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BackgroundDuring resonance frequency (RF) hyperthermia treatment, the temperature of the tumor tissue is elevated to the range of 39–44°C. Accurate temperature monitoring is essential to guide treatments and ensure precise heat delivery and treatment quality. Magnetic resonance (MR) thermometry is currently the only clinical method to measure temperature noninvasively in a volume during treatment. However, several studies have shown that this approach is not always sufficiently accurate for thermal dosimetry in areas with motion, such as the pelvic region. Model-based temperature estimation is a promising approach to correct and supplement 3D online temperature estimation in regions where MR thermometry is unreliable or cannot be measured. However, complete 3D temperature modeling of the pelvic region is too complex for online usage.PurposeThis study aimed to evaluate the use of proper orthogonal decomposition (POD) model reduction combined with Kalman filtering to improve temperature estimation using MR thermometry. Furthermore, we assessed the benefit of this method using data from hyperthermia treatment where there were limited and unreliable MR thermometry measurements.MethodsThe performance of POD–Kalman filtering was evaluated in several heating experiments and for data from patients treated for locally advanced cervical cancer. For each method, we evaluated the mean absolute error (MAE) concerning the temperature measurements acquired by the thermal probes, and we assessed the reproducibility and consistency using the standard deviation of error (SDE). Furthermore, three patient groups were defined according to susceptibility artifacts caused by the level of intestinal gas motion to assess if the POD–Kalman filtering could compensate for missing and unreliable MR thermometry measurements.ResultsFirst, we showed that this method is beneficial and reproducible in phantom experiments. Second, we demonstrated that the combined method improved the match between temperature prediction and temperature acquired by intraluminal thermometry for patients treated for locally advanced cervical cancer. Considering all patients, the POD–Kalman filter improved MAE by 43% (filtered MR thermometry = 1.29°C, POD–Kalman filtered temperature = 0.74°C). Moreover, the SDE was improved by 47% (filtered MR thermometry = 1.16°C, POD–Kalman filtered temperature = 0.61°C). Specifically, the POD–Kalman filter reduced the MAE by approximately 60% in patients whose MR thermometry was unreliable because of the great amount of susceptibilities caused by the high level of intestinal gas motion.ConclusionsWe showed that the POD–Kalman filter significantly improved the accuracy of temperature monitoring compared to MR thermometry in heating experiments and hyperthermia treatments. The results demonstrated that POD–Kalman filtering can improve thermal dosimetry during RF hyperthermia treatment, especially when MR thermometry is inaccurate.

Environmental temperature has effects on sperm quality with differences in susceptibility between cattle subspecies and breeds, but very little is known about the seminal plasma protein (SPP) changes resulting from testicular heat stress. Scrotal insulation (SI) for 48 hr was applied to Brahman (Bos indicus) bulls. Semen was collected at 3-day intervals from before, until 74 days post-SI. The changes in sperm morphology and motility following SI were comparable to previously reported and differences were detected in measures of sperm chromatin conformation as early as 8 days post-SI. New proteins spots, in the SPP two-dimensional (2-D) gels, were apparent when comparing pre-SI with 74 days post-SI, and SPP identified as associated with mechanisms of cellular repair and protection. Similar trends between 2-D gel and Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) data was observed, with SWATH-MS able to quantify individual SPP that otherwise were not resolved on 2-D gel. The SPP assessment at peak sperm damage (21-24 days) showed a significant difference in 29 SPP (adjusted p < .05), and identified six proteins with change in abundance in the SI group. In conclusion both spermatozoa and SPP composition of bulls are susceptible to temperature change incurred by SI, and SPP markers for testicular heat insults may be detected.

Previous studies have applied genomics and transcriptomics to identify immune and genetic markers as key indicator traits for cattle tick susceptibility/resistance; however, results differed between breeds, and there is lack of information on the use of host proteomics. Serum samples from Santa Gertrudis cattle (naïve and phenotyped over 105 days as tick‐resistant [TR] or tick‐susceptible [TS]) were used to conduct differential abundance analyses of protein profiles. Serum proteins were digested into peptides followed by identification and quantification using sequential window acquisition of all instances of theoretical fragment ion mass spectrometry. Before tick infestation, abundance of 28 proteins differed significantly (adjusted P < 10−5) between TR and TS. These differences were also observed following tick infestation (TR vs TS) with a further eight differentially abundant proteins in TR cattle, suggesting possible roles in adaptive responses. The intragroup comparisons (TS‐0 vs TS and TR‐0 vs TR) showed that tick infestation elicited quite similar responses in both groups of cattle, but with relatively stronger responses in TR cattle. Many of the significantly differentially abundant proteins in TR Santa Gertrudis cattle (before and after tick infestation) were associated with immune responses including complement factors, chemotaxis for immune cells and acute‐phase responses.

Background: Among persons with a mild intellectual disability or borderline intellectual functioning, differences in their characteristics imply that a differentiated approach is required to meet their needs. This retrospective study examined whether the history of support/treatment programs and the type of healthcare providers involved matched the specific support needs of persons with a mild intellectual disability or borderline intellectual functioning. Method: Five (previously identified) profiles of persons with a mild intellectual disability or borderline intellectual functioning were used to investigate to what extent the support needs of this group had been met. For the 250 persons with mild intellectual disability or borderline intellectual functioning who matched these five profiles, data were collected retrospectively from their case files. Results: Persons with mild intellectual disability or borderline intellectual functioning received a very similar amount and type of support/treatment programs. Differences between the profiles were found for non-verbal therapy, residential treatment and contacts with social work. Regarding the type of healthcare providers involved, differences between the profiles emerged for specialised intellectual disability services, youth services and specialised addiction services. Conclusions: The support programs for a heterogeneous population of persons with mild intellectual disability or borderline intellectual functioning seem to be suboptimal, indicating that more differentiation is required in the services offered to these individuals.

Background The lexical quality hypothesis proposes that successful reading comprehension requires high quality lexical representations, which allow for efficient retrieval. These retrieval operations have however not been specified. Methods We investigated the contribution of semantic retrieval to reading comprehension in 119 Dutch children in the upper grades of primary school, while taking decoding skills and vocabulary size into account in a longitudinal design. By using verbal fluency tasks, we measured retrieval in line with the structural organisation of the mental lexicon and additionally, a more controlled search through the mental lexicon. Results Semantic retrieval assessed in grade 5 accounted for variance in reading comprehension in grade 6, in addition to variance accounted for by vocabulary size and reading comprehension in grade 5. Conclusions The ability to search through the mental lexicon, along the lines of its hierarchical structure, is important for children's reading comprehension development in the upper primary grades.

Acetohydroxyacid synthase (AHAS) inhibitors are highly successful commercial herbicides. New kinetic data show that the binding of these compounds leads to reversible accumulative inhibition of AHAS. Crystallographic data (to a resolution of 2.17 Å) for an AHAS-herbicide complex shows that closure of the active site occurs when the herbicidal inhibitor binds, thus preventing exchange with solvent. This feature combined with new kinetic data shows that molecular oxygen promotes an accumulative inhibition leading to the conclusion that the exceptional potency of these herbicides is augmented by subversion of an inherent oxygenase side reaction. The reactive oxygen species produced by this reaction are trapped in the active site, triggering oxidation reactions that ultimately lead to the alteration of the redox state of the cofactor flavin adenine dinucleotide (FAD), a feature that accounts for the observed reversible accumulative inhibition.

The development of biomarkers of chemical exposure and effect in threatened wildlife is challenging because traditional methods for biomarker discovery that involve in vivo testing or destructive sampling cannot be utilised. These challenges have long since been acknowledged and the development of non‐destructive methods for the detection of biomarkers in wildlife has been examined for many decades. However, despite these efforts, progress in this field has been slow and the development or confirmation of non‐destructive biomarkers of exposure in threatened wildlife has been limited. The usefulness of cell lines along with non‐targeted omics has not been well explored in this context despite the potential for these methods to greatly enhance non‐destructive biomarker development. In order to explore the usefulness of global protein expression of primary cells cultured from wildlife, we optimised exposure and extraction methods and aimed to initially examine the effect of time and dose on global protein expression. Primary green sea turtle (Chelonia mydas) skin cells developed in our lab were exposed to two contaminants known to accumulate in sea turtles ‐ a polychlorinated biphenyl (PCB153) and perfluoronanoic acid (PFNA). Three environmentally relevant concentrations were chosen for exposure (1 μg/L, 0.1 μg/L, and 0.01 μg/L) and cells were exposed for both 24 or 48 hours. The global protein expression was then quantified using Sequential Windowed Acquisition of all Theoretical Fragment Ion Mass Spectra (SWATH‐MS) resulting in over 1000 unique protein identifications. Our results show that a large number of proteins are significantly differentially expressed when sea turtle primary cells are exposed to chemical contaminants. Over 700 proteins were differentially expressed by cells under exposure conditions and time and concentration had significant effects on overall differential expression as well as on the expression if individual proteins. Most significantly, a biomarker of PCB exposure that has previously been identified in sea turtles (superoxide dismutase) was expressed by the skin cells exposed to PCB indicating that these methods can potentially reflect biomarkers measured in whole organisms. Overall, the results from this study provide insight into the effects that time, dose and treatment have on global protein expression of green sea turtles cells, as well as preliminary evidence for the usefulness of non‐targeted proteomics for biomarker discovery. This indicates the potential of the methods described here to support higher throughput confirmation of biomarkers of exposure and effect while reducing the need for invasive sampling on threatened wildlife.

A unique combined pore approach to the sensitive detection of human insulin is developed. Through a systematic study to understand the impact of pore size and surface chemistry of nanoporous materials on their enrichment and purification performance, the advantages of selected porous materials are integrated to enhance detection sensitivity in a unified two-step process. In the first purification step, a rationally designed large pore material (ca. 100 nm in diameter) is chosen to repel the interferences from nontarget molecules. In the second enrichment step, a hydrophobically modified mesoporous material with a pore size of 5 nm is selected to enrich insulin molecules. A low detection limit of 0.05 ng mL(-1) in artificial urine is achieved by this advanced approach, similar to most antibody-based analysis protocols. This designer approach is efficient and low cost, and thus has great potential in the sensitive detection of biomolecules in complex biological systems.

High-altitude treatment has been applied for more than a century in the treatment of pulmonary diseases including asthma. Many uncontrolled and controlled studies have shown its beneficial effects in children and adolescents with house dust mite allergic asthma. A recent study also showed an improvement in markers of airway inflammation in adult patients with severe intrinsic asthma, suggesting that factors other than HDM avoidance may contribute to the beneficial influence of the high-altitude climate therapy on asthma. The dry mountain climate not only has decreased levels of mite allergens but also decreased levels of pollens, fungal spores and air pollution, as well as high exposure to UV light with immunomodulatory and anti-inflammatory effects. Treatments targeting environmental control have never been investigated systematically in severe asthma, which is surprising, as environmental factors have been recognized as important contributors to asthma severity for many years and more evidence has been accumulating ever since. Preliminary evidence shows the beneficial effects of high-altitude treatment in patients with severe refractory asthma on symptoms, lung function and oral corticosteroid requirement, irrespective of atopic status. In this narrative review, we will discuss why high-altitude treatment might be a promising therapeutic option for patients who suffer from this disabling disease.

Strains of Pseudomonas aeruginosa can be phenotypically classified by their mode of pathogenicity as either invasive, where the bacterium is internalised by host cells, or cytotoxic, where the host cell is killed without internalisation through the expression of cytotoxicity factors. These phenotypes are thought to depend primarily on the interactions of pseudomonal membrane and secreted proteins with host cells. We report here comparisons of outer membrane and extracellular protein-enriched fractions from invasive (PAO1) and cytotoxic (6206) strains of P. aeruginosa separated by two-dimensional (2-D) gel electrophoresis. Gel image comparisons revealed the two strains express essentially identical membrane protein profiles under the conditions investigated. Membrane protein strain differences were typically the result of minor amino acid sequence variations resulting in small mass and isoelectric point shifts visible on 2-D gels. Analysis of extracellular proteins from stationary phase growth, however, revealed significantly different protein profiles. Extracellular fractions from the invasive PAO1 strain were dominated by extracellular proteases including elastase (LasB), LasA protease and chitin-binding protein, as well as several previously designated 'hypothetical' proteins. LasB appeared to be highly processed with 28 discrete mass and isoelectric point forms detected in this study. The significant number of active extracellular proteases (including LasB itself) may account for this processing. Conversely, extracellular fractions from strain 6206 consisted mainly of cellular and membrane exposed proteins including GroEL, DnaK and flagellar subunits. These are thought to result from cellular turnover during growth and the reliance on the secretory mechanisms of this strain to produce high levels of cytotoxicity factors, such as ExoU, which may be produced only upon specific interactions with host cells. These studies will aid in elucidating the differences between invasive and cytotoxic P. aeruginosa at the proteome level.

Background Anti-allergic mattress encasing may provide clinical benefit in asthmatic patients. However, the effect of mattress encasings on allergen-specific parameters, such as bronchial reactions to house dust mite (HDM) challenge, is not clear. Objective To investigate the effect of anti-allergic mattress encasings on allergen sensitivity in patients with moderate to severe asthma. Methods Twenty-seven patients with asthma and HDM allergy were studied in a double-blind, placebo-controlled study. Concentrations of Dermatophagoides pteronyssinus (Der p 1) were measured in mattress dust before and after 1 year of treatment; bronchial histamine challenge, bronchial challenge with HDM and intradermal skin challenges with HDM were performed. The number of eosinophils in peripheral blood was assessed. Results In the active group, but not in the placebo group, there was a significant reduction in Der p 1 concentration in the dust collected from the mattresses after 1 year of treatment compared to before. There was a significant difference between the groups with respect to HDM-induced early-reaction (ER) in the airways and the number of blood eosinophils, which reflected an increase in ER and eosinophils in the placebo group without significant change in the active group. No significant improvement in PC20 histamine, late-reaction (LR) and skin tests was found in either groups. Conclusion Our data suggest that encasings protect against a further increase in allergen sensitivity in asthmatic patients, so their use should be recommended.

The monitoring of gene expression via the technologies encompassed under the term 'proteomics' allows proteins of significance to be related to phenotypes associated with strain variability, environmental influences and the effects of genetic manipulation. The characterizations of these molecules are routinely performed utilising two-dimensional (2-D) gel electrophoresis in association with mass spectrometry for the identification of proteins. Pathogenic bacteria are suitable for proteomic comparisons in the aim of elucidating proteins with vaccine and diagnostic applications, as well as determining novel targets for drug design and the effects of these drugs on cellular physiology. Strains exhibiting diverse phenotypes including antibiotic or chemical resistances, altered mode of pathogenicity, or differential capability of growth in similar environments, can be compared via protein differential display to correlate relative protein abundances associated with these conditions. Technically, proteins are 'mapped' on 2-D arrays under 'standard' conditions and visually compared to arrays of proteins from a variety of test conditions. High-throughput technologies allow molecules of significance to be elucidated rapidly from within complex mixtures using a combination of cellular pre fractionation to determine cellular location and pathway predictions to aid in overcoming the limitations of 2-D gel technology for the analysis of whole proteomes.

With the completion of many genome projects, a shift is now occurring from the acquisition of gene sequence to understanding the role and context of gene products within the genome. The opportunistic pathogen Pseudomonas aeruginosa is one organism for which a genome sequence is now available, including the annotation of open reading frames (ORFs). However, approximately one third of the ORFs are as yet undefined in function. Proteomics can complement genomics, by characterising gene products and their response to a variety of biological and environmental influences. In this study we have established the first two-dimensional gel electrophoresis reference map of proteins from the membrane fraction of P. aeruginosa strain PA01. A total of 189 proteins have been identified and correlated with 104 genes from the P. aeruginosa genome. Annotated membrane proteins could be grouped into three distinct categories: (i) those with functions previously characterised in P. aeruginosa (38%); (ii) those with significant sequence similarity to proteins with assigned function or hypothetical proteins in other organisms (46%); and (iii) those with unknown function (16%). Transmembrane prediction algorithms showed that each identified protein sequence contained at least one membrane-spanning region. Furthermore, the current methodology used to isolate the membrane fraction was shown to be highly specific since no contaminating cytosolic proteins were characterised. Preliminary analysis showed that at least 15 gel spots may be glycosylated in vivo, including three proteins that have not previously been functionally characterised. The reference map of membrane proteins from this organism is now the basis for determining surface molecules associated with antibiotic resistance and efflux, cell-cell signalling and pathogen-host interactions in a variety of P. aeruginosa strains.

Outer membrane proteins (OMPs) of Gram-negative bacteria are key molecules that interface the cell with the environment. Traditional biochemical and genetic approaches have yielded a wealth of knowledge relating to the function of OMPs. Nonetheless, with the completion of the Escherichia coli genome sequencing project there is the opportunity to further expand our understanding of the organization, expression and function of the OMPs in this Gram-negative bacterium. In this report we describe a proteomic approach which provides a platform for parallel analysis of OMPs. We propose a rapid method for isolation of bacterial OMPs using carbonate incubation, purification and protein array by two-dimensional electrophoresis, followed by protein identification using mass spectrometry. Applying this method to examine E. coli K-12 cells grown in minimal media we identified 21 out of 26 (80%) of the predicted integral OMPs that are annotated in SWISS-PROT release 37 and predicted to separate within the range of pH 4-7 and molecular mass 10-80 kDa. Five outer membrane lipoproteins were also identified and only minor contamination by nonmembrane proteins was observed. Importantly, this research readily demonstrates that integral OMPs, commonly missing from 2D gel maps, are amenable to separation by two-dimensional electrophoresis. Two of the identified OMPs (YbiL, YeaF) were previously known only from their ORFs, and their identification confirms the cognate genes are transcribed and translated. Furthermore, we show that like the E. coli iron receptors FhuE and FhuA, the expression of YbiL is markedly increased by iron limitation, suggesting a putative role for this protein in iron transport. In an additional demonstration we show the value of parallel protein analysis to document changes in E. coli OMP expression as influenced by culture temperature.

Progress in the field of proteomics is dependent upon an ability to visualise close to an entire protein complement via a given array technology. These efforts have previously centred upon two-dimensional gel electrophoresis in association with immobilised pH gradients in the first dimension. However, limitations in this technology, including the inability to separate hydrophobic, basic, and low copy number proteins have hindered the analysis of complete proteomes. The challenge is now to overcome these limitations through access to new technology and improvements in existing methodologies. Proteomics can no longer be equated with a single two-dimensional electrophoresis gel. Greater information can be obtained using targeted biological approaches based upon sample prefractionation into specific cellular compartments to determine protein location, while novel immobilised pH gradients spanning single pH units can be used to display poorly abundant proteins due to their increased resolving power and loading capacity. In this study, we show the effectiveness of a combined use of two differential subproteomes (as defined by relative solubilities, cellular location and narrow-range immobilised pH gradients) to increase the resolution of proteins contained on two-dimensional gels. We also present new results confirming that this method is capable of displaying up to a further 45% of a given microbial proteome. Subproteomics, utilising up to 40 two-dimensional gels per sample will become a powerful tool for near-to-total proteome analysis in the postgenome era. Furthermore, this new approach can direct biological focus towards molecules of specific interest within complex cells and thus simplify efforts in discovery-based proteome research.