Transvaginal ultrasound (TVUS)-guided biopsy is safe and effective in diagnosing peritoneal carcinomatosis and recurrent pelvic malignancy.

AIM: To assess safety and accuracy of transvaginal ultrasound (TVUS)-guided biopsy in achieving a diagnosis of peritoneal carcinomatosis (PC). MATERIALS AND METHODS: This was a retrospective study comprising a cohort of 54 consecutive women aged 18-85 years referred from the gynaecological oncology multidisciplinary team meeting (MDTM) who attended for TVUS-guided biopsy procedures in a tertiary oncology centre over a 4-year period (2010-2014). Clinicopathological validation was assessed using online patient records and radiological information systems. An independent oncologist assessed patient outcomes. RESULTS: The procedure was successful in all 19 patients with suspected recurrent malignancy with diagnosis validated against previous histology. Successful histological confirmation was achieved in 31 of 35 patients with suspected PC, which was thereafter validated by histology from subsequent surgery and favourable response to site-specific therapies (n=22). In three patients with suspected PC, the procedure did not result in biopsy as a suitable target could not be identified. Another woman had two false-negative biopsies. Thus overall a site-specific and subtype cancer diagnosis was obtained for 50 women giving an overall patient success rate of 93% (50/54). There were no procedure-related complications. CONCLUSION: TVUS core biopsy is a safe, effective, well-tolerated, and valuable technique in modern oncological management of PC when other diagnostic options are unavailable.

Influence of dietary protein level on body composition and energy expenditure in calorically restricted overweight cats.

High-protein (HP) diets help prevent loss of lean mass in calorie-restricted (CR) cats. However, it is not entirely known whether these diets also induce changes of energy expenditure during periods of CR. To investigate this issue, sixteen overweight cats were fed either a high-protein [(HP), 54.2% of metabolizable energy (ME)] or a moderate-protein [(MP), 31.5% of ME] diet at 70% of their maintenance energy intakes for 8 weeks, and energy expenditure, energy intake, body weight and composition, and serum metabolites and hormones were measured. While both groups of cats lost weight at a similar rate, only cats eating the HP diet maintained lean mass during weight loss. Indirect respiration calorimetry measurements revealed that both total and resting energy expenditure (kcal/d) significantly decreased during weight loss for both treatment groups. However, only cats eating the MP diet exhibited significant decreases of total and resting energy expenditures after energy expenditure was normalized for body weight or lean mass. Results from this study suggest that in addition to sparing the loss of lean mass, feeding HP diets to overweight cats in restricted amounts may be beneficial for preventing or minimizing decreases of mass-adjusted energy expenditure during weight loss.

Investigation of waste incineration of fluorotelomer-based polymers as a potential source of PFOA in the environment.

In light of the widespread presence of perfluorooctanoic acid (PFOA) in the environment, a comprehensive laboratory-scale study has developed data requested by the U.S. Environmental Protection Agency (EPA) to determine whether municipal and/or medical waste incineration of commercial fluorotelomer-based polymers (FTBPs) at end of life is a potential source of PFOA that may contribute to environmental and human exposures. The study was divided into two phases (I and II) and conducted in accordance with EPA Good Laboratory Practices (GLPs) as described in the quality assurance project plan (QAPP) for each phase. Phase I testing determined that the PFOA transport efficiency across the thermal reactor system to be used in Phase II was greater than 90%. Operating at 1000°C over 2s residence time with 3.2-6.6mgdscm(-1) hydrogen fluoride (HF), corrected to 7% oxygen (O2), and continuously monitored exhaust oxygen of 13%, Phase II testing of the FTBP composites in this thermal reactor system yielded results demonstrating that waste incineration of fluorotelomer-based polymers does not result in the formation of detectable levels of PFOA under conditions representative of typical municipal waste combustor (MWC) and medical waste incinerator (MWI) operations in the U.S. Therefore, waste incineration of these polymers is not expected to be a source of PFOA in the environment.

Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines.

Computing binding energies of protein-ligand complexes including their enthalpy and entropy terms by means of computational methods is an appealing approach for selecting initial hits and for further optimization in early stages of drug discovery. Despite the importance, computational predictions of thermodynamic components have evaded attention and reasonable solutions. In this study, support vector machines are used for developing scoring functions to compute binding energies and their enthalpy and entropy components of protein-ligand complexes. The binding energies computed from our newly derived scoring functions have better Pearson's correlation coefficients with experimental data than previously reported scoring functions in benchmarks for protein-ligand complexes from the PDBBind database. The protein-ligand complexes with binding energies dominated by enthalpy or entropy term could be qualitatively classified by the newly derived scoring functions with high accuracy. Furthermore, it is found that the inclusion of comprehensive descriptors based on ligand properties in the scoring functions improved the accuracy of classification as well as the prediction of binding energies including their thermodynamic components. The prediction of binding energies including the enthalpy and entropy components using the support vector machine based scoring functions should be of value in the drug discovery process.

Synthesis and properties of regenerated cellulose-based hydrogels with high strength and transparency for potential use as an ocular bandage.

Cellulose is a biologically derived material with excellent wound-healing properties. The high strength of cellulose fibers and the ability to synthesize gels with high optical transparency make these materials suitable for ocular applications. In this study, cellulose materials derived from wood pulp, cotton, and bacterial sources were dissolved in lithium chloride/N,N-dimethylacetamide to form regenerated cellulose hydrogels. Material properties of the resulting hydrogels, including water content, optical transparency, and tensile and tear strengths, were evaluated. Synthesis parameters, including activation time, dissolution time, relative humidity, and cellulose concentration, were found to impact the material properties of the resulting hydrogels. Overnight activation time improves the optical transparency of the hydrogels from 77% to 97% at 550 nm, whereas controlling cellulose concentration improves their tear strength by as much as 200%. On the basis of the measured transmittance and strength values of the regenerated hydrogels prepared via the optimized synthesis parameters, Avicel PH 101, Sigma-Aldrich microcrystalline cellulose 435236, and bacterial cellulose types were prioritized for future biocompatibility testing and potential clinical investigation.

Loss of coupling between calcium influx, energy consumption and insulin secretion associated with development of hyperglycaemia in the UCD-T2DM rat model of type 2 diabetes.

AIMS/HYPOTHESIS: Previous studies on isolated islets have demonstrated tight coupling between calcium (Ca(2+)) influx and oxygen consumption rate (OCR) that is correlated with insulin secretion rate (ISR). To explain these observations, we have proposed a mechanism whereby the activation of a highly energetic process (Ca(2+)/metabolic coupling process [CMCP]) by Ca(2+) mediates the stimulation of ISR. The aim of the study was to test whether impairment of the CMCP could play a role in the development of type 2 diabetes. METHODS: Glucose- and Ca(2+)-mediated changes in OCR and ISR in isolated islets were compared with the time course of changes of plasma insulin concentrations observed during the progression to hyperglycaemia in a rat model of type-2 diabetes (the University of California at Davis type 2 diabetes mellitus [UCD-T2DM] rat). Islets were isolated from UCD-T2DM rats before, 1 week, and 3 weeks after the onset of hyperglycaemia. RESULTS: Glucose stimulation of cytosolic Ca(2+) and OCR was similar for islets harvested before and 1 week after the onset of hyperglycaemia. In contrast, a loss of decrement in islet OCR and ISR in response to Ca(2+) channel blockade coincided with decreased fasting plasma insulin concentrations observed in rats 3 weeks after the onset of hyperglycaemia. CONCLUSIONS/INTERPRETATION: These results suggest that phenotypic impairment of diabetic islets in the UCD-T2DM rat is downstream of Ca(2+) influx and involves unregulated stimulation of the CMCP. The continuously elevated levels of CMCP induced by chronic hyperglycaemia in these islets may mediate the loss of islet function.

Consumption of fructose-sweetened beverages for 10 weeks reduces net fat oxidation and energy expenditure in overweight/obese men and women.

BACKGROUND/OBJECTIVES: The results of short-term studies in humans suggest that, compared with glucose, acute consumption of fructose leads to increased postprandial energy expenditure and carbohydrate oxidation and decreased postprandial fat oxidation. The objective of this study was to determine the potential effects of increased fructose consumption compared with isocaloric glucose consumption on substrate utilization and energy expenditure following sustained consumption and under energy-balanced conditions. SUBJECTS/METHODS: As part of a parallel arm study, overweight/obese male and female subjects, 40-72 years, consumed glucose- or fructose-sweetened beverages providing 25% of energy requirements for 10 weeks. Energy expenditure and substrate utilization were assessed using indirect calorimetry at baseline and during the 10th week of intervention. RESULTS: Consumption of fructose, but not glucose, led to significant decreases of net postprandial fat oxidation and significant increases of net postprandial carbohydrate oxidation (P<0.0001 for both). Resting energy expenditure (REE) decreased significantly from baseline values in subjects consuming fructose (P=0.031) but not in those consuming glucose. CONCLUSIONS: Increased consumption of fructose for 10 weeks leads to marked changes of postprandial substrate utilization including a significant reduction of net fat oxidation. In addition, we report that REE is reduced compared with baseline values in subjects consuming fructose-sweetened beverages for 10 weeks.

Verification and implementation of a modified split Hopkinson pressure bar technique for characterizing biological tissue and soft biosimulant materials under dynamic shear loading.

Modeling human body response to dynamic loading events and developing biofidelic human surrogate systems require accurate material properties over a range of loading rates for various human organ tissues. This work describes a technique for measuring the shear properties of soft biomaterials at high rates of strain (100-1000 s(-1)) using a modified split Hopkinson pressure bar (SHPB). Establishing a uniform state of stress in the sample is a fundamental requirement for this type of high-rate testing. Input pulse shaping was utilized to tailor and control the ramping of the incident loading pulse such that a uniform stress state could be maintained within the specimen from the start of the test. Direct experimental verification of the stress uniformity in the sample was obtained via comparison of the force measured by piezoelectric quartz force gages on both the input and the output sides of the shear specimen. The technique was demonstrated for shear loading of silicone gel biosimulant materials and porcine brain tissue. Finite element simulations were utilized to further investigate the effect of pulse shaping on the loading rate and rise time. Simulations also provided a means for visualization of the degree of shear stress and strain uniformity in the specimen during an experiment. The presented technique can be applied to verify stress uniformity and ensure high quality data when measuring the dynamic shear modulus of soft biological simulants and tissue.

Identification of protein binding surfaces using surface triplet propensities.

MOTIVATION: The ability to reliably predict protein-protein and protein-ligand interactions is important for identifying druggable binding sites and for understanding how proteins communicate. Most currently available algorithms identify cavities on the protein surface as potential ligand recognition sites. The method described here does not explicitly look for cavities but uses small surface patches consisting of triplets of adjacent surface atomic groups that can be touched simultaneously by a probe sphere representing a solvent molecule. A total of 455 different types of triplets can be identified. A training set of 309 protein-ligand protein X-ray structures has been used to generate interface propensities for the triplets, which can be used to predict their involvement in ligand-binding interactions. RESULTS: The success rate for locating protein-ligand binding sites on protein surfaces using this new surface triplet propensities (STP) algorithm is 88% which compares well with currently available grid-based and energy-based approaches. Q-SiteFinder's dataset (Laurie and Jackson, 2005. Bioinformatics, 21, 1908-1916) was used to show the favorable performance of STP. An analysis of the different triplet types showed that higher ligand binding propensity is related to more polarizable surfaces. The interaction statistics between triplet atoms on the protein surface and ligand atoms have been used to estimate statistical free energies of interaction. The ΔG(stat) for halogen atoms interacting with hydrophobic triplets is -0.6 kcal/mol and an estimate of the maximal ΔG(stat) for a ligand atom interacting with a triplet in a binding pocket is -1.45 kcal/mol. AVAILABILITY: Freely available online at http://opus.bch.ed.ac.uk/stp. Website implemented in Php, with all major browsers supported. CONTACT: m.walkinshaw@ed.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules.

BACKGROUND: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. RESULTS: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch13. CONCLUSION: The systematic framework for understanding structural variations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.

Use of deodorants during adjuvant breast radiotherapy: a survey of compliance with standard advice, impact on patients and a literature review on safety.

Proscription of antiperspirant or deodorant use during adjuvant breast radiotherapy is common. The investigators were seeking an information base to facilitate design of an appropriate controlled trial of the use of deodorants during radiotherapy. The first component consisted of a survey of women after adjuvant breast radiotherapy seeking information about routine deodorant use and potential concern if deodorants were not permitted during radiotherapy. The second component comprised a literature search for any existing controlled evidence regarding harm from deodorant use during radiotherapy. Four hundred fourteen women completed surveys. Two hundred eighty recalled advice against deodorants. Two hundred ninety-nine women routinely used deodorants, 70% of whom used roll-on products. Forty-five continued deodorant use during radiation, 20 of these despite recalling advice not to wear a deodorant. Of the 233 women who routinely wore a deodorant but abstained during radiotherapy, 19% expressed a lot of concern about body odour and 45% were slightly concerned. Three controlled studies totalling 310 patients report specific deodorants versus no deodorant use which did not show statistically significantly increased skin reactions, but had only a small subset with axillary irradiation. The proscription of deodorant use during radiotherapy is of unproven benefit and causes body odour concern to the majority of women who are usual deodorant users. The next most appropriate trial would compare use of the usual deodorant versus no deodorant, would encompass a significant number of women with radiotherapy to the axilla or application of deodorant to irradiated skin areas, and include endpoints other than skin reaction alone.

Predicting functional upstream open reading frames in Saccharomyces cerevisiae.

BACKGROUND: Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive. RESULTS: In this paper, a new computational approach to predicting functional uORFs in the yeast Saccharomyces cerevisiae is presented. Our approach is based on inductive logic programming and makes use of a novel combination of knowledge about biological conservation, Gene Ontology annotations and genes' responses to different conditions. Our method results in a set of simple and informative hypotheses with an estimated sensitivity of 76%. The hypotheses predict 301 further genes to have 398 novel functional uORFs. Three (RPC11, TPK1, and FOL1) of these 301 genes have been hypothesised, following wet-experiments, by a related study to have functional uORFs. A comparison with another related study suggests that eleven of the predicted functional uORFs from genes LDB17, HEM3, CIN8, BCK2, PMC1, FAS1, APP1, ACC1, CKA2, SUR1, and ATH1 are strong candidates for wet-lab experimental studies. CONCLUSIONS: Learning based prediction of functional uORFs can be done with a high sensitivity. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help to elucidate the regulatory roles of uORFs.

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation.

BACKGROUND: The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis. RESULTS: We have used comparative genomics to identify novel uORFs in yeast with a high likelihood of having a translational regulatory role. We examined uORFs, previously shown to play a role in regulation of translation in Saccharomyces cerevisiae, for evolutionary conservation within seven Saccharomyces species. Inspection of the set of conserved uORFs yielded the following three characteristics useful for discrimination of functional from spurious uORFs: a length between 4 and 6 codons, a distance from the start of the main ORF between 50 and 150 nucleotides, and finally a lack of overlap with, and clear separation from, neighbouring uORFs. These derived rules are inherently associated with uORFs with properties similar to the GCN4 locus, and may not detect most uORFs of other types. uORFs with high scores based on these rules showed a much higher evolutionary conservation than randomly selected uORFs. In a genome-wide scan in S. cerevisiae, we found 34 conserved uORFs from 32 genes that we predict to be functional; subsequent analysis showed the majority of these to be located within transcripts. A total of 252 genes were found containing conserved uORFs with properties indicative of a functional role; all but 7 are novel. Functional content analysis of this set identified an overrepresentation of genes involved in transcriptional control and development. CONCLUSION: Evolutionary conservation of uORFs in yeasts can be traced up to 100 million years of separation. The conserved uORFs have certain characteristics with respect to length, distance from each other and from the main start codon, and folding energy of the sequence. These newly found characteristics can be used to facilitate detection of other conserved uORFs.

PROPHECY--a yeast phenome database, update 2006.

Connecting genotype to phenotype is fundamental in biomedical research and in our understanding of disease. Phenomics--the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale--connects automated data generation with the development of novel tools for phenotype data integration, mining and visualization. Our yeast phenomics database PROPHECY is available at http://prophecy.lundberg.gu.se. Via phenotyping of 984 heterozygous diploids for all essential genes the genotypes analysed and presented in PROPHECY have been extended and now include all genes in the yeast genome. Further, phenotypic data from gene overexpression of 574 membrane spanning proteins has recently been included. To facilitate the interpretation of quantitative phenotypic data we have developed a new phenotype display option, the Comparative Growth Curve Display, where growth curve differences for a large number of mutants compared with the wild type are easily revealed. In addition, PROPHECY now offers a more informative and intuitive first-sight display of its phenotypic data via its new summary page. We have also extended the arsenal of data analysis tools to include dynamic visualization of phenotypes along individual chromosomes. PROPHECY is an initiative to enhance the growing field of phenome bioinformatics.

River flow and associated transport of sediments and solutes through a highly urbanised catchment, Bradford, West Yorkshire.

The hydrological characteristics of catchments become drastically modified in response to urbanisation. The total contributions and dynamics of runoff, suspended sediment and solutes may change significantly and have important implications downstream where they may affect flooding, instream ecological habitat, water quality and siltation of river channels and lakes. Although an appreciation of the likely hydrological changes is crucial for effective catchment management they are still poorly understood. In this paper we present data from a network of river monitoring stations throughout the heavily urbanised Bradford catchment, West Yorkshire. Sites are upstream, within and downstream of the highly urbanised central part of the catchment. Flow, turbidity (calibrated to suspended sediment concentration) and specific conductance (surrogate for solute concentration), logged at 15-min intervals, are presented for a 12-month period (June 2000 to June 2001). The total amounts and dynamics of flow, solute and suspended sediment transport were investigated. Estimated total flow and suspended sediment transport for the monitoring period were found to be high in response to the high total rainfall. Flow and sediment transport regimes were extremely 'flashy' throughout the catchment and became increasingly flashy in a downstream direction. Suspended sediment discharged from the Bradford subcatchment makes an important contribution to downstream sediment transport on the river Aire at Beal. Data suggest that the urbanised part of the Bradford catchment is extremely important in contributing solutes to the Beck (river). Although flow and sediment are also contributed to the Bradford Beck in the urbanised part of the catchment the data suggest that significant amounts may enter the combined sewer system and bypass the river. Understanding the spatial and temporal variations of flow and the transport of suspended sediment and solutes in rivers in urbanized subcatchments is crucial to their effective management and monitoring. Furthermore, this knowledge may be extremely important to the management and monitoring of downstream rivers in large scale mixed catchments.

Conformation of the exopolysaccharide of Burkholderia cepacia predicted with molecular mechanics (MM3) using genetic algorithm search.

We present a computational conformational analysis of the exopolysaccharide of Burkholderia cepacia, which is believed to play a role in colonization and persistence of B. cepacia in the lungs of cystic fibrosis patients. The repeating unit of the exopolysaccharide is a heptasaccharide with three branches, which cause significant steric restraints. Conformational searches using glygal, an in-house developed software using genetic algorithm search methods, were performed on fragments as well as on the complete repeating unit with wrap-over residues. The force field used for the calculations was MM3(96). The search showed four favored conformations for an isolated repeating unit. However, for a sequence of several repeating units, the calculations indicate a single, well-defined linear conformation.

The use of a genetic algorithm search for molecular mechanics (MM3)-based conformational analysis of oligosaccharides.

We have implemented a system called glygal that can perform conformational searches on oligosaccharides using several different genetic algorithm (GA) search methods. The searches are performed in the torsion angle conformational space, considering both the primary glycosidic linkages as well as the pendant groups (C-5-C-6 and hydroxyl groups) where energy calculations are performed using the MM3(96) force field. The system includes a graphical user interface for setting calculation parameters and incorporates a 3D molecular viewer. The system was tested using dozens of structures and we present two case studies for two previously investigated O-specific oligosaccharides of the Shigella dysenteriae type 2 and 4. The results obtained using glygal show a significant reduction in the number of structures that need to be sampled in order to find the best conformation, as compared to filtered systematic search.

PROPHECY--a database for high-resolution phenomics.

The rapid recent evolution of the field phenomics--the genome-wide study of gene dispensability by quantitative analysis of phenotypes--has resulted in an increasing demand for new data analysis and visualization tools. Following the introduction of a novel approach for precise, genome-wide quantification of gene dispensability in Saccharomyces cerevisiae we here announce a public resource for mining, filtering and visualizing phenotypic data--the PROPHECY database. PROPHECY is designed to allow easy and flexible access to physiologically relevant quantitative data for the growth behaviour of mutant strains in the yeast deletion collection during conditions of environmental challenges. PROPHECY is publicly accessible at http://prophecy.lundberg.gu.se.

Analysis of fish IL-1beta and derived peptide sequences indicates conserved structures with species-specific IL-1 receptor binding: implications for pharmacological design.

A large number of IL-1 protein sequences have become available recently from a range of vertebrate species and especially from bony fish. However, 3D structures are still only known for mammalian IL-1. In this review, we use a multiple sequence alignment of all published non-mammalian vertebrate IL-1beta proteins to locate the structurally important residues critical for maintaining the beta-trefoil fold and we investigate the degree to which functionally important residues involved in receptor binding are conserved across vertebrate species. We find that although there is a high level of variability of positions involved in receptor binding, the mode of binding and overall shape of the ligand-receptor complex is probably maintained. This implies that each species has evolved its own unique interleukin-1 signalling system through ligand-receptor co-evolution. Nonetheless, the IL-1beta processing mechanism in non-mammalian vertebrates remains unclear because, with the exception of three bony fish, all non-mammalian IL-1beta sequences discovered so far lack an ICE (Interleukin Converting Enzyme) cut site. The IL-1 system has become an important drug target because of its significance in inflammatory diseases. Research on peptides derived from IL-1beta has identified peptides that possess agonist activity in humans and in trout, and peptides with antagonist activity. The agonist peptides map to two distinct loop regions of IL-1beta that are known to interact with the flexible domain III of the corresponding receptor. Further analysis of the IL-1 system may prove useful in engineering IL-1 with improved features and in suggesting new avenues for therapeutic intervention.