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Countries in Africa have since joined their counterparts in other regions of the world in adopting IFRSs with over 30 countries either requiring or permitting its use for its companies. This study contributes to academic literature as it presents a bibliometric analysis on the state of IFRS research in Africa. The analysis involves 73 published articles listed on Scopus database between 2005 and 2018. Key findings in the study indicate that the first research document on Scopus database on IFRS in Africa was in 2005, despite its early adoption since 1993 in Zimbabwe. There is a continued upward growth in the volume of publications and citations over the years. The year of first IFRSs adoption is not associated with the volume of publication. Top five leaders in the volume of publication on IFRSs include Tunisia and Egypt, these countries are yet to adopt IFRSs. The dominant subject areas on IFRSs research are Business, Management & Accounting, Economics, Econometrics & Finance and Social Sciences. Only 21 authors and 18 institutions out of over 600 institutions in Africa contribute more than one publication to IFRS research. These institutions and authors are all in six African countries (South Africa, Nigeria, Tunisia, Egypt, Uganda and Ghana). Recommendations from the result include the need for higher visibility of research on IFRS. Approximately 87% of the publications are non-open access and the need for more academic conference on IFRS as conference proceedings accounts for only 11%.

Abstract Eosinophilic leukocytes accumulate in high numbers in the lungs of asthmatic patients, and are believed to be important in the pathogenisis of asthma. A potent eosinophil chemoattractant is produced in the asthmatic lung. This small protein, the chemokine eotaxin, is synthesized by a number of different cell types, and is stimulated by interleukin-4 and interleukin-13, which are produced by T-helper (Th)2 lymphocytes. Low molecular weight compounds have been developed that can block the eotaxin receptor C-C chemokine receptor (CCR)3, and prevent stimulation by eotaxin. This provides the potential for orally available drugs that can prevent eosinophil recruitment into the lung and the associated damage and dysfunction.

A summary of six LHCb results on the topic of charmless hadronic b-hadron decays is presented. These are comprised of: a search for the decay Bs0→Ks0K+K− and updated branching fraction measurements of B(s)0→Ks0h+h′− decays (h=K,π) [1]; the first observation of the decays B0→pp¯π+π−, Bs0→pp¯K+K−,Bs0→pp¯K+π− and strong evidence for the decay B0→pp¯K+K− [2]; the first observation of the decay Bs0→pΛ¯K− [3]; a search for the decay Bs0→φη′ [4]; the first observation of the decay Ξb−→pK−K− [5] and evidence for CP-violation in Λb0→pπ−π+π− decays [6].

Abstract Background Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. Results On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. Conclusions TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community.

Abstract Background MapReduce is a parallel framework that has been used effectively to design large-scale parallel applications for large computing clusters. In this paper, we evaluate the viability of the MapReduce framework for designing phylogenetic applications. The problem of interest is generating the all-to-all Robinson-Foulds distance matrix, which has many applications for visualizing and clustering large collections of evolutionary trees. We introduce MrsRF (MapReduce Speeds up RF), a multi-core algorithm to generate a t × t Robinson-Foulds distance matrix between t trees using the MapReduce paradigm. Results We studied the performance of our MrsRF algorithm on two large biological trees sets consisting of 20,000 trees of 150 taxa each and 33,306 trees of 567 taxa each. Our experiments show that MrsRF is a scalable approach reaching a speedup of over 18 on 32 total cores. Our results also show that achieving top speedup on a multi-core cluster requires different cluster configurations. Finally, we show how to use an RF matrix to summarize collections of phylogenetic trees visually. Conclusion Our results show that MapReduce is a promising paradigm for developing multi-core phylogenetic applications. The results also demonstrate that different multi-core configurations must be tested in order to obtain optimum performance. We conclude that RF matrices play a critical role in developing techniques to summarize large collections of trees.

Abstract Background Motor neurone disease (MND) is a devastating illness which leads to muscle weakness and death, usually within 2-3 years of symptom onset. Respiratory insufficiency is a common cause of morbidity, particularly in later stages of MND and respiratory complications are the leading cause of mortality in MND patients. Non Invasive Ventilation (NIV) is the current standard therapy to manage respiratory insufficiency. Some MND patients however do not tolerate NIV due to a number of issues including mask interface problems and claustrophobia. In those that do tolerate NIV, eventually respiratory muscle weakness will progress to a point at which intermittent/overnight NIV is ineffective. The NeuRx RA/4 Diaphragm Pacing System was originally developed for patients with respiratory insufficiency and diaphragm paralysis secondary to stable high spinal cord injuries. The DiPALS study will assess the effect of diaphragm pacing (DP) when used to treat patients with MND and respiratory insufficiency. Method/Design 108 patients will be recruited to the study at 5 sites in the UK. Patients will be randomised to either receive NIV (current standard care) or receive DP in addition to NIV. Study participants will be required to complete outcome measures at 5 follow up time points (2, 3, 6, 9 and 12 months) plus an additional surgery and 1 week post operative visit for those in the DP group. 12 patients (and their carers) from the DP group will also be asked to complete 2 qualitative interviews. Discussion The primary objective of this trial will be to evaluate the effect of Diaphragm Pacing (DP) on survival over the study duration in patients with MND with respiratory muscle weakness. The project is funded by the National Institute for Health Research, Health Technology Assessment (HTA) Programme (project number 09/55/33) and the Motor Neurone Disease Association and the Henry Smith Charity. Trial Registration: Current controlled trials ISRCTN53817913. The views and opinions expressed therein are those of the authors and do not necessarily reflect those of the HTA programme, NIHR, NHS or the Department of Health.

Abstract Background DNA methylation is an epigenetic mechanism associated with regulation of gene expression and it is modulated during chemical carcinogenesis. The zebrafish is increasingly employed as a human disease model; however there is a lack of information on DNA methylation in zebrafish and during fish tumorigenesis. Results A novel CpG island tiling array containing 44,000 probes, in combination with immunoprecipitation of methylated DNA, was used to achieve the first comprehensive methylation profiling of normal adult zebrafish liver. DNA methylation alterations were detected in zebrafish liver tumors induced by the environmental carcinogen 7, 12-dimethylbenz(a)anthracene. Genes significantly hypomethylated in tumors were associated particularly with proliferation, glycolysis, transcription, cell cycle, apoptosis, growth and metastasis. Hypermethylated genes included those associated with anti-angiogenesis and cellular adhesion. Of 49 genes that were altered in expression within tumors, and which also had appropriate CpG islands and were co-represented on the tiling array, approximately 45% showed significant changes in both gene expression and methylation. Conclusion The functional pathways containing differentially methylated genes in zebrafish hepatocellular carcinoma have also been reported to be aberrantly methylated during tumorigenesis in humans. These findings increase the confidence in the use of zebrafish as a model for human cancer in addition to providing the first comprehensive mapping of DNA methylation in the normal adult zebrafish liver.

Abstract Background Asthma management guidelines recommend a stepwise approach to instituting and adjusting anti-inflammatory controller therapy for children with asthma. The objective of this retrospective observational study was to describe prescribing patterns of asthma controller therapies for children in a primary care setting. Methods Data from the UK General Practice Research Database were examined for children with recorded asthma or recurrent wheezing who, from September 2006 through February 2007, were ≤ 14 years old at the time of a first asthma controller prescription after ≥ 6 months without a controller prescription. We evaluated demographic characteristics, asthma duration, comorbidities, asthma-related health care resource use, and prescribed daily dose of controller medication. In addition, physicians for 635 randomly selected patients completed a survey retrospectively classifying asthma severity at the prescription date and describing therapy and health care utilization for 6 prior months. Results We identified 10,004 children, 5942 (59.4%) of them boys, of mean (SD) age of 8.0 (3.8) years. Asthma controller prescriptions were for inhaled corticosteroid (ICS) monotherapy for 9059 (90.6%) children; ICS plus long-acting β2-agonist (LABA) for 698 (7.0%); leukotriene antagonist monotherapy for 91 (0.9%); ICS plus leukotriene antagonist for 55 (0.6%); and other therapy for 101 (1.0%), including 45 (0.45%) children who were prescribed LABA as monotherapy. High doses of ICS (> 400 μg) were prescribed for 44/2140 (2.1%) children < 5 years old and for 420/7452 (5.6%) children ≥ 5 years. Physicians reported asthma severity as intermittent for 346/635 (55%) patients and as mild, moderate, and severe persistent for 159 (25%), 71 (11%), and 11 (2%), respectively (severity data missing for 48 [8%]). The baseline characteristics and controller therapy prescriptions of the survey cohort were similar to those of the full cohort. Conclusions Physician classifications of asthma severity did not always correspond to guideline recommendations, as leukotriene receptor antagonists were rarely used and high-dose ICS or add-on LABA was prescribed even in intermittent and mild disease. In UK primary care, monotherapy with ICS is the most common controller therapy at all levels of asthma severity.

Abstract Background The present study is aimed at identifying potential candidate genes as prognostic markers in human oral tongue squamous cell carcinoma (SCC) by large scale gene expression profiling. Methods The gene expression profile of patients (n=37) with oral tongue SCC were analyzed using Affymetrix HG_U95Av2 high-density oligonucleotide arrays. Patients (n=20) from which there were available tumor and matched normal mucosa were grouped into stage (early vs. late) and nodal disease (node positive vs. node negative) subgroups and genes differentially expressed in tumor vs. normal and between the subgroups were identified. Three genes, GLUT3, HSAL2, and PACE4, were selected for their potential biological significance in a larger cohort of 49 patients via quantitative real-time RT-PCR. Results Hierarchical clustering analyses failed to show significant segregation of patients. In patients (n=20) with available tumor and matched normal mucosa, 77 genes were found to be differentially expressed (P< 0.05) in the tongue tumor samples compared to their matched normal controls. Among the 45 over-expressed genes, MMP-1 encoding interstitial collagenase showed the highest level of increase (average: 34.18 folds). Using the criterion of two-fold or greater as overexpression, 30.6%, 24.5% and 26.5% of patients showed high levels of GLUT3, HSAL2 and PACE4, respectively. Univariate analyses demonstrated that GLUT3 over-expression correlated with depth of invasion (PHSAL2 was positively associated with depth of invasion (P=0.015) and advanced T stage (P=0.047). In survival studies, only GLUT3 showed a prognostic value with disease-free (P=0.049), relapse-free (P=0.002) and overall survival (P=0.003). PACE4 mRNA expression failed to show correlation with any of the relevant parameters. Conclusion The characterization of genes identified to be significant predictors of prognosis by oligonucleotide microarray and further validation by real-time RT-PCR offers a powerful strategy for identification of novel targets for prognostication and treatment of oral tongue carcinoma.

Abstract Background Community acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) increasingly causes disease worldwide. USA300 has emerged as the predominant clone causing superficial and invasive infections in children and adults in the USA. Epidemiological studies suggest that USA300 is more virulent than other CA-MRSA. The genetic determinants that render virulence and dominance to USA300 remain unclear. Results We sequenced the genomes of two pediatric USA300 isolates: one CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at Texas Children's Hospital in Houston. DNA sequencing was performed by Sanger dideoxy whole genome shotgun (WGS) and 454 Life Sciences pyrosequencing strategies. The sequence of the USA300 MRSA strain was rigorously annotated. In USA300-MRSA 2658 chromosomal open reading frames were predicted and 3.1 and 27 kilobase (kb) plasmids were identified. USA300-MSSA contained a 20 kb plasmid with some homology to the 27 kb plasmid found in USA300-MRSA. Two regions found in US300-MRSA were absent in USA300-MSSA. One of these carried the arginine deiminase operon that appears to have been acquired from S. epidermidis. The USA300 sequence was aligned with other sequenced S. aureus genomes and regions unique to USA300 MRSA were identified. Conclusion USA300-MRSA is highly similar to other MRSA strains based on whole genome alignments and gene content, indicating that the differences in pathogenesis are due to subtle changes rather than to large-scale acquisition of virulence factor genes. The USA300 Houston isolate differs from another sequenced USA300 strain isolate, derived from a patient in San Francisco, in plasmid content and a number of sequence polymorphisms. Such differences will provide new insights into the evolution of pathogens.

Introduction: Carotenoids are naturally occurring pigments in plants and are responsible for the orange, yellow, and red color of fruits and vegetables. Carrots are one of the primary dietary sources of carotenoids. The biological activities of carotenoids in higher organisms, including their immunomodulatory activities, are well documented in most tissues but not the large intestine. The gastrointestinal barrier acts as a line of defense against the systemic invasion of pathogenic bacteria, especially at the colonic level., Methods: To test whether carotenoids in orange carrots can alleviate obesity-associated gut inflammation and strengthen the intestinal barrier function, male C57BL/6J mice were randomized to one of four experimental diets for 20 weeks (n = 20 animals/group): Low-fat diet (LFD, 10% calories from fat), high-fat diet (HFD, 45% calories from fat), HFD with white carrot powder (HFD+WC), or HFD with orange carrot powder (HFD + OC). Colon tissues were harvested to analyze the biochemical effects of carotenoids in carrots. The distal sections were subjected to isobaric labeling-based quantitative proteomics in which tryptic peptides were labeled with tandem mass tags, followed by fractionation and LC-MS/MS analysis in an Orbitrap Eclipse Tribrid instrument., Results: High-performance liquid chromatography results revealed that the HFD+WC pellets were carotenoid-deficient, and the HFD+OC pellets contained high concentrations of provitamin A carotenoids, specifically α-carotene and β-carotene. As a result of the quantitative proteomics, a total of 4410 differentially expressed proteins were identified. Intestinal barrier-associated proteins were highly upregulated in the HFD+OC group, particularly mucin-2 (MUC-2). Upon closer investigation into mucosal activity, other proteins related to MUC-2 functionality and tight junction management were upregulated by the HFD+OC dietary intervention., Discussion: Collectively, our findings suggest that carotenoid-rich foods can prevent high-fat diet-induced intestinal barrier disruption by promoting colonic mucus synthesis and secretion in mammalian organisms. Data are available via ProteomeXchange with identifier PXD054150., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Balbuena, Milhem, Kiremitci, Williams, Collins, Shu and Eroglu.)

Lay Abstract: Research has shown that autistic individuals often have unusually good musical skills and that combining words and music helps autistic individuals to focus on spoken words. This study tests the idea that music will help with early language learning of preschool autistic children. The results show that when caregivers sing words to autistic children, the children pay more attention to the caregiver than when the words are spoken and that they learn word combinations more easily., Competing Interests: Declaration of conflicting interestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship and/or publication of this article.

Atypical predictive processing has been associated with autism across multiple domains, based mainly on artificial antecedents and consequents. As structured sequences where expectations derive from implicit learning of combinatorial principles, language and music provide naturalistic stimuli for investigating predictive processing. In this study, we matched melodic and sentence stimuli in cloze probabilities and examined musical and linguistic prediction in Mandarin- (Experiment 1) and English-speaking (Experiment 2) autistic and non-autistic individuals using both production and perception tasks. In the production tasks, participants listened to unfinished melodies/sentences and then produced the final notes/words to complete these items. In the perception tasks, participants provided expectedness ratings of the completed melodies/sentences based on the most frequent notes/words in the norms. While Experiment 1 showed intact musical prediction but atypical linguistic prediction in autism in the Mandarin sample that demonstrated imbalanced musical training experience and receptive vocabulary skills between groups, the group difference disappeared in a more closely matched sample of English speakers in Experiment 2. These findings suggest the importance of taking an individual differences approach when investigating predictive processing in music and language in autism, as the difficulty in prediction in autism may not be due to generalized problems with prediction in any type of complex sequence processing., (© 2024 The Authors. Autism Research published by International Society for Autism Research and Wiley Periodicals LLC.)

Background & Aims: Activated CD8 + T cells are elevated in Nonalcoholic steatohepatitis (NASH) and are important for driving fibrosis and inflammation. Despite this, mechanisms of CD8 + T cell activation in NASH are largely limited. Specific CD8 + T cell subsets may become activated through metabolic signals or cytokines. However, studies in NASH have not evaluated the impact of antigen presentation or the involvement of specific antigens. Therefore, we determined if activated CD8 + T cells are dependent on MHC class I expression in NASH to regulate fibrosis and inflammation., Methods: We used H2Kb and H2Db deficient (MHC I KO ) , Kb transgenic mice, and myeloid cell Kb deficient mice (LysM Kb KO) to investigate how MHC class I impacts CD8 + T cell function and NASH. Flow cytometry, gene expression, and histology were used to examine hepatic inflammation and fibrosis. The hepatic class I immunopeptidome was evaluated by mass spectrometry., Results: In NASH, MHC class I isoform H2Kb was upregulated in myeloid cells. MHC I KO demonstrated protective effects against NASH-induced inflammation and fibrosis. Kb mice exhibited increased fibrosis in the absence of H2Db while LysM Kb KO mice showed protection against fibrosis but not inflammation. H2Kb restricted peptides identified a unique NASH peptide Ncf2 capable of CD8 + T cell activation in vitro . The Ncf2 peptide was not detected during fibrosis resolution., Conclusion: These results suggest that activated hepatic CD8 + T cells are dependent on myeloid cell MHC class I expression in diet induced NASH to promote inflammation and fibrosis. Additionally, our studies suggest a role of NADPH oxidase in the production of Ncf2 peptide generation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Adams, Collins, Williams, Holmes, Hess, Atkins, Scheidemantle, Liu, Lodge, Johnson and Kennedy.)

Host-cell proteins (HCPs) are the foremost class of process-related impurities to be controlled and removed in downstream processing steps in monoclonal antibody (mAb) manufacturing. However, some HCPs may evade clearance in multiple purification steps and reach the final drug product, potentially threatening drug stability and patient safety. This study extends prior work on HCP characterization and persistence in mAb process streams by using mass spectrometry (MS)-based methods to track HCPs through downstream processing steps for seven mAbs that were generated by five different cell lines. The results show considerable variability in HCP identities in the processing steps but extensive commonality in the identities and quantities of the most abundant HCPs in the harvests for different processes. Analysis of HCP abundance in the harvests shows a likely relationship between abundance and the reproducibility of quantification measurements and suggests that some groups of HCPs may hinder the characterization. Quantitative monitoring of HCPs persisting through purification steps coupled with the findings from the harvest analysis suggest that multiple factors, including HCP abundance and mAb-HCP interactions, can contribute to the persistence of individual HCPs and the identification of groups of common, persistent HCPs in mAb manufacturing., (© 2023 Wiley Periodicals LLC.)

Mass spectrometry (MS) has steadily moved into the forefront of quantification-centered protein research. Protein cleavage isotope dilution MS is a proven way for quantifying proteins by using an isotope-labeled analogue of a peptide fragment of the parent protein as an internal standard. Parallel reaction monitoring (PRM) has become the go-to approach for such quantification on an Orbitrap-based instrument as it is assumed that the instrument sensitivity is enhanced. We performed a comparative study on data-dependent acquisition (DDA) and PRM-based workflows to quantify egg yolk protein precursors or vitellogenins (VTGs) Aa, Ab, and C in striped bass ( Morone saxatilis ). VTG proportions serve as a developmental measure of egg quality, possibly changing with the environment, and have been studied as an indicator of the health of North Carolina stocks. Based on single-factor analysis of variance comparisons of mean VTG amounts across fish from the same sample groupings, our results indicate that there is no statistical difference between MS1-based and MS2-based VTG quantification. We further conclude that DDA is able to deliver both discovery data and absolute quantification data in the same experiment., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Rationale: Discovery proteomics has been popularized to be essential in the investigator's biological toolbox. Many biological problems involve the interplay of multiple organisms. Herein, a bottom-up proteomics workflow was developed to study a system containing multiple organisms to promote a thorough understanding of how each interacts with the others., Methods: A label-free quantification proteomics workflow was developed with nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS). This protocol describes a bottom-up proteomics workflow used to study differential protein expression in the context of fleas (Ctenocephalides felis felis) experimentally infected by the bacterium Bartonella henselae, the etiological agent of Cat Scratch Disease (CSD)., Results: Step-by-step instructions are provided for protein extraction, protein cleanup, total protein measurement, nanoLC-MS/MS data acquisition, and data analysis using Proteome Discoverer software. Comprehensive and exhaustive details are included to promote the adoption of this proteomics workflow in other laboratories., Conclusion: A proteomics protocol is detailed for a system containing multiple proteomes from different taxonomic lineages using CSD (cats bitten by fleas infected with Bartonella henselae) as a model. The operating protocol can be readily applied to other label-free proteomics work involving multiple proteomes from taxonomically distinct organisms., (© 2022 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.)

We describe a label-free proteomics protocol for the interrogation of the placental proteome. Step-by-step directions, including tissue cleanup and preparation, proteolytic digestion, nanoLC-MS/MS data collection and data analysis, are provided. The workflow has been applied toward exploring differential protein expression patterns in placentas from women who have been exposed to drugs during pregnancy relative to those who have not. We collected 20 tissue specimens, each representing a combination of spatially diverse sections across the placenta. These specimens were analyzed in the work described here, to survey information across the entire organ. This protocol can be scaled up or down as needed., (© 2021 John Wiley & Sons Ltd.)

Chlamydia protein associating with death domains (CADD) is involved in the biosynthesis of para -aminobenzoate (pABA), an essential component of the folate cofactor that is required for the survival and proliferation of the human pathogen Chlamydia trachomatis . The pathway used by Chlamydiae for pABA synthesis differs from the canonical multi-enzyme pathway used by most bacteria that relies on chorismate as a metabolic precursor. Rather, recent work showed pABA formation by CADD derives from l-tyrosine. As a member of the emerging superfamily of heme oxygenase-like diiron oxidases (HDOs), CADD was proposed to use a diiron cofactor for catalysis. However, we report maximal pABA formation by CADD occurs upon the addition of both iron and manganese, which implicates a heterobimetallic Fe:Mn cluster is the catalytically active form. Isotopic labeling experiments and proteomics studies show that CADD generates pABA from a protein-derived tyrosine (Tyr27), a residue that is ∼14 Å from the dimetal site. We propose that this self-sacrificial reaction occurs through O 2 activation by a probable Fe:Mn cluster through a radical relay mechanism that connects to the "substrate" Tyr, followed by amination and direct oxygen insertion. These results provide the molecular basis for pABA formation in C. trachomatis , which will inform the design of novel therapeutics.

Ependymal cells (ECs) line the ventricular surfaces of the mammalian central nervous system (CNS) and their development is indispensable to structural integrity and functions of the CNS. We previously reported that EC-specific genetic deletion of the myristoylated alanine-rich protein kinase C substrate (Marcks) disrupts barrier functions and elevates oxidative stress and lipid droplet accumulation in ECs causing precocious cellular aging. However, little is known regarding the mechanisms that mediate these changes in ECs. To gain insight into Marcks-mediated mechanisms, we performed mass spectrometric analyses on Marcks-associated proteins in young and aged ECs in the mouse forebrain using an integrated approach. Network analysis on annotated proteins revealed that the identified Marcks-associated complexes are in part involved in protein transport mechanisms in young ECs. In fact, we found perturbed intracellular vesicular trafficking in cultured ECs with selective deletion of Marcks (Marcks-cKO mice), or upon pharmacological alteration to phosphorylation status of Marcks. In comparison, Marcks-associated protein complexes in aged ECs appear to be involved in regulation of lipid metabolism and responses to oxidative stress. Confirming this, we found elevated signatures of inflammation in the cerebral cortices and the hippocampi of young Marcks-cKO mice. Interestingly, behavioral testing using a water maze task indicated that spatial learning and memory is diminished in young Marcks-cKO mice similar to aged wildtype mice. Taken together, our study provides first line of evidence for potential mechanisms that may mediate differential Marcks functions in young and old ECs, and their effect on forebrain homeostasis during aging., (© 2022. The Author(s), under exclusive licence to American Aging Association.)

The growth of advanced analytics in manufacturing monoclonal antibodies (mAbs) has highlighted the challenges associated with the clearance of host cell proteins (HCPs). Of special concern is the removal of "persistent" HCPs, including immunogenic and mAb-degrading proteins, that co-elute from the Protein A resin and can escape the polishing steps. Responding to this challenge, we introduced an ensemble of peptide ligands that target the HCPs in Chinese hamster ovary (CHO) cell culture fluids and enable mAb purification via flow-through affinity chromatography. This study describes their integration into LigaGuard™, an affinity adsorbent featuring an equilibrium binding capacity of ~30 mg of HCPs per mL of resin as well as dynamic capacities up to 16 and 22 mg/ml at 1- and 2-min residence times, respectively. When evaluated against cell culture harvests with different mAb and HCP titers and properties, LigaGuard™ afforded high HCP clearance, with logarithmic removal values (LRVs) up to 1.5, and mAb yield above 90%. Proteomic analysis of the effluents confirmed the removal of high-risk HCPs, including cathepsins, histones, glutathione-S transferase, and lipoprotein lipases. Finally, combining LigaGuard™ for HCP removal with affinity adsorbents for product capture afforded a global mAb yield of 85%, and HCP and DNA LRVs > 4., (© 2022 Wiley Periodicals LLC.)

Among the Ctenocephalides felis felis -borne pathogens, Bartonella henselae , the main aetiological agent of cat scratch disease (CSD), is of increasing comparative biomedical importance. Despite the importance of B. henselae as an emergent pathogen, prevention of the diseases caused by this agent in cats, dogs and humans mostly relies on the use of ectoparasiticides. A vaccine targeting both flea fitness and pathogen competence is an attractive choice requiring the identification of flea proteins/metabolites with a dual effect. Even though recent developments in vector and pathogen -omics have advanced the understanding of the genetic factors and molecular pathways involved at the tick-pathogen interface, leading to discovery of candidate protective antigens, only a few studies have focused on the interaction between fleas and flea-borne pathogens. Taking into account the period of time needed for B. henselae replication in flea digestive tract, the present study investigated flea-differentially abundant proteins (FDAP) in unfed fleas, fleas fed on uninfected cats, and fleas fed on B. henselae -infected cats at 24 hours and 9 days after the beginning of blood feeding. Proteomics approaches were designed and implemented to interrogate differentially expressed proteins, so as to gain a better understanding of proteomic changes associated with the initial B. henselae transmission period (24 hour timepoint) and a subsequent time point 9 days after blood ingestion and flea infection. As a result, serine proteases, ribosomal proteins, proteasome subunit α-type, juvenile hormone epoxide hydrolase 1, vitellogenin C, allantoinase, phosphoenolpyruvate carboxykinase, succinic semialdehyde dehydrogenase, glycinamide ribotide transformylase, secreted salivary acid phosphatase had high abundance in response of C. felis blood feeding and/or infection by B. henselae . In contrast, high abundance of serpin-1, arginine kinase, ribosomal proteins, peritrophin-like protein, and FS-H/FSI antigen family member 3 was strongly associated with unfed cat fleas. Findings from this study provide insights into proteomic response of cat fleas to B. henselae infected and uninfected blood meal, as well as C. felis response to invading B. henselae over an infection time course, thus helping understand the complex interactions between cat fleas and B. henselae at protein levels., Competing Interests: RGM is a co-founder and the Chief Technical Officer for Galaxy Diagnostics Inc. In conjunction with Dr. S. Sontakke and North Carolina State University, EBB holds US Patent No. 7,115,385 Media and Methods for Cultivation of Microorganisms, which was issued on October 3rd, 2006. He is a co-founder, shareholder and Chief Scientific Officer for Galaxy Diagnostics, a company that provides advanced diagnostic testing for the detection of Bartonella spp. infections. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 André, Neupane, Lappin, Herrin, Smith, Williams, Collins, Bai, Jorge, Balbuena, Bradley, Maggi and Breitschwerdt.)

Plant parasitic nematode (PPN) control has historically relied on the use of synthetic chemical nematicides, however many are toxic to both human health and the environment. The withdrawal of the more harmful nematicides coupled with increases in soil temperatures and increased occurrence of pests and diseases associated with climate change, may enable PPN to increase in numbers and spread globally. The need for sustainable and environmentally friendly management options is necessary while facing future food security scares in order to feed the ever-growing population. Seaweed extracts have been used for decades in agriculture and horticulture as soil biostimulants, however there is a growing body of evidence to suggest that they could be used to reduce the occurrence of damaging PPN infections. Using meta-analysis, we investigated whether seaweed extracts applied to soil could reduce root knot nematode (RKN) abundance and whether there could be confounding factors that influence their efficacy. We found that seaweed extracts reduce RKN performance and that various factors affected the efficacy of seaweed, including the seaweed species itself and the crop the seaweed was applied to. Ascophyllum nodosum extracts were found to be the most effective. Particular RKN species were more sensitive than others to seaweed species used and, in some cases, specific seaweed species only affected particular RKN species . Different life cycle stages were also differentially susceptible to seaweed application, where both egg hatching and population abundance could be reduced via seaweed use. This research indicates that seaweed extracts could potentially be used to help reduce RKN attack on plants., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)

Background: About 30% of children with autism spectrum disorder (ASD) do not develop functional speech and remain non-verbal or minimally verbal even after years of speech, language and educational interventions. A wide range of interventions have been developed for improving communication in ASD, but none have proved effective in eliciting functional language in ASD children. Research has found that people with ASD are more likely to have perfect pitch and prefer music to language. Further, it seems that language delay tends to co-occur with better musical skills. Brain imaging research has found that music alongside words increases the attention that people with ASD pay to spoken words., Methods: In this protocol, we describe our music-assisted programmes (MAP) that will use music to attract the attention of people with ASD to speech. MAP may open the brain pathways to language and therefore help improve communication skills for people with ASD more than standard communication protocols. In particular, we aim to develop and test whether individualised, easily used MAP would increase spoken language in 24-60-month-old, nonverbal or minimally verbal children with ASD. We will develop a structured training method, delivered through naturalistic, interactive activities (e.g. songs) to teach language to ASD children. We will test this by comparing two groups: one undertaking music-assisted programmes, and the other receiving speech and language therapy in the way that is recommended in NHS clinics. Participants will be allocated to groups randomly. The feasibility of MAP will be assessed through estimations of recruitment and retention rates, the sensitivity and reliability of the outcome measures, the intensity and frequency of the trial, the usability of the MAP app (beta version), and the burden of the assessments for the children and parents., Discussion: This feasibility randomised controlled trial will establish the acceptability and estimate the power of the MAP intervention to improve early word learning in children with ASD. In the longer term, this research will help us develop an app for parents or carers of children with ASD to design their own songs and implement their own individualised MAP., Trial Registration: ISRCTN, ISRCTN12536062 . Registered on 26 June 2019., (© 2021. The Author(s).)

Capture of host cell proteins (HCPs) from cell culture production harvests is critical to ensure the maximum levels specified by international regulatory bodies of product purity for therapeutic monoclonal antibodies (mAbs). Peptide ligands that selectively target the whole spectrum of the HCPs, while letting the mAb product flow through unbound, are an ideal complement to the affinity-based capture step via Protein A chromatography. In this work, we describe the development of HCP-binding peptide ligands, especially focusing on the steps of (1) peptide selection via library screening and (2) quantification of HCP removal via proteomics by mass spectrometry.

The clearance of host cell proteins (HCPs) is of crucial importance in biomanufacturing, given their diversity in composition, structure, abundance, and occasional structural homology with the product. The current approach to HCP clearance in the manufacturing of monoclonal antibodies (mAbs) relies on product capture with Protein A followed by removal of residual HCPs in flow-through mode using ion exchange or mixed-mode chromatography. Recent studies have highlighted the presence of "problematic HCP" species, which are either difficult to remove (Group I), can degrade the mAb product (Group II), or trigger immunogenic reactions (Group III). To improve the clearance of these species, we developed a family of synthetic peptides that target HCPs and exhibit low binding to IgG product. In this study, these peptides were conjugated onto chromatographic resins and evaluated in terms of HCP clearance and mAb yield, using an industrial mAb-producing CHO harvest as model supernatant. To gather detailed knowledge on the binding of individual HCPs, the unbound fractions were subjected to shotgun proteomic analysis by mass spectrometry. It was found that these peptide ligands exhibit superior HCP binding capability compared to those of the benchmark commercial resins commonly used in mAb purification. In addition, some peptide-based resins resulted in much lower losses of product yield compared to these commercial supports. The proteomic analysis showed effective capture of many "problematic HCPs" by the peptide ligands, especially some that are weakly bound by commercial media. Collectively, these results indicate that these peptides show great promise toward the development of next-generation adsorbents for safer and cost-effective manufacturing of biologics., (© 2019 Wiley Periodicals, Inc.)

Background: Viral kinetics impact humoral immune response to HIV; antibody avidity testing helps distinguish recent (<6 months) and long-term HIV infection. This study aims to determine the frequency of recent HIV-1 infection among clients attending ICTC (Integrated Counselling and Testing Centre) using a commercial EIA, to correlate it with a modified in-house avidity assay and to study the impact of ART on anti-HIV-1 antibody maturation., Methods: Commercial LAg Avidity EIA was used to detect antibody avidity among 117 treatment naïve HIV-1 infected individuals. A second-generation HIV ELISA was modified for in-house antibody avidity testing and cutoff was set based on Receiver Operating Characteristic (ROC) analysis. Archived paired samples from 25 HIV-1 infected individuals before ART and after successful ART; samples from 7 individuals responding to ART and during virological failure were also tested by LAg Avidity EIA., Results: Six individuals (5.1%) were identified as recently infected by a combination of LAg avidity assay and HIV-1 viral load testing. The modified in-house avidity assay demonstrated sensitivity and specificity of 100% and 98.2%, respectively, at AI=0.69 by ROC analysis. Median ODn values of individuals when responding to ART were significantly lower than pre-ART [4.136 (IQR 3.437- 4.827) vs 4.455 (IQR 3.748-5.120), p=0.006] whereas ODn values were higher during virological failure [4.260 (IQR 3.665 - 4.515) vs 2.868 (IQR 2.247 - 3.921), p=0.16]., Conclusion: This modified in-house antibody avidity assay is an inexpensive method to detect recent HIV-1 infection. ART demonstrated significant effect on HIV-1 antibody avidity owing to changes in viral kinetics., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: There has been an abundance of studies that have employed quantitative methods to research obsessive compulsive disorder (OCD) and its neurobiology and neurochemistry. However, there appears to be a paucity of research investigating how OCD is experienced by those living with the diagnosis, particularly young people., Method: A qualitative cross-sectional semistructured interview design was used to address this lack of research. Ten young people, aged 14-17 years old, with a diagnosis of OCD were recruited from Child and Adolescent Mental Health Services in the United Kingdom. Thematic analysis was used to analyse the data., Results: Four themes were identified: 'Traumatic and stressful life events', 'Responses to signs of OCD', 'The battle of living with OCD' and 'Ambivalent relationship to help'. Young people reported experiencing stressful or traumatic life events prior to obsessive and compulsive behaviour. OCD behaviours were misunderstood by the young people and others, leading to delays in finding help. A sense of shame among the young people led them to keep their OCD secret due to feeling 'crazy'. The all-encompassing nature of OCD led the young people to withdraw socially. Most of the young people experienced an inner conflict between fighting and giving in to the compulsions., Conclusions: Traumatic experiences may be an important factor in the development of OCD for young people, which might indicate a direction for prevention. The sense of shame and stigma needs addressing if young people are to access help earlier. Education of the public, medical professionals and educators should be a priority., (© 2017 Association for Child and Adolescent Mental Health.)

Background: Deep pressure is widely used by occupational therapists for people with autism spectrum disorders. There is limited research evaluating deep pressure., Objective: To evaluate the immediate effects of deep pressure on young people with autism and severe intellectual disabilities., Methods: Mood and behaviour were rated for 13 pupils with ASD and severe ID before and after deep pressure sessions., Results: Sufficient data was available from 8 participants to be analysed using Tau-U, a nonparametric technique that allows for serial dependence in data. Six showed benefits statistically. Five of these showed benefits across all domains, and one showed benefits on three out of five domains., Relevance to Clinical Practice: Deep pressure appears to be of immediate benefit to this population with autism and severe ID, but the heterogeneity of response suggests that careful monitoring of response should be used and deep pressure discontinued when it is no longer of benefit., Limitations: This is an open label evaluation study using rating scales., Recommendations for Future Research: Future studies of the use of deep pressure should use physiological response measures, in addition to blinded raters for aspects of behaviours such as attitude to learning psychological health not captured physiologically., Competing Interests: The authors declare that they have no competing interests.

Morphing fears (also called transformation obsessions) involve concerns that a person may become contaminated by and acquire undesirable characteristics of others. These symptoms are found in patients with obsessive-compulsive disorder (OCD) and are thought to be related to mental contamination. Given the high levels of distress and interference morphing fears can cause, a reliable and valid assessment measure is needed. This article describes the development and evaluation of the Morphing Fear Questionnaire (MFQ), a 13-item measure designed to assess for the presence and severity of morphing fears. A sample of 900 participants took part in the research. Of these, 140 reported having a current diagnosis of OCD (SR-OCD) and 760 reported never having had OCD (N-OCD; of whom 24 reported a diagnosis of an anxiety disorder and 23 reported a diagnosis of depression). Factor structure, reliability and construct and criterion-related validity were investigated. Exploratory and confirmatory factor analyses supported a one-factor structure replicable across the N-OCD and SR-OCD group. The MFQ was found to have high internal consistency and good temporal stability and showed significantly greater associations with convergent measures (assessing obsessive-compulsive symptoms, mental contamination, thought-action fusion and magical thinking) than with divergent measures (assessing depression and anxiety). Moreover, the MFQ successfully discriminated between the SR-OCD sample and the N-OCD group, anxiety disorder sample and depression sample. These findings suggest that the MFQ has sound psychometric properties and that it can be used to assess morphing fear. Clinical implications are discussed. Copyright © 2015 John Wiley & Sons, Ltd., Key Practitioner Message: Little remains known about morphing fears, but it is an important area of investigation due to symptoms being highly distressing and often debilitating Because morphing fears commonly present as obscure symptoms, they may not be recognized as a type of OCD The MFQ is a robust measure with clinical utility; it can facilitate recognition and assessment of morphing fears The MFQ will allow for further investigations of the prevalence, correlates and treatment outcomes of morphing fears., (Copyright © 2015 John Wiley & Sons, Ltd.)

We evaluated changes in the striped bass (Morone saxatilis) ovary proteome during the annual reproductive cycle using label-free quantitative mass spectrometry and a novel machine learning analysis based on K-means clustering and support vector machines. Modulated modularity clustering was used to group co-variable proteins into expression modules and Gene Ontology (GO) biological process and KEGG pathway enrichment analyses were conducted for proteins within those modules. We discovered that components of the ribosome along with translation initiation and elongation factors generally decrease as the annual ovarian cycle progresses toward ovulation, concomitant with a slight increase in components of the 26S-proteasome. Co-variation within more than one expression module of components from these two multi-protein complexes suggests that they are not only co-regulated, but that co-regulation occurs through more than one sub-network. These components also co-vary with subunits of the TCP-1 chaperonin system and enzymes of intermediary metabolic pathways, suggesting that protein folding and cellular bioenergetic state play important roles in protein synthesis and degradation. We provide further evidence to suggest that protein synthesis and degradation are intimately linked, and our results support function of a proteasome-ribosome supercomplex known as the translasome.

Most organisms rely on olfaction for survival and reproduction. The olfactory system of Drosophila melanogaster is one of the best characterized chemosensory systems and serves as a prototype for understanding insect olfaction. Olfaction in Drosophila is mediated by multigene families of odorant receptors and odorant binding proteins (OBPs). Although molecular response profiles of odorant receptors have been well documented, the contributions of OBPs to olfactory behavior remain largely unknown. Here, we used RNAi-mediated suppression of Obp gene expression and measurements of behavioral responses to 16 ecologically relevant odorants to systematically dissect the functions of 17 OBPs. We quantified the effectiveness of RNAi-mediated suppression by quantitative real-time polymerase chain reaction and used a proteomic liquid chromatography and tandem mass spectrometry procedure to show target-specific suppression of OBPs expressed in the antennae. Flies in which expression of a specific OBP is suppressed often show altered behavioral responses to more than one, but not all, odorants, in a sex-dependent manner. Similarly, responses to a specific odorant are frequently affected by suppression of expression of multiple, but not all, OBPs. These results show that OBPs are essential for mediating olfactory behavioral responses and suggest that OBP-dependent odorant recognition is combinatorial., (© 2011 The Authors. Genes, Brain and Behavior © 2011 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.)

Background: An inflated sense of responsibility is characteristic of obsessive-compulsive disorder (OCD). No previous studies have investigated its origins. Five potential pathways to inflated responsibility beliefs have been proposed; these are tested in this study., Method: A novel measure, the Origins Questionnaire for Adolescents (OQA), was developed to assess experiences on these five pathways. Reliability of the OQA was investigated. The experiences on the five pathways to inflated responsibility beliefs of 16 adolescents with a history of OCD were compared to 16 adolescents with no history of OCD. Parents also reported on adolescents' experiences on the five pathways., Results: Test-retest reliability was high. The internal consistency of the subscales was only partly satisfactory. The groups differed on one pathway; the clinical group reported a higher sense of responsibility for significant incidents with a negative outcome prior to onset of OCD., Conclusions: An inflated sense of responsibility, in combination with the occurrence of specific incidents, might act as a vulnerability factor for development of OCD. Future research should consider how to measure the subtle effects of experiences of responsibility over the course of development.

Two studies examine the experience of 'earworms', unwanted catchy tunes that repeat. Survey data show that the experience is widespread but earworms are not generally considered problematic, although those who consider music to be important to them report earworms as longer, and harder to control, than those who consider music as less important. The tunes which produce these experiences vary considerably between individuals but are always familiar to those who experience them. A diary study confirms these findings and also indicates that, although earworm recurrence is relatively uncommon and unlikely to persist for longer than 24 h, the length of both the earworm and the earworm experience frequently exceed standard estimates of auditory memory capacity. Active attempts to block or eliminate the earworm are less successful than passive acceptance, consistent with Wegner's theory of ironic mental control.

Cognitive behaviour therapy (CBT) for young people with obsessive compulsive disorder (OCD) has become the treatment of first choice. However, the literature is largely based on studies emphasising exposure and response prevention. In this study, we report on a randomised controlled trial of CBT for young people carried out in typical outpatient clinic conditions which focused on cognitions. A randomised controlled trial compares 10 sessions of manualised cognitive behavioural treatment with a 12-week waiting list for adolescents and children with OCD. Assessors were blind to treatment allocation. 21 consecutive patients with OCD aged between 9 and 18 years were recruited. The group who received treatment improved more than a comparison group who waited for 3 months. The second group was treated subsequently using the same protocol and made similar gains. In conclusion, CBT can be delivered effectively to young people with OCD in typical outpatient settings.

The olfactory system of Drosophila melanogaster is one of the best characterized chemosensory systems. Identification of proteins contained in the third antennal segment, the main olfactory organ, has previously relied primarily on immunohistochemistry, and although such studies and in situ hybridization studies are informative, they focus generally on one or few gene products at a time, and quantification is difficult. In addition, purification of native proteins from the antenna is challenging because it is small and encased in a hard cuticle. Here, we describe a simple method for the large-scale detection of soluble proteins from the Drosophila antenna by chromatographic separation of tryptic peptides followed by tandem mass spectrometry with femtomole detection sensitivities. Examination of the identities of these proteins indicates that they originate both from the extracellular perilymph and from the cytoplasm of disrupted cells. We identified enzymes involved with intermediary metabolism, proteins associated with regulation of gene expression, nucleic acid metabolism and protein metabolism, proteins associated with microtubular transport, 8 odorant-binding proteins, protective enzymes associated with antibacterial defense and defense against oxidative damage, cuticular proteins, and proteins of unknown function, which represented about one-third of all soluble proteins. The procedure described here opens the way for precise quantification of any target protein in the Drosophila antenna and should be readily applicable to antennae from other insects.

The coordination-driven self-assembly of two metal-carbonyl-cluster-coordinated dipyridyl donors, (4-C(5)H(4)N)(2)C[triple bond]CCo(2)(CO)(6) (1) and (4-C(5)H(4)N)(2)C[triple bond]CMo(2)Cp(2)(CO)(4) (2), with a linear diplatinum(II) acceptor ligand was investigated. The structures of the resulting self-assembled polygons were found to be controlled by the steric bulk of the metal-carbonyl cluster adduct. The use of a sterically less imposing ligand 1 resulted in a pentagon-hexagon mixture, which was characterized by electrospray ionization time-of-flight mass spectroscopy. The exclusive formation of a [5 + 5] pentagon was achieved by the self-assembly of the bulkier molybdenum donor ligand 2 with a linear organoplatinum(II) acceptor ligand. Molecular force field modeling was used to study the structural details of the pentagonal and hexagonal architectures. The first Fe(3)-Co(6)-Pt(6) trimetal [3 + 3] hexagon was also synthesized via the combination of 1 with a 120 degrees ferrocenyldiplatinum(II) acceptor.

We report the development of split-less nano-flow liquid chromatography mass spectrometric analysis of glycans chemically cleaved from glycoproteins in plasma. Porous graphitized carbon operating under reverse-phase conditions and an amide-based stationary phase operating under hydrophilic interaction conditions are quantitatively compared for glycan separation. Both stationary phases demonstrated similar column efficiencies and excellent retention time reproducibility without an internal standard to correct for retention time shift. The 95% confidence intervals of the mean retention times were +/-4 s across 5 days of analysis for both stationary phases; however, the amide stationary phase was observed to be more robust. The high mass measurement accuracy of less than 2 ppm and fragmentation spectra provided highly confident identifications along with structural information. In addition, data are compared among samples derived from 10 healthy controls, 10 controls with a differential diagnosis of benign gynecologic tumors, and 10 diseased epithelial ovarian cancer patients (EOC). Two fucosylated glycans were found to be up-regulated in healthy controls and provided an accurate diagnostic value with an area under the receiver operator characteristic curve of 0.87. However, these same glycans provided a significantly less diagnostic value when used to differentiate EOC from benign tumor control samples with an area under the curve of 0.73.

Operation of any mass spectrometer requires implementation of mass calibration laws to translate experimentally measured physical quantities into a m/z range. While internal calibration in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) offers several attractive features, including exposure of calibrant and analyte ions to identical experimental conditions (e.g. space charge), external calibration affords simpler pulse sequences and higher throughput. The automatic gain control method used in hybrid linear trap quadrupole (LTQ) FT-ICR-MS to consistently obtain the same ion population is not readily amenable to matrix-assisted laser desorption/ionization (MALDI) FT-ICR-MS, due to the heterogeneous nature and poor spot-to-spot reproducibility of MALDI. This can be compensated for by taking external calibration laws into account that consider magnetic and electric fields, as well as relative and total ion abundances. Herein, an evaluation of external mass calibration laws applied to MALDI-FT-ICR-MS is performed to achieve higher mass measurement accuracy (MMA)., (Copyright (c) 2008 John Wiley & Sons, Ltd.)

Posttranslational modifications such as glycosylation can play a fundamental role in signaling pathways that transform an ordinary cell into a malignant one. The development of a protocol to detect these changes in the preliminary stages of disease can lead to a sensitive and specific diagnostic for the early detection of malignancies such as ovarian cancer in which differential glycan patterns are linked to etiology and progression. Small variations in instrument parameters and sample preparation techniques are known to have significant influence on the outcome of an experiment. For an experiment to be effective and reproducible, these parameters must be optimized for the analyte(s) under study. We present a detailed examination of sample preparation and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS) analysis of O-linked glycans globally cleaved from mucin glycoproteins. Experiments with stable isotope-labeled biomolecules allowed for the establishment of appropriate acquisition times and excitation voltages for MALDI-FT-ICR-MS of oligosaccharides. Quadrupole ion guide optimization studies with mucin glycans identified conditions for the comprehensive analysis of the entire mass range of O-linked carbohydrates in this glycoprotein. Separately optimized experimental parameters were integrated in a method that allowed for the effective study of O-linked glycans.

Recent investigations have implicated aberrant glycosylations in various malignancies, including epithelial ovarian cancer (EOC). The protocol here identifies O-linked carbohydrate patterns in EOC plasma glycoproteins through chemical cleavage and purification of these glycans. Dialyzed plasma is subjected to reductive beta-elimination with alkaline borohydride to release O-linked oligosaccharides from glycoproteins. Enrichment of released glycans, as well as removal of peptide and other contaminants, is followed by carbohydrate pattern analysis with MALDI-FT-ICR-MS.

We report the use of desorption electrospray ionization hybrid Fourier transform ion cyclotron resonance mass spectrometry (DESI-FT-ICR-MS) for the analysis of carbohydrates. Spectra of neat carbohydrates are presented along with their mass measurement accuracies and limits of detection. Furthermore, a comparison is made between the analyses of O-linked glycans from mucin by DESI-FT-ICR-MS and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry. Finally, glycans from mucin are identified by using the high mass measurement accuracy and tandem MS capabilities afforded by the hybrid FT-ICR-MS platform.

Cancer research in recent years has immensely benefited from the development of novel technologies that enable scientists to perform detailed investigations of genomes, transcriptomes, proteomes, and metabolomes. This has invariably furthered knowledge of tumorigenesis and etiology of cancer. The resulting information can, in the foreseeable future, effect a significant change in the pace of cancer research, thereby producing improvements in patient care. Ovarian cancer in particular has received the interest of the scientific community, being the most frequent cause of death from gynecological cancers, characterized by few early symptoms, diagnosis at an advanced stage, as well as poor prognosis. Ovarian cancer is a malignancy in which normal ovarian cells begin to grow in an uncontrolled, abnormal manner and produce tumors in one or both ovaries. Epithelial cancers, the most common ovarian cancers (>80%), develop from cells lining the ovarian surface. Most ovarian cancer research is primarily focused on the early detection and treatment of epithelial ovarian cancer, the more common ovarian malignancy. This review offers an introduction to ovarian cancer, with particular emphasis on human epithelial ovarian cancer. Current methods of detection and therapy are discussed. A survey of promising new protein, gene, and metabolite biomarkers on the horizon is provided. Future prospects for improved diagnosis are offered.

Objective: To compare the frequency of nail biting in 4 settings (interventions) designed to elicit the functions of nail biting and to compare the results with a self-report questionnaire about the functions of nail biting., Design: Randomised allocation of participants to order of conditions., Setting: University Psychology Department., Subjects: Forty undergraduates who reported biting their nails., Interventions: Left alone (boredom), solving maths problems (frustration), reprimanded for nail biting (contingent attention), continuous conversation (noncontingent attention)., Main Outcome Measures: Number of times the undergraduates bit their nails., Results: Nail biting occurred most often in two conditions, boredom and frustration., Conclusion: Nail biting in young adults occurs as a result of boredom or working on difficult problems, which may reflect a particular emotional state. It occurs least often when people are engaged in social interaction or when they are reprimanded for the behavior.

Clostridium thermocellum, a cellulolytic, thermophilic anaerobe, has potential for commercial exploitation in converting fibrous biomass to ethanol. However, ethanol concentrations above 1% (w/v) are inhibitory to growth and fermentation, and this limits industrial application of the organism. Recent work with ethanol-adapted strains suggested that protein changes occurred during ethanol adaptation, particularly in the membrane proteome. A two-stage Bicine-doubled sodium dodecyl sulfate-polyacrylamide gel electrophoresis protocol was designed to separate membrane proteins and circumvent problems associated with membrane protein analysis using traditional gel-based proteomics approaches. Wild-type and ethanol-adapted C. thermocellum membranes displayed similar spot diversity and approximately 60% of proteins identified from purified membrane fractions were observed to be differentially expressed in the two strains. A majority (73%) of differentially expressed proteins were down-regulated in the ethanol-adapted strain. Based on putative identifications, a significant proportion of these down-regulated proteins were involved with carbohydrate transport and metabolism. Approximately one-third of the up-regulated proteins in the ethanol-adapted species were associated with chemotaxis and signal transduction. Overall, the results suggested that membrane-associated proteins in the ethanol-adapted strain are either being synthesized in lower quantities or not properly incorporated into the cell membrane.

Sample preparation techniques for carbohydrate analysis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) are explored, with particular emphasis on analyte/matrix co-crystallization procedures. While carbohydrates are known to prefer 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix of choice, these analytes are quite specific about matrix crystal structure, which in turn is dependent on the rate of drying of analyte/matrix spots on the MALDI target. With N-acetylglucosamine (GlcNAc) and N-acetylneuraminic acid (sialic acid or NeuAc) as test monosaccharides, significant increases in ion abundances are demonstrated with 2,5-DHB/NeuAc spots (>10-fold improvement) and 2,5-DHB/GlcNAc spots ( approximately 5-fold improvement) with active drying. The fine structure of crystals generated in active and passive drying was investigated using powder diffraction. Passively dried samples were shown to consist of an ordered polymorph, crystallizing in the space group P2(1)/a, while the actively dried samples produced a disordered phase crystallizing in the space group Pa. These data provide the wherewithal to engineer a matrix best suited for carbohydrate analyses., (Copyright (c) 2007 John Wiley & Sons, Ltd.)

Previous studies have found beneficial effects of aromatherapy massage for agitation in people with dementia, for pain relief and for poor sleep. Children with autism often have sleep difficulties, and it was thought that aromatherapy massage might enable more rapid sleep onset, less sleep disruption and longer sleep duration. Twelve children with autism and learning difficulties (2 girls and 10 boys aged between 12 years 2 months to 15 years 7 months) in a residential school participated in a within subjects repeated measures design: 3 nights when the children were given aromatherapy massage with lavender oil were compared with 14 nights when it was not given. The children were checked every 30 min throughout the night to determine the time taken for the children to settle to sleep, the number of awakenings and the sleep duration. One boy's data were not analyzed owing to lengthy absence. Repeated measures analysis revealed no differences in any of the sleep measures between the nights when the children were given aromatherapy massage and nights when the children were not given aromatherapy massage. The results suggest that the use of aromatherapy massage with lavender oil has no beneficial effect on the sleep patterns of children with autism attending a residential school. It is possible that there are greater effects in the home environment or with longer-term interventions.

Previous studies show increased levels of lipid peroxidation and neurotoxic by-products of lipid peroxidation including 4-hydroxynonenal (HNE) and acrolein in vulnerable regions of the Alzheimer's disease (AD) brain. To determine if lipid peroxidation occurs early in progression of AD, we analyzed levels of HNE and acrolein in the hippocampus/parahippocampal gyrus (HPG), superior and middle temporal gyrus (SMTG) and cerebellum (CER) of 7 subjects with Mild Cognitive Impairment (MCI), six subjects with early AD (EAD) and sevem age-matched control subjects using liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI/MS/MS). Our data show that there is a statistically significant (P<0.05) increase in HNE in HPG, SMTG and CER in MCI compared to age-matched control subjects. Specimens of SMTG also showed a significant increase in levels of acrolein in MCI. Comparison of EAD and control subjects showed a statistically significant increase in HNE in HPG and SMTG and a significant increase in acrolein in all three brain regions studied. We did not observe any statistically significant differences between MCI and EAD specimens. These results suggest that lipid peroxidation occurs early in the pathogenesis of AD.