Search

Sperm DNA damage is a useful biomarker for male infertility diagnosis and prediction of assisted reproduction outcomes. It is associated with reduced fertilization rates, embryo quality and pregnancy rates, and higher rates of spontaneous miscarriage and childhood diseases. This review provides a synopsis of the most recent studies from each of the authors, all of whom have major track records in the field of sperm DNA damage in the clinical setting. It explores current laboratory tests and the accumulating body of knowledge concerning the relationship between sperm DNA damage and clinical outcomes. The paper proceeds to discuss the strengths, weaknesses and clinical applicability of current sperm DNA tests. Next, the biological significance of DNA damage in the male germ line is considered. Finally, as sperm DNA damage is often the result of oxidative stress in the male reproductive tract, the potential contribution of antioxidant therapy in the clinical management of this condition is discussed. DNA damage in human spermatozoa is an important attribute of semen quality. It should be part of the clinical work up and properly controlled trials addressing the effectiveness of antioxidant therapy should be undertaken as a matter of urgency. Sperm DNA damage is a useful biomarker for male infertility diagnosis and prediction of assisted reproduction outcomes. It is associated with reduced fertilization rates, embryo quality and pregnancy rates, and higher rates of spontaneous miscarriage and childhood diseases. With all of these fertility check points, it shows more promise than conventional semen parameters from a diagnostic perspective. Despite this, few infertility clinics use it routinely. This review provides a synopsis of the most recent studies from each of the authors, all of whom have major track records in the field of sperm DNA damage in the clinical setting. It explores current laboratory tests and the accumulating body of knowledge concerning the relationship between sperm DNA damage and clinical outcomes. The paper proceeds to discuss the strengths and weaknesses and clinical applicability of current sperm DNA fragmentation tests. Next, the biological significance of DNA damage in the male germ line is considered. Finally, as sperm DNA damage is often the result of increased oxidative stress in the male reproductive tract, the potential contribution of antioxidant therapy in the clinical management of this condition is discussed. As those working in this field of clinical research, we conclude that DNA damage in human spermatozoa is an important attribute of semen quality which should be carefully assessed in the clinical work up of infertile couples and that properly controlled trials addressing the effectiveness of antioxidant therapy should be undertaken as a matter of urgency., (Copyright © 2013 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.)

Recently, the inshore reefs of the Great Barrier Reef have declined rapidly because of deteriorating water quality. Increased catchment runoff is one potential culprit. The impacts of land-use on coral growth and reef health however are largely circumstantial due to limited long-term data on water quality and reef health. Here we use a 60 year coral core record to show that phosphorus contained in the skeletons (P/Ca) of long-lived, near-shore Porites corals on the Great Barrier Reef correlates with annual records of fertiliser application and particulate phosphorus loads in the adjacent catchment. Skeletal P/Ca also correlates with Ba/Ca, a proxy for fluvial sediment loading, again linking near-shore phosphorus records with river runoff. Coral core records suggest that phosphorus levels increased 8 fold between 1949 and 2008 with the greatest levels coinciding with periods of high fertiliser-phosphorus use. Periods of high P/Ca correspond with intense agricultural activity and increased fertiliser application in the river catchment following agricultural expansion and replanting after cyclone damage. Our results demonstrate how coral P/Ca records can be used to assess terrestrial nutrient loading of vulnerable near-shore reefs.

Aims: We have previously reported alterations in cardiolipin content and inner mitochondrial membrane (IMM) proteomic make-up specifically in interfibrillar mitochondria (IFM) in the type 1 diabetic heart; however, the mechanism underlying this alteration is unknown. The goal of this study was to determine how the cardiolipin biosynthetic pathway and cardiolipin-IMM protein interactions are impacted by type 1 diabetes mellitus., Main Methods: Male FVB mice were made diabetic by multiple low-dose streptozotocin injections and sacrificed five weeks post-diabetic onset. Messenger RNA was measured and cardiac mitochondrial subpopulations were isolated. Further mitochondrial functional experimentation included evaluating the protein expression of the enzymes directly responsible for cardiolipin biosynthesis, as well as ATP synthase activity. Interactions between cardiolipin and ATP synthase subunits were also examined., Key Findings: Western blot analysis revealed a significant decrease in cardiolipin synthase (CRLS) protein content in diabetic IFM, with a concomitant decrease in its activity. ATP synthase activity was also significantly decreased. We identified two novel direct interactions between two subunits of the ATP synthase F0 complex (ATP5F1 and ATP5H), both of which were significantly decreased in diabetic IFM., Significance: Overall, these results indicate that type 1 diabetes mellitus negatively impacts the cardiolipin biosynthetic pathway specifically at CRLS, contributing to decreased cardiolipin content and loss of interactions with key ATP synthase F0 complex constituents in the IFM., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.

Reaction of 6-methyl-1-phenylhept-3-yne-2,6-diol with various aldehydes under Lewis acid conditions provides an atom economical, two-component cascade reaction sequence to novel 2,4-dihydro-1H-benzo[f]isochromene compounds. Aliphatic aldehydes as well as electron-deficient and -rich aromatic aldehydes can be used.

Purpose: To examine factors that influence intraocular pressure (IOP) measurement agreement between Goldmann applanation (GAT), Ocular Response Analyzer (ORA), and Pascal Dynamic Contour tonometers (DCT)., Patients and Methods: In subjects who were diagnosed with primary open-angle glaucoma, ocular hypertension, glaucoma suspect, and normal, we used ORA, DCT, and GAT to obtain corneal hysteresis (CH), corneal resistance factor (CRF), ocular pulse amplitude, and 4 IOP values (ORA-IOPcc; ORA-IOPg; DCT-IOP; and GAT-IOP.) We also obtained corneal curvature, corneal thickness, axial length, retinal nerve fiber layer thickness, visual field parameters, diabetes diagnostic status, and topical IOP-lowering treatment data. Analysis of variance, Bland-Altman, and regression analyses were used to examine IOP agreement and associated factors., Results: In 243 eyes of the 243 subjects, mean DCT-IOP (18.73±4.92) was not different from mean ORA-IOPcc (18.96±5.41) but both were significantly higher than ORA-IOPg (16.97±5.49) and GAT-IOP (16.37±4.97). In multivariate regression models, intermethod differences between IOPg, IOPcc, and DCT-IOP were explained almost completely by variations in CH, CRF, and level of IOP (r(2)=0.98 to 0.99); conversely, intermethod variability between GAT-IOP and the other 3 IOP metrics was only partially explained by the factors evaluated in this study (r(2)=0.31 to 0.65)., Conclusions: Consistent with other studies, we found that the 4 IOP variables examined in this study are not interchangeable. The most consistent confounders of IOP measurement agreement were the ORA-measured corneal parameters, CH and CRF. Thus, accounting for these factors may be important in efforts to obtain accurate transcorneal estimates of IOP.

A synthetic approach to complanadine alkaloids is described which employs a Kondrat'eva reaction to construct the pyridine rings. The viability of this approach is demonstrated by its application to a model substrate accessed from unfunctionalized decalin. The key transformation affords the desired tetracyclic architecture with unprecedented incorporation of substituents on the pyridine ring, implicating the oxazole α-hydroxy group as an active participant in the cycloadduct fragmentation process.

Objectives: Safety net health centers (SNHCs), which include federally qualified health centers (FQHCs) provide primary care for underserved, minority and low income patients. SNHCs across the country are in the process of adopting the patient centered medical home (PCMH) model, based on promising early implementation data from demonstration projects. However, previous demonstration projects have not focused on the safety net and we know little about PCMH transformation in SNHCs., Design: This qualitative study characterizes early PCMH adoption experiences at SNHCs., Setting and Participants: We interviewed 98 staff (administrators, providers, and clinical staff) at 20 of 65 SNHCs, from five states, who were participating in the first of a five-year PCMH collaborative, the Safety Net Medical Home Initiative., Main Measures: We conducted 30-45 minute, semi-structured telephone interviews. Interview questions addressed benefits anticipated, obstacles encountered, and lessons learned in transition to PCMH., Results: Anticipated benefits for participating in the PCMH included improved staff satisfaction and patient care and outcomes. Obstacles included staff resistance and lack of financial support for PCMH functions. Lessons learned included involving a range of staff, anticipating resistance, and using data as frequent feedback., Conclusions: SNHCs encounter unique challenges to PCMH implementation, including staff turnover and providing care for patients with complex needs. Staff resistance and turnover may be ameliorated through improved health care delivery strategies associated with the PCMH. Creating predictable and continuous funding streams may be more fundamental challenges to PCMH transformation.

Neurodegenerative diseases present a wide and complex range of biological and clinical features. Animal models are key to translational research, yet typically only exhibit a subset of disease features rather than being precise replicas of the disease. Consequently, connecting animal to human conditions using direct data-mining strategies has proven challenging, particularly for diseases of the nervous system, with its complicated anatomy and physiology. To address this challenge we have explored the use of ontologies to create formal descriptions of structural phenotypes across scales that are machine processable and amenable to logical inference. As proof of concept, we built a Neurodegenerative Disease Phenotype Ontology (NDPO) and an associated Phenotype Knowledge Base (PKB) using an entity-quality model that incorporates descriptions for both human disease phenotypes and those of animal models. Entities are drawn from community ontologies made available through the Neuroscience Information Framework (NIF) and qualities are drawn from the Phenotype and Trait Ontology (PATO). We generated ~1200 structured phenotype statements describing structural alterations at the subcellular, cellular and gross anatomical levels observed in 11 human neurodegenerative conditions and associated animal models. PhenoSim, an open source tool for comparing phenotypes, was used to issue a series of competency questions to compare individual phenotypes among organisms and to determine which animal models recapitulate phenotypic aspects of the human disease in aggregate. Overall, the system was able to use relationships within the ontology to bridge phenotypes across scales, returning non-trivial matches based on common subsumers that were meaningful to a neuroscientist with an advanced knowledge of neuroanatomy. The system can be used both to compare individual phenotypes and also phenotypes in aggregate. This proof of concept suggests that expressing complex phenotypes using formal ontologies provides considerable benefit for comparing phenotypes across scales and species.

Mitochondrial dysfunction is a contributor to diabetic cardiomyopathy. Previously, we observed proteomic decrements within the inner mitochondrial membrane (IMM) and matrix of diabetic cardiac interfibrillar mitochondria (IFM) correlating with dysfunctional mitochondrial protein import. The goal of this study was to determine whether overexpression of mitochondria phospholipid hydroperoxide glutathione peroxidase 4 (mPHGPx), an antioxidant enzyme capable of scavenging membrane-associated lipid peroxides in the IMM, could reverse proteomic alterations, dysfunctional protein import, and ultimately, mitochondrial dysfunction associated with the diabetic heart. MPHGPx transgenic mice and controls were made diabetic by multiple low-dose streptozotocin injections and examined after 5 wk of hyperglycemia. Five weeks after hyperglycemia onset, in vivo analysis of cardiac contractile function revealed decreased ejection fraction and fractional shortening in diabetic hearts that was reversed with mPHGPx overexpression. MPHGPx overexpression increased electron transport chain function while attenuating hydrogen peroxide production and lipid peroxidation in diabetic mPHGPx IFM. MPHGPx overexpression lessened proteomic loss observed in diabetic IFM. Posttranslational modifications, including oxidations and deamidations, were attenuated in diabetic IFM with mPHGPx overexpression. Mitochondrial protein import dysfunction in diabetic IFM was reversed with mPHGPx overexpression correlating with protein import constituent preservation. Ingenuity Pathway Analyses indicated that oxidative phosphorylation, tricarboxylic acid cycle, and fatty acid oxidation processes most influenced in diabetic IFM were preserved by mPHGPx overexpression. Specific mitochondrial networks preserved included complex I and II, mitochondrial ultrastructure, and mitochondrial protein import. These results indicate that mPHGPx overexpression can preserve the mitochondrial proteome and provide cardioprotective benefits to the diabetic heart.

The functionalisation of decalin by means of an "aliphatic Friedel-Crafts" reaction was reported over fifty years ago by Baddeley et al. This protocol is of current relevance in the context of C-H activation and here we demonstrate its applicability to a range of other saturated hydrocarbons. Structural elucidation of the products is described and a mechanistic rationale for their formation is presented. The "aliphatic Friedel-Crafts" procedure allows for production of novel oxygenated building blocks from abundant hydrocarbons and as such can be considered to add significant synthetic value in a single step.

Numerous disease syndromes are associated with regions of copy number variation (CNV) in the human genome and, in most cases, the pathogenicity of the CNV is thought to be related to altered dosage of the genes contained within the affected segment. However, establishing the contribution of individual genes to the overall pathogenicity of CNV syndromes is difficult and often relies on the identification of potential candidates through manual searches of the literature and online resources. We describe here the development of a computational framework to comprehensively search phenotypic information from model organisms and single-gene human hereditary disorders, and thus speed the interpretation of the complex phenotypes of CNV disorders. There are currently more than 5000 human genes about which nothing is known phenotypically but for which detailed phenotypic information for the mouse and/or zebrafish orthologs is available. Here, we present an ontology-based approach to identify similarities between human disease manifestations and the mutational phenotypes in characterized model organism genes; this approach can therefore be used even in cases where there is little or no information about the function of the human genes. We applied this algorithm to detect candidate genes for 27 recurrent CNV disorders and identified 802 gene-phenotype associations, approximately half of which involved genes that were previously reported to be associated with individual phenotypic features and half of which were novel candidates. A total of 431 associations were made solely on the basis of model organism phenotype data. Additionally, we observed a striking, statistically significant tendency for individual disease phenotypes to be associated with multiple genes located within a single CNV region, a phenomenon that we denote as pheno-clustering. Many of the clusters also display statistically significant similarities in protein function or vicinity within the protein-protein interaction network. Our results provide a basis for understanding previously un-interpretable genotype-phenotype correlations in pathogenic CNVs and for mobilizing the large amount of model organism phenotype data to provide insights into human genetic disorders.

Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of phenotype information between species. We have generated a cross-species phenotype ontology for human, mouse and zebrafish that contains classes from the Human Phenotype Ontology, Mammalian Phenotype Ontology, and generated classes for zebrafish phenotypes. We also provide up-to-date annotation data connecting human genes to phenotype classes from the generated ontology. We have included the data generation pipeline into our continuous integration system ensuring stable and up-to-date releases. This article describes the data generation process and is intended to help interested researchers access both the phenotype annotation data and the associated cross-species phenotype ontology. The resource described here can be used in sophisticated semantic similarity and gene set enrichment analyses for phenotype data across species. The stable releases of this resource can be obtained from http://purl.obolibrary.org/obo/hp/uberpheno/.

Sperm DNA damage has a negative impact on pregnancy rates following assisted reproduction treatment (ART). The aim of the present study was to examine the relationship between sperm DNA fragmentation and live-birth rates after IVF and intracytoplasmic sperm injection (ICSI). The alkaline Comet assay was employed to measure sperm DNA fragmentation in native semen and in spermatozoa following density-gradient centrifugation in semen samples from 203 couples undergoing IVF and 136 couples undergoing ICSI. Men were divided into groups according to sperm DNA damage. Following IVF, couples with <25% sperm DNA fragmentation had a live-birth rate of 33%; in contrast, couples with >50% sperm DNA fragmentation had a much lower live-birth rate of 13%. Following ICSI, no significant differences in sperm DNA damage were found between any groups of patients. Sperm DNA damage was also associated with low live-birth rates following IVF in both men and couples with idiopathic infertility: 39% of couples and 41% of men with idiopathic infertility have high sperm DNA damage. Sperm DNA damage assessed by the Comet assay has a close inverse relationship with live-birth rates after IVF. Sperm DNA damage has a negative impact on assisted reproduction treatment outcome, in particular, on pregnancy rates. The aim of the present study was to examine the relationship between sperm DNA fragmentation and live-birth rates after IVF and intracytoplasmic sperm injection (ICSI). The alkaline Comet assay was employed to measure sperm DNA fragmentation in native semen and in spermatozoa following density-gradient centrifugation in semen samples from 203 couples undergoing IVF and 136 couples undergoing ICSI. Men were divided into groups according to sperm DNA damage and treatment outcome. Following IVF, couples with <25% sperm DNA fragmentation had a live birth rate of 33%. In contrast, couples with >50% sperm DNA fragmentation had a much lower live-birth rate of 13% following IVF. Following ICSI, there were no significant differences in levels of sperm DNA damage between any groups of patients. Sperm DNA damage was also associated with the very low live-birth rates following IVF in both men and couples with idiopathic infertility: 39% of couples and 41% of men have high level of sperm DNA damage. Sperm DNA damage assessed by the Comet assay has a close inverse relationship with live-birth rates after IVF., (Copyright © 2012 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.)

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

Objective: To evaluate the association between electronic health record (EHR) satisfaction and job satisfaction in primary care physicians (PCPs)., Method: Cross-sectional survey of PCPs at 825 primary care practices in North Carolina., Results: Surveys were returned from 283 individuals across 214 practices (26% response rate for practices), of whom 122 were physicians with EHRs and no missing information. We found that for each point increase in EHR satisfaction, job satisfaction increased by ∼0.36 points both in an unadjusted and an adjusted model (β 0.359 unadjusted, 0.361 adjusted; p < 0.001 for both models)., Conclusion: We found that EHR satisfaction was associated with job satisfaction in a cross-sectional survey of PCPs. Our conclusions are limited by suboptimum survey response rate, but if confirmed may have substantial implications for how EHR vendors develop their product to support the needs of PCPs.

Biooxidation of benzoic acid by Ralstonia eutropha B9 provides an unusual cyclohexadiene carboxy diol that contains a quaternary stereocentre. Tricarbonyliron derivatives of this chiron, on treatment with acid, give two isomeric η(5)-cyclohexadienyl complexes as observed by NMR spectroscopy. Both of these can be subjected to the addition of nucleophiles to provide isomeric cyclohexadiene complexes with new substituent patterns, several of which have been characterised crystallographically. De-metallation of these provides a versatile library of cyclohexadiene building blocks, the utility of which is demonstrated by formal syntheses of oseltamivir. The mechanism of product formation and its stereochemical implications are discussed, as are the procedures undertaken to establish the enantiopurity of a representative cyclohexadiene product., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Acanthocephalan parasites can manipulate the behavior of their amphipod intermediate hosts in ways that increase the amphipod's risk of being eaten by a predator that serves as the final host for the parasite. Some asocial amphipod species have been shown to increase the likelihood of aggregation in response to chemical cues associated with predators. If such aggregation has anti-predation benefits, it might be subject to manipulation by parasites. We tested this hypothesis by comparing the preference of parasitized and unparasitized amphipods (Gammarus pseudolimnaeus) for associating with a group of unparasitized conspecifics, both in the presence and absence of chemical cues from predatory brook sticklebacks (Culaea inconstans). Amphipods with encysted parasites (Corynosoma sp.) avoided aggregating, whereas unparasitized amphipods preferred to aggregate. We also found that the risk of predation by sticklebacks faced by an individual amphipod was significantly lower when the amphipod was in a group compared to when it was alone. This suggests that the aggregation response of unparasitized amphipods is an adaptive response to escape predation. This study provides evidence for a novel parasitic manipulation of intermediate host behavior that is likely to increase transmission to the definitive host., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Recent societal acceptance of cannabinoids as recreational and therapeutic drugs has posed a potential hazard to male reproductive health. Mammals have a highly sophisticated endogenous cannabinoid (ECS) system that regulates male (and female) reproduction and exo-cannabinoids may influence it adversely. Therefore it is imperative to determine their effects on male reproduction so that men can make informed choices as to their use. Here, an animal model was used to administer HU210, a synthetic analogue of Δ9-tetrahydrocannabinol (THC) and potent cannabinoid receptor (CB) agonist to determine its effects on reproductive organ weights, spermatogenesis, testicular histology and sperm motility. Its effects on the physiological endocannabinoid system were also investigated. Spermatogenesis was markedly impaired with reductions in total sperm count after 2 weeks of exposure. Spermatogenic efficiency was depleted, and Sertoli cell number decreased as exposure time increased with seminiferous tubules showing germ cell depletion developing into atrophy in some cases. Sperm motility was also adversely affected with marked reductions from 2 weeks on. HU210 also acted on the sperm's endocannabinoid system. Long-term use of exo-cannabinoids has adverse effects on both spermatogenesis and sperm function. These findings highlight the urgent need for studies evaluating the fertility potential of male recreational drug users. HU210, a selective agonist for CB1 and CB2 cannabinoid receptors impairs spermatogenesis and sperm motility and deregulates the endocannabinoid system., (© 2012 The Authors. International Journal of Andrology © 2012 European Academy of Andrology.)

Representing phenotype in a way that can be linked to thousands of molecular genetic and environmental databases is an unresolved research challenge. A recent meeting of the Phenotype Research Coordination Network (RCN) aimed to coordinate and leverage current efforts. The three day summit meeting was hosted by NESCent (The National Evolutionary Synthesis Center) in Durham, North Carolina on the 23(rd) - 25(th) of February, 2012.

The 2010-2011 wet season was one of extreme weather for the State of Queensland, Australia. Major rivers adjacent to the Great Barrier Reef (GBR) were discharging at rates 1.5 to >3 times higher than their long term median. Exposure to photosystem II herbicides has been routinely monitored over a period of up to 5 years at 12 inshore GBR sites. The influence of this wet season on exposure to photosystem II herbicides was examined in the context of this long-term monitoring record and during flood plume events in specific regions. Median exposures expressed as diuron equivalent concentration were an average factor of 2.3 times higher but mostly not significantly different (p<0.05) to the median for the long-term monitoring record. The herbicides metolachlor and tebuthiuron were frequently detected in flood plume waters at concentrations that reached or exceeded relevant water quality guidelines (by up to 4.5 times)., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Mouse phenotype data represents a valuable resource for the identification of disease-associated genes, especially where the molecular basis is unknown and there is no clue to the candidate gene's function, pathway involvement or expression pattern. However, until recently these data have not been systematically used due to difficulties in mapping between clinical features observed in humans and mouse phenotype annotations. Here, we describe a semantic approach to solve this problem and demonstrate highly significant recall of known disease-gene associations and orthology relationships. A Web application (MouseFinder; www.mousemodels.org) has been developed to allow users to search the results of our whole-phenome comparison of human and mouse. We demonstrate its use in identifying ARTN as a strong candidate gene within the 1p34.1-p32 mapped locus for a hereditary form of ptosis., (© 2012 Wiley Periodicals, Inc.)

We report the enantioselective total syntheses of zeylenol (+)-1, as well as its congeners (-)-7 and 16, and of 3-O-debenzoylzeylenone 28. To this end, a new variant of the Kornblum-DeLaMare rearrangement, which utilises neighbouring-group participation to impart regioselectivity, has been developed. The approach employs photooxygenation of building blocks derived from a microbial arene oxidation product., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Objective: To test the hypothesis that patients with chronic low back pain (CLBP) would have reduced paraspinal muscle activity when wearing a heat wrap and that this would be associated with increased stature recovery and short-term improvements in psychological factors., Design: A within-subject repeated-measures design. Muscle activity and stature recovery were assessed before and after a 40-minute unloading period, both without a heat wrap and after 2 hours of wear. Questionnaires were completed after both sessions., Setting: Hospital physiotherapy department., Participants: Patients with CLBP (n=24; age, 48.0±9.0 y; height, 166.6±7.3 cm; body mass, 80.2±12.9 kg) and asymptomatic participants (n=11; age, 47.9±15.4 y; height, 168.7±11.6 cm; body mass, 69.3±13.1 kg) took part in the investigation. Patients on the waiting list for 2 physiotherapist-led rehabilitation programs, and those who had attended the programs during the previous 2 years, were invited to participate., Intervention: Superficial heat wrap., Main Outcome Measures: Paraspinal muscle activity, stature recovery over a 40-minute unloading period, pain, disability, and psychological factors., Results: For the CLBP patients only, the heat wrap was associated with a reduction in nonnormalized muscle activity and a positive short-term effect on self-report of disability, pain-related anxiety, catastrophizing, and self-efficacy. Changes in muscle activity were correlated with changes in stature recovery, and both were also correlated to changes in psychological factors., Conclusions: Use of the heat wrap was associated with a decrease in muscle activity and a short-term improvement in certain aspects of well-being for the CLBP patients. The results confirm the link between the biomechanical and psychological outcome measures., (Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.)

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org.

Background: We sought to determine whether perceived patient-centered medical home (PCMH) characteristics are associated with staff morale, job satisfaction, and burnout in safety net clinics., Methods: Self-administered survey among 391 providers and 382 clinical staff across 65 safety net clinics in 5 states in 2010. The following 5 subscales measured respondents' perceptions of PCMH characteristics on a scale of 0 to 100 (0 indicates worst and 100 indicates best): access to care and communication with patients, communication with other providers, tracking data, care management, and quality improvement. The PCMH subscale scores were averaged to create a total PCMH score., Results: Six hundred three persons (78.0%) responded. In multivariate generalized estimating equation models, a 10% increase in the quality improvement subscale score was associated with higher morale (provider odds ratio [OR], 2.64; 95% CI, 1.47-4.75; staff OR, 3.62; 95% CI, 1.84-7.09), greater job satisfaction (provider OR, 2.45; 95% CI, 1.42-4.23; staff OR, 2.55; 95% CI 1.42-4.57), and freedom from burnout (staff OR, 2.32; 95% CI, 1.31-4.12). The total PCMH score was associated with higher staff morale (OR, 2.63; 95% CI, 1.47-4.71) and with lower provider freedom from burnout (OR, 0.48; 95% CI, 0.30-0.77). A separate work environment covariate correlated highly with the quality improvement subscale score and the total PCMH score, and PCMH characteristics had attenuated associations with morale and job satisfaction when included in models., Conclusions: Providers and staff who perceived more PCMH characteristics in their clinics were more likely to have higher morale, but the providers had less freedom from burnout. Among the PCMH subscales, the quality improvement subscale score particularly correlated with higher morale, greater job satisfaction, and freedom from burnout.

Coral cores were collected along an environmental and water quality gradient through the Whitsunday Island group, Great Barrier Reef (Australia), for trace element and stable isotope analysis. The primary aim of the study was to examine if this gradient could be detected in coral records and, if so, whether the gradient has changed over time with changing land use in the adjacent river catchments. Y/Ca was the trace element ratio which varied spatially across the gradient, with concentrations progressively decreasing away from the river mouths. The Ba/Ca and Y/Ca ratios were the only indicators of change in the gradient through time, increasing shortly after European settlement. The Mn/Ca ratio responded to local disturbance related to the construction of tourism infrastructure. Nitrogen isotope ratios showed no apparent trend over time. This study highlights the importance of site selection when using coral records to record regional environmental signals., (Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.)

The Great Barrier Reef (GBR) is a World Heritage Area and contains extensive areas of coral reef, seagrass meadows and fisheries resources. From adjacent catchments, numerous rivers discharge pollutants from agricultural, urban, mining and industrial activity. Pollutant sources have been identified and include suspended sediment from erosion in cattle grazing areas; nitrate from fertiliser application on crop lands; and herbicides from various land uses. The fate and effects of these pollutants in the receiving marine environment are relatively well understood. The Australian and Queensland Governments responded to the concerns of pollution of the GBR from catchment runoff with a plan to address this issue in 2003 (Reef Plan; updated 2009), incentive-based voluntary management initiatives in 2007 (Reef Rescue) and a State regulatory approach in 2009, the Reef Protection Package. This paper reviews new research relevant to the catchment to GBR continuum and evaluates the appropriateness of current management responses., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Male infertility is a major cause of problems for many couples in conceiving a child. Recently, lifestyle pastimes such as alcohol, tobacco and marijuana have been shown to have further negative effects on male reproduction. The endocannabinoid system (ECS), mainly through the action of anandamide (AEA) and 2-arachidonoylglycerol (2-AG) at cannabinoid (CB(1), CB(2)) and vanilloid (TRPV1) receptors, plays a crucial role in controlling functionality of sperm, with a clear impact on male reproductive potential. Here, sperm from fertile and infertile men were used to investigate content (through LC-ESI-MS), mRNA (through quantitative RT-PCR), protein (through Western Blotting and ELISA) expression, and functionality (through activity and binding assays) of the main metabolic enzymes of AEA and 2-AG (NAPE-PLD and FAAH, for AEA; DAGL and MAGL for 2-AG), as well as of their binding receptors CB(1), CB(2) and TRPV1. Our findings show a marked reduction of AEA and 2-AG content in infertile seminal plasma, paralleled by increased degradation: biosynthesis ratios of both substances in sperm from infertile versus fertile men. In addition, TRPV1 binding was detected in fertile sperm but was undetectable in infertile sperm, whereas that of CB(1) and CB(2) receptors was not statistically different in the two groups. In conclusion, this study identified unprecedented alterations of the ECS in infertile sperm, that might impact on capacitation and acrosome reaction, and hence fertilization outcomes. These alterations might also point to new biomarkers to determine male reproductive defects, and identify distinct ECS elements as novel targets for therapeutic exploitation of ECS-oriented drugs to treat male fertility problems.

This study examined the temporal variability in herbicide delivery to the Great Barrier Reef (GBR) lagoon (Australia) from one of the GBR catchment's major sugarcane growing regions. Annual loads of measured herbicides were consistently in the order of 200+kg. Atrazine, it's degradate desethylatrazine, and diuron contributed approximately 90% of annual herbicide load, with early 'first-flush' events accounting for the majority of herbicide loads leaving the catchment. Assessment of herbicide water-sediment partitioning in flood runoff highlighted the majority of herbicides were transported in predominantly dissolved form, although a considerable fraction of diuron was transported in particulate-bound form (ca. 33%). Diuron was also the herbicide demonstrating the highest concentrations and frequency of detection in sediments collected from catchment waterways and adjacent estuarine-marine environments, an outcome aligning with previous research. Herbicide physico-chemical properties appear to play a crucial role in partitioning between water column and sediment habitat types in GBR receiving ecosystems., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

The extreme 2010-2011 wet season resulted in highly elevated Burdekin River discharge into the Great Barrier Reef lagoon for a period of 200 days, resulting in a large flood plume extending >50km offshore and >100km north during peak conditions. Export of suspended sediment was dominated by clay and fine silt fractions and most sediment initially settled within ∼10km of the river mouth. Biologically-mediated flocculation of these particles enhanced deposition in the initial low salinity zone. Fine silt and clay particles and nutrients remaining in suspension, were carried as far as 100km northward from the mouth, binding with planktonic and transparent exopolymer particulate matter to form large floc aggregates (muddy marine snow). These aggregates, due to their sticky nature, likely pose a risk to benthic organisms e.g. coral and seagrass through smothering, and also by contributing to increased turbidity during wind-induced resuspension events., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Herbicide residues have been measured in the Great Barrier Reef lagoon at concentrations which have the potential to harm marine plant communities. Monitoring on the Great Barrier Reef lagoon following wet season discharge show that 80% of the time when herbicides are detected, more than one are present. These herbicides have been shown to act in an additive manner with regards to photosystem-II inhibition. In this study, the area of the Great Barrier Reef considered to be at risk from herbicides is compared when exposures are considered for each herbicide individually and also for herbicide mixtures. Two normalisation indices for herbicide mixtures were calculated based on current guidelines and PSII inhibition thresholds. The results show that the area of risk for most regions is greatly increased under the proposed additive PSII inhibition threshold and that the resilience of this important ecosystem could be reduced by exposure to these herbicides., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Objective: Consumer-run mental health programs that include advocacy, peer counseling, and mentoring are somewhat commonplace in community mental health services, yet fully peer-operated mental health centers remain novel in the public mental health landscape. This ethnographic study of a consumer-run mental health center had two major aims: to learn what is distinctive about consumer-run services-for example, how they might strengthen personal capacity for social integration-and to explore how the development of these capacities might promote recovery., Methods: Data collection for this modified ethnographic study consisted of ten months of participant observation, coupled with semistructured interviews (N=25), a focus group (N=22), and dramatic skits (N=17), to identify and define the distinctive features of the program, both structurally and from the point of view of participants. Inquiry was framed theoretically by the capabilities approach., Results: Participants in this consumer-run mental health program experienced themselves as accountable for and to their peers in what amounts to a shared project of recovery., Conclusions: As part of a capacity-building approach in consumer-run services, programs should aim to not only provide social support for participants but also foster a culture in which service users are accountable for their peers. Such reciprocity may help to strengthen socialization skills, which could better prepare consumers for participation in the community at large.

A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the "functional similarity" between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the "ortholog conjecture" (or, more properly, the "ortholog functional conservation hypothesis"). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an "open world assumption" (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis.

In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.

We report the first synthesis of a cobalt Cp diene complex wherein the diene is derived by microbial dearomatising dihydroxylation of an aromatic ring. The complex has been characterised crystallographically and its structure is compared to that of an uncomplexed diene precursor.

Background: Existing tools to measure patient-centered medical home (PCMH) adoption are not designed for research evaluation in safety-net clinics., Objective: Develop a scale to measure PCMH adoption in safety-net clinics., Research Design: Cross-sectional survey., Subjects: Sixty-five clinics in five states., Main Measures: Fifty-two-item Safety Net Medical Home Scale (SNMHS). The total score ranges from 0 (worst) to 100 (best) and is an average of multiple subscales (0-100): Access and Communication, Patient Tracking and Registry, Care Management, Test and Referral Tracking, Quality Improvement, and External Coordination. The scale was tested for internal consistency reliability and tested for convergent validity using The Assessment of Chronic Illness Care (ACIC) and the Patient-Centered Medical Home Assessment (PCMH-A). The scale was applied to centers in the sample. In addition, linear regression models were used to measure the association between clinic characteristics and medical home adoption., Results: The SNMHS had high internal consistency reliability (Cronbach's alpha = 0.84). The SNMHS score correlated moderately with the ACIC score (r = 0.64, p < 0.0001) and the PCMH-A (r = 0.56, p < 0.001). The mean SNMHS score was 61 ± SD 13. Among the subscales, External Coordination (66 ± 16) and Access and Communication (65 ± 14) had the highest mean scores, while Quality Improvement (55 ± 17) and Care Management (55 ± 16) had lower mean scores. Clinic characteristics positively associated with total SNMHS score were having more providers (β 15.8 95% CI 8.1-23.4 >8 provider FTEs compared to <4 FTEs) and participation in financial incentive programs (β 8.4 95% 1.6-15.3)., Conclusion: The SNMHS demonstrated reliability and convergent validity for measuring PCMH adoption in safety-net clinics. Some clinics have significant PCMH adoption. However, room for improvement exists in most domains, especially for clinics with fewer providers.

The exchange of histones with protamines in sperm DNA results in sperm chromatin compaction and protection. Variations in sperm protamine expression are associated with male infertility. The aim of this study was to investigate relationships between DNA fragmentation, sperm protamines and assisted reproduction treatment. Semen and spermatozoa prepared by density-gradient centrifugation (DGC) from 73 men undergoing IVF and 24 men undergoing intracytoplasmic sperm injection (ICSI) were included in the study. Nuclear DNA fragmentation was assessed using the alkaline Comet assay and protamines were separated by acid-urea polyacrylamide gels. Sperm DNA fragmentation and protamine content (P1-DNA, P2-DNA, P1+P2-DNA) decreased in spermatozoa after DGC. Abnormally high and low P1/P2 ratios were associated with increased sperm DNA fragmentation. Couples with idiopathic infertility had abnormally high P1/P2 ratios. Fertilization rates and embryo quality decreased as sperm DNA fragmentation or protamines increased. Sperm DNA fragmentation was lower in couples achieving pregnancies after IVF, but not after ICSI. There was no correlation between protamine content (P1-DNA, P2-DNA, P1+P2-DNA) or P1/P2 ratios and IVF or ICSI pregnancies. Increased sperm DNA fragmentation was associated with abnormal protamination and resulted in lower fertilization rates, poorer embryo quality and reduced pregnancy rates., (Copyright © 2011 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.)

TRPA1 is a unique sensor of noxious stimuli and, hence, a potential drug target for analgesics. Here we show that the antinociceptive effects of spinal and systemic administration of acetaminophen (paracetamol) are lost in Trpa1(-/-) mice. The electrophilic metabolites N-acetyl-p-benzoquinoneimine and p-benzoquinone, but not acetaminophen itself, activate mouse and human TRPA1. These metabolites also activate native TRPA1 and, as a consequence, reduce voltage-gated calcium and sodium currents in primary sensory neurons. The N-acetyl-p-benzoquinoneimine metabolite L-cysteinyl-S-acetaminophen was detected in the mouse spinal cord after systemic acetaminophen administration. In the hot-plate test, intrathecal administration of N-acetyl-p-benzoquinoneimine, p-benzoquinone and the electrophilic TRPA1 activator cinnamaldehyde produced antinociception that was lost in Trpa1(-/-) mice. Intrathecal injection of a non-electrophilic cannabinoid, Δ(9)-tetrahydrocannabiorcol, also produced TRPA1-dependent antinociception in this test. Our study provides a molecular mechanism for the antinociceptive effect of acetaminophen and discloses spinal TRPA1 activation as a potential pharmacological strategy to alleviate pain.

Catalytic quantities of bismuth(III) triflate efficiently initiate the rearrangement of epoxides to aldehydes, which subsequently react with (Z)-δ-hydroxyalkenylsilanes to afford 2,6-disubstituted 3,6-dihydro-2H-pyrans. Isolated yields of desired products using Bi(OTf)(3) were compared with yields obtained when the reactions were run with TfOH and TMSOTf in the presence and absence of several additives. These studies, as well as NMR spectroscopic analyses, indicate an initial Lewis acid/base interaction between Bi(OTf)(3) and substrates providing TfOH in situ.

The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods.

The model organism Encyclopedia of DNA Elements (modENCODE) project is a National Human Genome Research Institute (NHGRI) initiative designed to characterize the genomes of Drosophila melanogaster and Caenorhabditis elegans. A Data Coordination Center (DCC) was created to collect, store and catalog modENCODE data. An effective DCC must gather, organize and provide all primary, interpreted and analyzed data, and ensure the community is supplied with the knowledge of the experimental conditions, protocols and verification checks used to generate each primary data set. We present here the design principles of the modENCODE DCC, and describe the ramifications of collecting thorough and deep metadata for describing experiments, including the use of a wiki for capturing protocol and reagent information, and the BIR-TAB specification for linking biological samples to experimental results. modENCODE data can be found at http://www.modencode.org.

(+)-Grandifloracin was synthesized from sodium benzoate by means of a dearomatizing dihydroxylation that proceeds with unusual regioselectivity. Iron diene complexes formed from the arene oxidation product permit the use of otherwise inaccessible transformations. The synthetic material was shown to be antipodal to the natural product, thus determining the absolute configuration of grandifloracin for the first time., (© 2011 American Chemical Society)

Limited data exist in regard to productivity and staffing in the anatomic pathology laboratory. In 2004, the National Society for Histotechnology (NSH) conducted a pilot study to examine productivity and staffing in the histology laboratory. After review of the data, The College of American Pathologists (CAP)/NSH Histotechnology Committee concluded that a larger survey was required to further address and expand on the pilot study findings. In 2007, a total of 2674 surveys were sent out to North American laboratories. From the responses, comparisons of laboratory demographics and productivity were examined by institution type and workload volume. Productivity was measured as the number of paraffin-embedded tissue blocks processed per full-time equivalent per year. This manuscript presents and discusses the data collected from the CAP/NSH Workload Study.

Sperm progressive motility has been reported to be one of the key factors influencing in vitro fertilization rates. However, recent studies have shown that sperm DNA fragmentation is a more robust predictor of assisted reproductive outcomes including reduced fertilization rates, embryo quality, and pregnancy rates. This study aimed to compare the usefulness of sperm progressive motility and DNA damage as predictive tools of in vitro fertilization rates. Here, 136 couples provided 1,767 eggs with an overall fertilization rate of 64.2%. The fertilization rate in vitro correlated with both sperm progressive motility (r² = 0.236; P = 0.002) and DNA fragmentation (r² = -0.318; P < 0.001). The relative risk of a poor fertilization rate was 9.5 times higher in sperm of men with high DNA fragmentation (>40%) compared with 2.6 times in sperm with poor motility (<40%). Further, sperm DNA fragmentation gave a higher specificity (93.3%) in predicting the fertilization rate than progressive motility (77.8%). Finally, the odds ratio to determine fertilization rate (>70%) was 4.81 (1.89-12.65) using progressive motility compared with 24.18 (5.21-154.51) using DNA fragmentation. This study shows that fertilization rates are directly dependent upon both sperm progressive motility and DNA fragmentation, but sperm DNA fragmentation is a much stronger test.

Metabolism of meta-bromobenzoic acid by the blocked mutant Ralstonia eutrophus B9 affords an enantiopure dearomatised halodiene-diol which we demonstrate is a versatile chiron for organic synthesis. The presence of the halogen leads to reactivity that is distinct to that observed for the non-halogenated analogue and also serves as a synthetic handle for further functionalisation.

Microbial 1,2-dihydroxylation of sodium benzoate permits the rapid construction of novel inositol-amino acid hybrid structures. Both β- and γ-amino acids are accessible by means of an acylnitroso Diels-Alder cycloaddition., (© The Royal Society of Chemistry 2011)

Objective: To evaluate sperm DNA fragmentation and semen parameters to diagnose male factor infertility and predict pregnancy after IVF., Design: Prospective study., Setting: Academic research laboratory., Patient(s): Seventy-five couples undergoing IVF and 28 fertile donors., Intervention(s): Sperm DNA fragmentation was measured by the alkaline Comet assay in semen and sperm after density gradient centrifugation (DGC). Binary logistic regression was used to analyze odds ratios (OR) and relative risks (RR) for IVF outcomes., Main Outcome Measure(s): Semen parameters and sperm DNA fragmentation in semen and DGC sperm compared with fertilization rates, embryo quality, and pregnancy., Result(s): Men with sperm DNA fragmentation at more than a diagnostic threshold of 25% had a high risk of infertility (OR: 117.33, 95% confidence interval [CI]: 12.72-2,731.84, RR: 8.75). Fertilization rates and embryo quality decreased as sperm DNA fragmentation increased in semen and DGC sperm. The risk of failure to achieve a pregnancy increased when sperm DNA fragmentation exceeded a prognostic threshold value of 52% for semen (OR: 76.00, CI: 8.69-1,714.44, RR: 4.75) and 42% for DGC sperm (OR: 24.18, CI: 2.89-522.34, RR: 2.16)., Conclusion(s): Sperm DNA testing by the alkaline Comet assay is useful for both diagnosis of male factor infertility and prediction of IVF outcome., (Copyright © 2011 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.)