MIDA–Vinylsilanes: Selective Cross-Couplings and Applications to the Synthesis of Functionalized Stilbenes

A rapid and stereodefined synthesis of MIDA−boryl vinylsilanes has been achieved through the hydrosilylation of an alkynylboronic ester. The E products which contain a silyl and boryl group can be selectively cross-coupled in a two-step bidirectional sequence to provide a rapid and high-yielding synthesis of complex styrenes.

An alkyne hydrosilylation–Hiyama coupling approach to highly functionalised 1,3-dienes

A high yielding and robust protocol for the stereodefined synthesis of 1,3-dienes has been established through a hydrosilylation–Hiyama coupling strategy. In all cases the products were formed as single E,E isomers and conditions are tolerant of a wide range of functional groups not compatible with other methods.

BOB CAT: a Large-Scale Review and Delphi Consensus for Management of Barrett’s Esophagus With No Dysplasia, Indefinite for, or Low-Grade Dysplasia

OBJECTIVES: Barrett’s esophagus (BE) is a common premalignant lesion for which surveillance is recommended. This strategy is limited by considerable variations in clinical practice. We conducted an international, multidisciplinary, systematic search and evidence-based review of BE and provided consensus recommendations for clinical use in patients with nondysplastic, indefinite, and low-grade dysplasia (LGD). METHODS: We defined the scope, proposed statements, and searched electronic databases, yielding 20,558 publications that were screened, selected online, and formed the evidence base. We used a Delphi consensus process, with an 80% agreement threshold, using GRADE (Grading of Recommendations Assessment, Development and Evaluation) to categorize the quality of evidence and strength of recommendations. RESULTS: In total, 80% of respondents agreed with 55 of 127 statements in the final voting rounds. Population endoscopic screening is not recommended and screening should target only very high-risk cases of males aged over 60 years with chronic uncontrolled reflux. A new international definition of BE was agreed upon. For any degree of dysplasia, at least two specialist gastrointestinal (GI) pathologists are required. Risk factors for cancer include male gender, length of BE, and central obesity. Endoscopic resection should be used for visible, nodular areas. Surveillance is not recommended for <5 years of life expectancy. Management strategies for indefinite dysplasia (IND) and LGD were identified, including a de-escalation strategy for lower-risk patients and escalation to intervention with follow-up for higher-risk patients. CONCLUSIONS: In this uniquely large consensus process in gastroenterology, we made key clinical recommendations for the escalation/de-escalation of BE in clinical practice. We made strong recommendations for the prioritization of future research.

The inclusion of open-ended questions on quantitative surveys of children: Dealing with unanticipated responses relating to child abuse and neglect

Web surveys have been shown to be a viable, and relatively inexpensive, method of data collection with children. For this reason, the Kids’ Life and Times (KLT) was developed as an annual online survey of 10 and 11 year old children. Each year, approximately 4,000 children participate in the survey. Throughout the six years that KLT has been running, a range of questions has been asked that are both policy-relevant and important to the lives of children. Given the method employed by the survey, no extremely sensitive questions that might cause the children distress are included. The majority of questions on KLT are closed yielding quantitative data that are analysed statistically; however, one regular open-ended question is included at the end of KLT each year so that the children can suggest questions that they think should be asked on the survey the following year. While most of the responses are innocuous, each year a small minority of children suggest questions on child abuse and neglect. This paper reports the responses to this question and reflects on how researchers can, and should, deal with this issue from both a methodological and an ethical perspective.

Bacteria microarrays as sensitive tools for exploring pathogen surface epitopes and recognition by host receptors

We describe a protocol for the generation and validation of bacteria microarrays and their application to the study of specific features of the pathogen's surface and interactions with host receptors. Bacteria were directly printed on nitrocellulose-coated glass slides, using either manual or robotic arrayers, and printing quality, immobilization efficiency and stability of the arrays were rigorously controlled by incorporating a fluorescent dye into the bacteria. A panel of wild type and mutant strains of the human pathogen Klebsiella pneumoniae, responsible for nosocomial and community-acquired infections, was selected as model bacteria, and SYTO-13 was used as dye. Fluorescence signals of the printed bacteria were found to exhibit a linear concentration-dependence in the range of 1 x 10(8) to 1 x 10(9) bacteria per ml. Similar results were obtained with Pseudomonas aeruginosa and Acinetobacter baumannii, two other human pathogens. Successful validation of the quality and applicability of the established microarrays was accomplished by testing the capacity of the bacteria array to detect recognition by anti-Klebsiella antibodies and by the complement subcomponent C1q, which binds K. pneumoniae in an antibody-independent manner. The biotin/AlexaFluor-647-streptavidin system was used for monitoring binding, yielding strain-and dose-dependent signals, distinctive for each protein. Furthermore, the potential of the bacteria microarray for investigating specific features, e.g. glycosylation patterns, of the cell surface was confirmed by examining the binding behaviour of a panel of plant lectins with diverse carbohydrate-binding specificities. This and other possible applications of the newly developed arrays, as e.g. screening/evaluation of compounds to identify inhibitors of host-pathogen interactions, make bacteria microarrays a useful and sensitive tool for both basic and applied research in microbiology, biomedicine and biotechnology.

An alternative methodology in Schottky diode physics

The fabrication and electrical characterization of Schottky junction diodes have been extensively researched for three-quarters of a century since the original work of Schottky in 1938. This study breaks from the highly standardized regime of such research and provides an alternative methodology that prompts novel, more efficient applications of the adroit Schottky junction in areas such as chemical and thermal sensing. The core departure from standard Schottky diode configuration is that the metal electrode is of comparable or higher resistance than the underlying semiconductor. Further, complete electrical characterization is accomplished through recording four-probe resistance-temperature (R-D-T) characteristics of the device, where electrical sourcing and sensing is done only via the metal electrode and not directly through the semiconductor. Importantly, this results in probing a nominally unbiased junction while eliminating the need for an Ohmic contact to the semiconductor. The characteristic R-D-T plot shows two distinct regions of high (metal) and low (semiconductor) resistances at low and high temperatures, respectively, connected by a crossover region of width, DT, within which there is a large negative temperature coefficient of resistance. The R-D-T characteristic is highly sensitive to the Schottky barrier height; consequently, at a fixed temperature, R-D responds appreciably to small changes in barrier height such as that induced by absorption of a chemical species (e.g., H-2) at the interface. A theoretical model is developed to simulate the R-D-T data and applied to Pd/p-Si and Pt/p-Si Schottky diodes with a range of metal electrode resistance. The analysis gives near-perfect fits to the experimental R-D-T characteristics, yielding the junction properties as fit parameters. The modelling not only helps elucidate the underlying physics but also helps to comprehend the parameter space essential for the discussed applications. Although the primary regime of application is limited to a relatively narrow range (DT) for a given type of diode, the alternative methodology is of universal applicability to all metal-semiconductor combinations forming Schottky contacts. (C) 2015 AIP Publishing LLC.

Establishing a population-based patient-reported outcomes study (PROMs) using national cancer registries across two jurisdictions: The Prostate Cancer Treatment, your experience (PiCTure) study

Objective: To establish an international patient-reported outcomes (PROMs) study among prostate cancer survivors, up to 18 years postdiagnosis, in two countries with different healthcare systems and ethical frameworks. Design: A cross-sectional, postal survey of prostate cancer survivors sampled and recruited via two population-based cancer registries. Healthcare professionals (HCPs) evaluated patients for eligibility to participate. Questionnaires contained validated instruments to assess health-related quality of life and psychological well-being, including QLQ-C30, QLQPR-25, EQ-5D-5L, 21-question Depression, Anxiety and Stress Scale (DASS-21) and the Decisional Regret Scale. Setting: Republic of Ireland (RoI) and Northern Ireland (NI). Primary outcome measures: Registration completeness, predictors of eligibility and response, data missingness, unweighted and weighted PROMs. Results: Prostate cancer registration was 80% (95% CI 75% to 84%) and 91% (95% CI 89% to 93%) complete 2 years postdiagnosis in NI and RoI, respectively. Of 12 322 survivors sampled from registries, 53% (n=6559) were classified as eligible following HCP screening. In the multivariate analysis, significant predictors of eligibility were: being ≤59 years of age at diagnosis (p<0.001), short-term survivor (<5 years postdiagnosis; p<0.001) and from RoI (p<0.001). 3348 completed the questionnaire, yielding a 54% adjusted response rate. 13% of men or their families called the study freephone with queries for assistance with questionnaire completion or to talk about their experience. Significant predictors of response in multivariate analysis were: being ≤59 years at diagnosis (p<0.001) and from RoI (p=0.016). Mean number of missing questions in validated instruments ranged from 0.12 (SD 0.71; EQ-5D-5L) to 3.72 (SD 6.30; QLQ-PR25). Weighted and unweighted mean EQ-5D-5L, QLQ-C30 and QLQ-PR25 scores were similar, as were the weighted and unweighted prevalences of depression, anxiety and distress. Conclusions: It was feasible to perform PROMs studies across jurisdictions, using cancer registries as sampling frames; we amassed one of the largest, international, population-based data set of prostate cancer survivors. We highlight improvements which could inform future PROMs studies, including utilising general practitioners to assess eligibility and providing a freephone service.

Seismic damage detection for a steel braced frame structure

A new approach for global detection of seismic damage in a single-storey steel concentrically braced frame (CBF) structure is presented. The filtered lateral in-plane acceleration response of the CBF structure is integrated twice to provide the lateral in-plane displacement which is used to infer buckling and yielding damage. The level of interstorey drift of the CBF during a seismic excitation allows the yield and buckling of the bracing members to be identified and indirectly detects damage based on exceedance of calculated lateral in-plane displacement limits. A band-pass filter removes noise from the acceleration signal followed by baseline correction being used to reduce the drift in velocity and displacement during numerical integration. This pre-processing results in reliable numerical integration of the frame acceleration that predicts the displacement response accurately when compared to the measured lateral displacement of the CBF structure. Importantly, the structural damage is not assumed through removal of bracing members, rather damage is induced through actual seismic loading. The buckling and yielding displacement threshold limits used to identify damage are demonstrated to accurately identify the initiation of buckling and yielding.

14C as a tool to trace terrestrial carbon in a complex lake system: implications for food-web structure and carbon cycling

Globally lakes bury and remineralise significant quantities of terrestrial C, and the associated flux of terrestrial C strongly influences their functioning. Changing deposition chemistry, land use and climate induced impacts on hydrology will affect soil biogeochemistry and terrestrial C export¹ and hence lake ecology with potential feedbacks for regional and global C cycling. C and nitrogen stable isotope analysis (SIA) has identified the terrestrial subsidy of freshwater food webs. The approach relies on different ¹³C fractionation in aquatic and terrestrial primary producers, but also that inorganic C demands of aquatic primary producers are partly met by ¹³C depleted C from respiration of terrestrial C, and ‘old’ C derived from weathering of catchment geology. SIA thus fails to differentiate between the contributions of old and recently fixed terrestrial C. Natural abundance ¹⁴C can be used as an additional biomarker to untangle riverine food webs² where aquatic and terrestrial δ ¹³C overlap, but may also be valuable for examining the age and origin of C in the lake. Primary production in lakes is based on dissolved inorganic C (DIC). DIC in alkaline lakes is partially derived from weathering of carbonaceous bedrock, a proportion of which is¹⁴C-free. The low ¹⁴C activity yields an artificial age offset leading samples to appear hundreds to thousands of years older than their actual age. As such, ¹⁴C can be used to identify the proportion of autochthonous C in the food-web. With terrestrial C inputs likely to increase, the origin and utilisation of ‘fossil’ or ‘recent’ allochthonous C in the food-web can also be determined. Stable isotopes and 14C were measured for biota, particulate organic matter (POM), DIC and dissolved organic carbon (DOC) from Lough Erne, Northern Ireland, a humic alkaline lake. Temporal and spatial variation was evident in DIC, DOC and POM C isotopes with implications for the fluctuation in terrestrial export processes. Ramped pyrolysis of lake surface sediment indicates the burial of two C components. ¹⁴C activity (507 ± 30 BP) of sediment combusted at 400˚C was consistent with algal values and younger than bulk sediment values (1097 ± 30 BP). The sample was subsequently combusted at 850˚C, yielding 14C values (1471 ± 30 BP) older than the bulk sediment age, suggesting that fossil terrestrial carbon is also buried in the sediment. Stable isotopes in the food web indicate that terrestrial organic C is also utilised by lake organisms. High winter δ ¹⁵N values in calanoid zooplankton (δ ¹⁵N = 24%¸) relative to phytoplankton and POM (δ ¹⁵N = 6h and 12h respectively) may reflect several microbial trophic levels between terrestrial C and calanoids. Furthermore winter calanoid 14C ages are consistent with DOC from an inflowing river (75 ± 24 BP), not phytoplankton (367 ± 70 BP). Summer calanoid δ ^13C, δ ¹⁵N and ¹⁴C (345 ± 80 BP) indicate greater reliance on phytoplankton.

¹ Monteith, D.T et al., (2007) Dissolved organic carbon trends resulting from changes in atmospheric deposition chemistry. Nature, 450:537-535

² Caraco, N., et al.,(2010) Millennial-aged organic carbon subsidies to a modern river food web. Ecology,91: 2385-2393.

Parasite neuropeptide biology:Seeding rational drug target selection?

The rationale for identifying drug targets within helminth neuromuscular signalling systems is based on the premise that adequate nerve and muscle function is essential for many of the key behavioural determinants of helminth parasitism, including sensory perception/host location, invasion, locomotion/orientation, attachment, feeding and reproduction. This premise is validated by the tendency of current anthelmintics to act on classical neurotransmitter-gated ion channels present on helminth nerve and/or muscle, yielding therapeutic endpoints associated with paralysis and/or death. Supplementary to classical neurotransmitters, helminth nervous systems are peptide-rich and encompass associated biosynthetic and signal transduction components - putative drug targets that remain to be exploited by anthelmintic chemotherapy. At this time, no neuropeptide system-targeting lead compounds have been reported, and given that our basic knowledge of neuropeptide biology in parasitic helminths remains inadequate, the short-term prospects for such drugs remain poor. Here, we review current knowledge of neuropeptide signalling in Nematoda and Platyhelminthes, and highlight a suite of 19 protein families that yield deleterious phenotypes in helminth reverse genetics screens. We suggest that orthologues of some of these peptidergic signalling components represent appealing therapeutic targets in parasitic helminths.

Deep Salience: Visual Salience Modeling via Deep Belief Propagation

Visual salience is an intriguing phenomenon observed in biological neural systems. Numerous attempts have been made to model visual salience mathematically using various feature contrasts, either locally or globally. However, these algorithmic models tend to ignore the problem’s biological solutions, in which visual salience appears to arise during the propagation of visual stimuli along the visual cortex. In this paper, inspired by the conjecture that salience arises from deep propagation along the visual cortex, we present a Deep Salience model where a multi-layer model based on successive Markov random fields (sMRF) is proposed to analyze the input image successively through its deep belief propagation. As a result, the foreground object can be automatically separated from the background in a fully unsupervised way. Experimental evaluation on the benchmark dataset validated that our Deep Salience model can consistently outperform eleven state-of-the-art salience models, yielding the higher rates in the precision-recall tests and attaining the best F-measure and mean-square error in the experiments.

Antibiofilm Activity of the Brown Alga Halidrys siliquosa against Clinically Relevant Human Pathogens

The marine brown alga Halidrys siliquosa is known to produce compounds with antifouling activity against several marine bacteria. The aim of this study was to evaluate the antimicrobial and antibiofilm activity of organic extracts obtained from the marine brown alga H. siliquosa against a focused panel of clinically relevant human pathogens commonly associated with biofilm-related infections. The partially fractionated methanolic extract obtained from H. siliquosa collected along the shores of Co. Donegal; Ireland; displayed antimicrobial activity against bacteria of the genus Staphylococcus; Streptococcus; Enterococcus; Pseudomonas; Stenotrophomonas; and Chromobacterium with MIC and MBC values ranging from 0.0391 to 5 mg/mL. Biofilms of S. aureus MRSA were found to be susceptible to the algal methanolic extract with MBEC values ranging from 1.25 mg/mL to 5 mg/mL respectively. Confocal laser scanning microscopy using LIVE/DEAD staining confirmed the antimicrobial nature of the antibiofilm activity observed using the MBEC assay. A bioassay-guided fractionation method was developed yielding 10 active fractions from which to perform purification and structural elucidation of clinically-relevant antibiofilm compounds.

Molecular pathology of prostate cancer:the key to identifying new biomarkers of disease

Microarray technology has recently accelerated the study of the molecular events involved in prostate cancer, offering the prospect of more precise prognosis and new therapeutic strategies. This review summarises current knowledge of the molecular pathology of prostate cancer. The expression and function of numerous genes have been shown to be altered in prostate cancer. Many of these genes are involved in cell cycle regulation, steroid hormone metabolism or regulation of gene expression. The mechanisms by which androgen independence arises are discussed, including cross-activation, gene amplification and point mutations of the androgen receptor. Analysis of changes in the levels of expression of large numbers of genes during prostate cancer progression have provided a better understanding of the basis of the disease, yielding new molecular markers, such as hepsin, with potential use in diagnosis and prognosis.

Characterization of a reference material for BCR-ABL (M-BCR) mRNA quantitation by real-time amplification assays:towards new standards for gene expression measurements

Monitoring of BCR-ABL transcripts has become established practice in the management of chronic myeloid leukemia. However, nucleic acid amplification techniques are prone to variations which limit the reliability of real-time quantitative PCR (RQ-PCR) for clinical decision making, highlighting the need for standardization of assays and reporting of minimal residual disease (MRD) data. We evaluated a lyophilized preparation of a leukemic cell line (K562) as a potential quality control reagent. This was found to be relatively stable, yielding comparable respective levels of ABL, GUS and BCR-ABL transcripts as determined by RQ-PCR before and after accelerated degradation experiments as well as following 5 years storage at -20 degrees C. Vials of freeze-dried cells were sent at ambient temperature to 22 laboratories on four continents, with RQ-PCR analyses detecting BCR-ABL transcripts at levels comparable to those observed in primary patient samples. Our results suggest that freeze-dried cells can be used as quality control reagents with a range of analytical instrumentations and could enable the development of urgently needed international standards simulating clinically relevant levels of MRD.

Improved shear strength model for FRP-strengthened RC beams accounting for adverse FRP-steel interaction

RC beams shear-strengthened with externally-bonded FRP side strips or U-strips usually fail by debonding. As such debonding occurs in a brittle manner at relatively small shear crack widths, some of the internal steel stirrups may not have reached yielding at beam shear failure. Consequently, the internal steel stirrups cannot be fully utilized. This adverse shear interaction between internal steel stirrups and external FRP strips may significantly reduce the benefit of shear-strengthening FRP but has not been considered by any of the existing FRP strengthening design guidelines. In this paper, an improved shear strength model capable of accounting for the effect of the above shear interaction is first presented, in which the unfavorable effect of shear interaction is reflected through a reduction factor (i.e. shear interaction factor). Using a large test database established in the present study, the performance of the proposed model as well as that of three other shear strength models is then assessed. This assessment shows that the proposed shear strength model performs better than the three existing models. The assessment also shows that the inclusion of the proposed shear interaction factor in the existing models can significantly improve their performance.