold to sevenfold. Diastolic blood pressure was not increased by E + C 20 mg/200 mg, whereas the other two combinations increased it by approximately 4 mm Hg more than placebo. E + C 20 mg/100 mg and 20 mg/200 mg increased heart rate more than placebo, while E + C 10 mg/200 mg had no effect on heart rate. As expected, all combinations increased plasma glucose, insulin, and C-peptide from their ephedrine content. No significant effects of the combinations were found on plasma lactate, glycerol, nonesterified fatty acids (NEFA), triglyceride, potassium, or sodium.(ABSTRACT TRUNCATED AT 250 WORDS)