bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Novel Inhibitors of UDP‐Galactopyranose Mutase by Structure‐Based Virtual Screening
Authors: Karunan Partha Sarathy , Sadeghi‐Khomami Ali , Cren Sylvaine , Robinson Richard I. , Woodward Simon , Slowski Kate , Berast Lindsey , Zheng Blake , Thomas Neil R. , Sanders David A. R.
Published: September 2011

UDP‐galactopyranose mutase (UGM) is a flavo‐enzyme involved in the bacterial cell wall biosynthesis. UGM catalyzes the reversible isomerization of UDP‐galactopyranose (UDP‐Galp) to UDP‐galactofuranose (UDP‐Galf). UDP‐Galf is the activated precursor of galactofuranose (Galf) residues that are essential components of the cell wall of certain pathogenic bacteria such as Klebsiella pneumoniae and Mycobacterium tuberculosis. Neither UGM nor Galf residues are found in humans, making Galf biosynthesis a potential drug target for developing antibacterial agents. We report the identification of novel inhibitors of UGM by in silico docking of the LeadQuest compound database against UGM from Escherichia coli. The 13 most promising inhibitors were then evaluated against K. pneumonia and M. tuberculosis UGMs by enzyme inhibition studies. Two inhibitors were identified with IC50 values of ∼1 µM and subsequently these compounds were docked into the recently solved X‐ray structure of Deinococcus radiodurans UGM. The structure‐activity relationships of the initial 13 compounds evaluated as inhibitors are discussed.
A Microarray Tool Provides Pathway and GO Term Analysis
Authors: Koch Martin , Royer Hans‐Dieter , Wiese Michael
Published: September 2011

Analysis of gene expression profiles is no longer exclusively a task for bioinformatic experts. However, gaining statistically significant results is challenging and requires both biological knowledge and computational know‐how. Here we present a novel, user‐friendly microarray reporting tool called maRt. The software provides access to bioinformatic resources, like gene ontology terms and biological pathways by use of the DAVID and the BioMart web‐service. Results are summarized in structured HTML reports, each presenting a different layer of information. In these report, contents of diverse sources are integrated and interlinked. To speed up processing, maRt takes advantage of the multi‐core technology of modern desktop computers by using parallel processing. Since the software is built upon a RCP infrastructure it might be an outset for developers aiming to integrate novel R based applications. Availability: Installer, documentation and various kinds of tutorials are available under LGPL license at the website of our institute http://www.pharma.uni‐bonn.de/www/mart. This software is free for academic use.
SAHA Capture Compound – A novel tool for the profiling of histone deacetylases and the identification of additional vorinostat binders
Authors: Fischer Jenny J. , Michaelis Simon , Schrey Anna K. , Diehl Anne , Graebner Olivia Y. , Ungewiss Jan , Horzowski Sabine , Glinski Mirko , Kroll Friedrich , Dreger Mathias , Koester Hubert
Published: September 2011

Suberoylanilide hydroxamic acid (SAHA) is a potent histone deacetylase (HDAC) inhibitor. Inhibitors of HDACs are used in cancer therapy based on the role HDACs play in transcription by regulating chromatin compaction and non‐histone proteins such as transcription factors. Profiling of HDAC expression is of interest in the functional proteomics analysis of cancer. Also, non‐HDAC proteins may interact with HDAC inhibitor drugs and contribute to the drug mode of action. We here present a tool for the unbiased chemical proteomic profiling of proteins that specifically interact with SAHA. We designed and synthesized a trifunctional Capture Compound containing SAHA as selectivity and identified HDACs1, 2, 3 and 6, known and predicted HDAC interactors from human‐derived HepG2 cell lysate, as well as a set of new potential non‐HDAC targets of SAHA. One of these non‐HDAC targets, isochorismatase domain‐containing protein 2 (ISOC2) is putative hydrolase associated with the negative regulation of the tumor‐suppressor p16(INK4a). We demonstrated the direct and dose‐dependent interaction of SAHA to the purified recombinant ISOC2 protein. Using SAHA Capture Compound mass spectrometry, we thus identified potential new SAHA target proteins in an entirely unbiased chemical proteomics approach.
Autoimmune polyendocrine syndrome type 1: Utility of KCNRG autoantibodies as a marker of active pulmonary disease and successful treatment with rituximab
Authors: Popler Jonathan , Alimohammadi Mohammad , Kämpe Olle , Dalin Frida , Dishop Megan K. , Barker Jennifer M. , Moriarty‐Kelsey Margaret , Soep Jennifer B. , Deterding Robin R.
Published: September 2011

Autoimmune polyendocrine syndrome type 1 (APS‐1), also known as Autoimmune Polyendocrinopathy Candidiasis and Ectodermal Dysplasia (APECD) is a disorder caused by mutations in the autoimmune regulator (AIRE) gene. In some APS‐1 patients, significant pulmonary disease is observed. Autoantibodies directed against the potassium channel regulatory protein (KCNRG), found in epithelial cells of terminal bronchioles, have been suggested as a marker for pulmonary disease in APS‐1 patients. We report two patients with APS‐1; one with and one without lung disease. Patient 1 had multiple admissions for pneumonia and respiratory insufficiency, required non‐invasive ventilation, and had findings of bronchiectasis on thoracic imaging and significant lymphocytic infiltrates of the airways on lung biopsy. To verify the autoimmune cause of pulmonary symptoms APS‐1 patients, both were tested in a blinded manner for the presence of autoantibodies to KCNRG in serum. We found that only Patient 1 had autoantibodies present. Additionally, Patient 1 had progressive disease despite treatment with several immunomodulating agents, including corticosteroids, azathioprine, and mycophenolate. Patient 1 had a lung biopsy performed which was consistent with B cell lymphocytic aggregates. Rituximab treatment was initiated with apparent good response. This report illustrates the practical use of KCNRG autoantibodies to identify APS‐1 patients with pulmonary risk and the successful use of the monoclonal antibody, Rituximab, to treat pulmonary disease in APS‐1 patients. Pediatr Pulmonol. Pediatr Pulmonol. 2012; 47:84–87. © 2010 Wiley Periodicals, Inc.
Hospital readmissions for newly discharged pediatric home mechanical ventilation patients
Authors: Kun Sheila S. , Edwards Jeffrey D. , Davidson Ward Sally L. , Keens Thomas G.
Published: September 2011

Background

Ventilator‐dependent children have complex chronic conditions that put them at risk for acute illness and repeated hospitalizations.

Objectives

To determine the 12‐month incidence of and risk factors for non‐elective readmission in children with chronic respiratory failure (CRF) after initiation on home mechanical ventilation (HMV) via tracheostomy.

Methods

A retrospective cohort study of 109 HMV patients initiated and followed at an university‐affiliated children's hospital between 2003 and 2009. Patient characteristics are presented using descriptive statistics; generalized estimated equations are used to estimate adjusted odds ratios of select predictor variables for readmission.

Results

The 12‐month incidence of non‐elective readmission was 40%. Close to half of these readmissions occurred within the first 3 months post‐index discharge. Pneumonia and tracheitis were the most common reasons for readmission; 64% were pulmonary‐ or tracheostomy‐related. Most demographic and clinical patient characteristics were not statistically associated with non‐elective readmissions. Although, a change in the child's management within 7 days before discharge was associated readmissions shortly after index discharge.

Conclusion

Non‐elective readmissions of newly initiated pediatric HMV patients were common and likely multifactorial. Many of these readmissions were airway‐related, and some may have been potentially preventable. Pediatr Pulmonol. 2012; 47:409–414. © 2011 Wiley Periodicals, Inc.
Lower airway microbiology and cellularity in children with newly diagnosed non‐CF bronchiectasis
Authors: Kapur Nitin , Grimwood Keith , Masters I. Brent , Morris Peter S. , Chang Anne B.
Published: September 2011

Background

Infection and inflammation are important in the pathogenesis of bronchiectasis. However, there are few published data describing the lower airway microbiology and cellularity in children.

Methods

Children with non‐cystic fibrosis (CF) bronchiectasis who underwent bronchoalveolar lavage (BAL) within 4 weeks of diagnosis were identified by a retrospective patient‐record review. The effects of infection (≥105 colony‐forming units of respiratory bacteria/ml; or detectable Pseudomonas aeruginosa; mycobacteria, fungi, mycoplasma, or respiratory viruses) on airway cellularity and the impact of age, gender, indigenous status, immune function, radiographic involvement and antibiotic usage on infection risk were evaluated.

Results

Of 113 children [median age 63 months (IQR 32–95)] with newly diagnosed bronchiectasis, 77 (68%) had positive BAL cultures for respiratory bacterial pathogens. Haemophilus influenzae was most commonly detected, being present in 53 (47%) BAL specimens. P. aeruginosa was found in just 7 (6%) children, five of whom had an underlying disorder, while mycobacterial and fungal species were not detected. Respiratory viruses were identified in 14 (12%) children and Mycoplasma pneumoniae in two others. Overall, 56 (49.5%) children fulfilled our definition of a lower airway infection and of these, 35 (63%) had more than one pathogen present. Compared to children without infection, children with infection had higher total cell counts (610 vs. 280 × 106/L), neutrophil counts (351 vs. 70 × 106/L), and neutrophil percentages (69% vs. 34%). Age at diagnosis was most strongly associated with infection.

Conclusions

BAL microbiology of children with newly diagnosed bronchiectasis is dominated by H. influenzae. In the absence of CF, isolation of P. aeruginosa may suggest a serious co‐morbidity in this group. Airway neutrophilia is common, especially with higher bacterial loads. Pediatr Pulmonol. 2012; 47:300–307. © 2011 Wiley Periodicals, Inc.
Respiratory effects associated with wood fuel use: A cross‐sectional biomarker study among adolescents
Authors: Van Miert Erik , Sardella Antonia , Nickmilder Marc , Bernard Alfred
Published: September 2011

The use of wood as heating and cooking fuel can result in elevated levels of indoor air pollution, but to what extent this is related to respiratory diseases and allergies is still inconclusive. Here, we report a cross‐sectional study among 744 school adolescents (median age 15 years) using as main outcomes respiratory symptoms and diseases, exhaled nitric oxide, total and aeroallergen‐specific IgE in serum, and two epithelial biomarkers in nasal lavage fluid (NALF) or serum, that is, Clara cell protein (CC16) and surfactant‐associated protein D (SPD). Information about the wood fuel use and potential confounders was collected via a personal interview of the adolescent and a questionnaire filled out by the parents. Two approaches were used to limit the possible influence of confounders, that is, multivariate analysis using the complete study population or pairwise analysis of matched sub‐populations obtained using an automated procedure. Wood fuel use was associated with a decrease of CC16 and an increase of SPD in serum, which resulted in a decreased serum CC16/SPD ratio (median −9%, P = 0.001). No consistent differences were observed for the biomarkers measured in exhaled breath or NALF. Wood fuel use was also associated with increased odds for asthma [odds ratio (OR) 2.2, 95% CI: 1.1–4.4, P = 0.02], hay fever (OR = 2.4, 95% CI: 1.4–4.3, P = 0.002), and sensitization against pollen allergens (OR = 2.1, 95% CI: 1.3–3.4, P = 0.002). The risks of respiratory tract infections, self‐reported symptoms, and sensitization against house‐dust mite were not increased by wood fuel use. The increased risks of asthma, hay fever and aeroallergen sensitization, and the changes of lung‐specific biomarkers consistently pointed towards respiratory effects associated with the use of wood fuel. Pediatr Pulmonol. 2012; 47:358–366. © 2011 Wiley Periodicals, Inc.
The linear interaction energy method for the prediction of protein stability changes upon mutation
Authors: Wickstrom Lauren , Gallicchio Emilio , Levy Ronald M.
Published: September 2011

The coupling of protein energetics and sequence changes is a critical aspect of computational protein design, as well as for the understanding of protein evolution, human disease, and drug resistance. To study the molecular basis for this coupling, computational tools must be sufficiently accurate and computationally inexpensive enough to handle large amounts of sequence data. We have developed a computational approach based on the linear interaction energy (LIE) approximation to predict the changes in the free‐energy of the native state induced by a single mutation. This approach was applied to a set of 822 mutations in 10 proteins which resulted in an average unsigned error of 0.82 kcal/mol and a correlation coefficient of 0.72 between the calculated and experimental ΔΔG values. The method is able to accurately identify destabilizing hot spot mutations; however, it has difficulty in distinguishing between stabilizing and destabilizing mutations because of the distribution of stability changes for the set of mutations used to parameterize the model. In addition, the model also performs quite well in initial tests on a small set of double mutations. On the basis of these promising results, we can begin to examine the relationship between protein stability and fitness, correlated mutations, and drug resistance. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Raman spectroscopy of thin‐film silicon on woven polyester
Authors: Lind Helena , Wilson John , Mather Robert
Published: September 2011

Thin‐film silicon deposited by plasma‐enhanced chemical vapour deposition (PECVD), encompasses both hydrogenated amorphous silicon (a‐Si:H) and ‘nanocrystalline silicon’ (nc‐Si), the latter being a two‐phase mixture of discrete nanocrystallites in an amorphous matrix. It is distinguished from a‐Si:H by a characteristic Raman spectrum. As the film structure moves from amorphous to more crystalline, the Raman TO phonon spectral region no longer consists of a broad amorphous peak at ∼480 cm−1 but instead has an obvious narrower peak located at higher wavenumber. The accepted signature peak for nc‐Si lies between these two and most probably arises from the hexagonal, wurtzite structure of the nanocrystals. Here we use Raman spectroscopy to show how the structure of thin‐film silicon on woven polyester is influenced by the substrate as well as by the deposition conditions. We find that the rough surface of the textile substrate enables nc‐Si formation, provided that the correct deposition conditions are employed and that the substrate temperature does not exceed 210 °C. Although the gas mixture is the dominant parameter for determining the film structure, and input power also has a significant effect, we find that a specific combination of these interrelated parameters is essential to control the final structure.
Carrier‐density dependence of the hole mobility in doped and undoped regioregular poly(3‐hexylthiophene)
Authors: Brondijk Jakob J. , Maddalena Francesco , Asadi Kamal , van Leijen Herman J. , Heeney Martin , Blom Paul W. M. , de Leeuw Dago M.
Published: September 2011

We investigate the mobility of poly(3‐hexylthiophene) (P3HT) over a carrier‐density range from 1015 to 1020 cm−3. Hole‐only diodes were used for densities below 1016 cm−3 and field‐effect transistors were used for carrier densities higher than 1018 cm−3. To fill the gap, intermediate densities were probed using chemically doped Schottky diodes and transistors. Combining of the mobilities in doped and undoped devices experimentally establishes the full relation of the mobility over the whole carrier‐density range.
Cyclic loading test of T‐shaped mid‐rise shear wall
Authors: Pin‐Le Zhang , Qing‐ning Li
Published: September 2011

Shear wall systems are the most commonly used lateral load resisting systems in high‐rise buildings. Six 1:2 scale mid‐rise T‐shaped reinforced concrete shear wall specimens with aspect ratio of 1.75, 2.15 and 2.80 were respectively tested under reversed cyclic loading. The seismic behavior and displacement ductility were investigated. The effects of aspect ratio, axial load level and transverse steel ratio on the seismic behavior and displacement ductility were also analyzed. Test results were discussed and compared with T‐shaped steel–concrete composite shear wall. Results mainly showed that the T‐shaped shear wall specimens mainly presented bending–shear failure mode and were all destroyed because of the concrete crushing at the web (negative direction) and the longitudinal reinforcement of the web reaching the limited deformation (positive direction), showing that the web was the weakest part of T‐shape shear wall. The ductility of the specimens was decreased, and the ultimate load‐bearing capacity was increased by increasing the axial load. To specimens with smaller aspect ratio and higher axial load ratio, the special transverse steel ratio of the web should be increased to improve the crushing strain of the confined concrete of the web in order to satisfy the ductility of the walls. The seismic performance was obviously improved in the T‐shaped steel–concrete shear wall compared with that of the T‐shaped reinforced concrete shear wall. Copyright © 2011 John Wiley & Sons, Ltd.
Gold‐gold junction electrodes:the disconnection method
Authors: Dale Sara E. C. , Vuorema Anne , Ashmore Ellen M. Y. , Kasprzyk‐Horden Barbara , Sillanpää Mika , Denuault Guy , Marken Frank
Published: September 2011

The formation of gold‐gold junction electrodes for application in electroanalysis is described here based on electro‐deposition from a non‐cyanide gold plating bath. Converging growth of two hemispherical gold deposits on two adjacent platinum microelectrodes (both 100 µm diameter in glass, ca. 45 µm gap) followed by careful etching in aqueous chloride solution was employed. During growth both gold hemispheres “connect” and during etching “disconnection” is evident in a drop in current. Gold‐gold junctions with sub‐micron gaps are formed and applied for the electroanalytical detection of sub‐micromolar concentrations of hydroquinone in 0.1 M phosphate buffer pH 7 (Erev = 0.04 V vs. SCE) and sub‐micromolar concentration of dopamine in 0.1 M phosphate buffer pH 7 (Erev = 0.14 V vs. SCE). The potential future uses in analysis and limitations of gold‐gold junction electrodes are discussed. DOI 10.1002/tcr.201100008
Effects of decabromodiphenyl ether (BDE‐209) on mRNA transcription of thyroid hormone pathway and spermatogenesis associated genes in Chinese rare minnow (Gobiocypris rarus)
Authors: Li Wei , Zhu Lifei , Zha Jinmiao , Wang Zijian
Published: September 2011

Polybrominated diphenyl ethers (PBDEs) are widely used as flame retardants, which are ubiquitous environmental contaminant found in both abiotic and biotic environmental samples. Deca‐BDE (BDE‐209) is the principal component, which is currently used worldwide. In this study, the effect of BDE‐209 on the mRNA levels of thyroid hormone (TH) related genes and spermatogenesis associated genes were determined from larvae and adult rare minnow (Gobiocypris rarus) exposed to concentrations 0.01, 0.1, 1, and 10 μg/L for 21 days. The results showed that the type II deiodinase (dio2) and sodium iodide symporter (nis) mRNA levels were significantly up‐regulated in the larvae at 10 μg/L treatment. In adult, histopathological observations showed that liver of female fish were degenerated at 10 μg/L treatment, and inhibition of spermatogenesis were observed in testis of male fish. In addition, the thyroid hormone receptor α (trα), dio2, and nis mRNA levels in the liver of male and female fish were significantly up‐regulated, whereas dio2 and nis mRNA levels were significantly down‐regulated in the brain. These results indicate that exposure to BDE‐209 could result in tissue‐specific alternations of TH‐related genes expression in adults. Moreover, the mRNA levels of the testis‐specific apoptosis genes, the spermatogenesis‐associated 4 (spata4) and spermatogenesis‐associated 17 (spata17), were down‐regulated at 10 μg/L treatment in testis of male fish. Our results suggest that BDE‐209 may pose threat to normal thyroid and reproductive function in fish. © 2011 Wiley Periodicals, Inc. Environ Toxicol 29: 1–9, 2014.
Visual matrix explorer for collaborative seriation
Authors: Liiv Innar , Opik Rain , Ubi Jaan , Stasko John
Published: September 2011

In this article, we present a web‐based open source tool to support cross‐disciplinary collaborative seriation with the following goals: to compare different matrix permutations, to discover patterns from the data, annotate it, and accumulate knowledge. Seriation is an unsupervised data mining technique that reorders objects into a sequence along a one‐dimensional continuum to make sense of the whole series. Clustering assigns objects to groups, whereas seriation assigns objects to a position within a sequence. Seriation has been applied to a variety of disciplines including archaeology and anthropology; cartography, graphics, and information visualization; sociology and sociometry; psychology and psychometrics; ecology; biology and bioinformatics; cellular manufacturing; and operations research. Interestingly, across those different disciplines, there are several commonly emerging similar structural patterns. Visual Matrix Explorer allows users to explore and link those patterns, share an online workplace and instantly transmit changes in the system to other users. WIREs Comp Stat 2012, 4:85–97. doi: 10.1002/wics.193

This article is categorized under:

Statistical Learning and Exploratory Methods of the Data Sciences > Clustering and Classification

Statistical Learning and Exploratory Methods of the Data Sciences > Exploratory Data Analysis

Statistical and Graphical Methods of Data Analysis > Statistical Graphics and Visualization
Monte Carlo methods
Authors: Kroese Dirk P. , Rubinstein Reuven Y.
Published: September 2011

Many quantitative problems in science, engineering, and economics are nowadays solved via statistical sampling on a computer. Such Monte Carlo methods can be used in three different ways: (1) to generate random objects and processes in order to observe their behavior, (2) to estimate numerical quantities by repeated sampling, and (3) to solve complicated optimization problems through randomized algorithms. WIREs Comp Stat 2012, 4:48–58. doi: 10.1002/wics.194

This article is categorized under:

Statistical and Graphical Methods of Data Analysis > Markov Chain Monte Carlo (MCMC)
Spontaneous burrowing behaviour in the rat is reduced by peripheral nerve injury or inflammation associated pain
Authors: Andrews N. , Legg E. , Lisak D. , Issop Y. , Richardson D. , Harper S. , Pheby T. , Huang W. , Burgess G. , Machin I. , Rice A.S.C.
Published: September 2011

Pain influences many aspects of daily living and effective analgesics should reinstate normal spontaneous daily behaviours. Experiments are described herein which show that the innate, spontaneous behaviour of burrowing by rats, which can be simply and objectively assessed by measuring the amount of gravel left in a hollow tube 1 h after presentation to the rat, is reduced by peripheral nerve injury (tibial nerve transection (TNT), L5 spinal nerve transection (SNT) and partial sciatic nerve ligation (PSNL)) and also following inflammation induced by intra‐plantar injection of Complete Freund's Adjuvant (CFA). Gabapentin (100 mg/kg sc) but not at 30 mg/kg sc significantly reduced burrowing activity in naive rats. All peripheral nerve injuries and CFA reduced burrowing compared with shams and rats naive to surgery. The level of mechanical hypersensitivity in rats with peripheral nerve injury did not correlate with the deficit in burrowing indicating that different parameters of the holistic pain experience are measured in these paradigms. Gabapentin at 30 mg/kg sc, but not 100 mg/kg sc, reversed the deficit in burrowing induced by TNT and ibuprofen (30 mg/kg sc) reversed the effect of CFA on burrowing. These experiments show that measurement of burrowing is a simple, objective assay of innate rodent behaviour affected by pain that is ethologically relevant to the rat, does not rely wholly on evoking a reflex and can dissociate a selective analgesic dose of gabapentin from one inducing motor impairment in the same animal.
Inviting questions
Authors: Khan Uzma , Tormala Zakary L.
Published: September 2011

Consumers are frequently invited to ask questions in everyday life. The current research provides an initial examination of how inviting consumers to ask questions influences their attitudes and intentions. Two experiments show that inviting questions can have a positive or negative effect depending on whether consumers actually ask them. Experiment 1 shows that merely inviting questions has a positive effect, but that this effect reverses when consumers actually ask questions. Following a similar logic, Experiment 2 shows that inviting questions has a positive effect under low involvement conditions, but a negative effect under high involvement conditions where the likelihood of generating questions is higher.
Evaluation of the immune benefits of two probiotic strains Bifidobacterium animalis ssp. lactis, BB-12® and Lactobacillus paracasei ssp. paracasei, L. casei 431® in an influenza vaccination model: a randomised, double-blind, placebo-controlled study
Authors: Rizzardini Giuliano , Eskesen Dorte , Calder Philip C. , Capetti Amedeo , Jespersen Lillian , Clerici Mario
Published: September 2011

The present study investigated the ability of Bifidobacterium animalis ssp. lactis (BB-12®) and Lactobacillus paracasei ssp. paracasei (L. casei 431®) to modulate the immune system using a vaccination model in healthy subjects. A randomised, double-blind, placebo-controlled, parallel-group study was conducted in 211 subjects (56 % females, mean age 33·2 (sd 13·1) years). Subjects consumed a minimum of 109 colony-forming units of BB-12® (capsule) or L. casei 431® (dairy drink) or a matching placebo once daily for 6 weeks. After 2 weeks, a seasonal influenza vaccination was given. Plasma and saliva samples were collected at baseline and after 6 weeks for the analysis of antibodies, cytokines and innate immune parameters. Changes from baseline in vaccine-specific plasma IgG, IgG1 and IgG3 were significantly greater in both probiotic groups v. the corresponding placebo group (L. casei 431®, P = 0·01 for IgG; P < 0·001 for remaining comparisons). The number of subjects obtaining a substantial increase in specific IgG (defined as ≥ 2-fold above baseline) was significantly greater in both probiotic groups v. placebo (BB-12®, P < 0·001 for IgG, IgG1 and IgG3; L. casei 431®, P < 0·001 for IgG1 and IgG3). Significantly greater mean fold increases for vaccine-specific secretory IgA in saliva were observed in both probiotic groups v. placebo (BB-12®, P = 0·017; L. casei 431®, P = 0·035). Similar results were observed for total antibody concentrations. No differences were found for plasma cytokines or innate immune parameters. Data herein show that supplementation with BB-12® or L. casei 431® may be an effective means to improve immune function by augmenting systemic and mucosal immune responses to challenge.
Marine collagen peptides protect against early alcoholic liver injury in rats
Authors: Lin Bing , Zhang Feng , Yu Yongchao , Jiang Qinghao , Zhang Zhaofeng , Wang Junbo , Li Yong
Published: September 2011

Marine collagen peptides (MCP) have been reported to exhibit antioxidative activity, which is the common property of numerous hepatoprotective agents. Previous studies have shown that MCP have biological functions including anti-hypertension, anti-ulcer, anti-skin ageing and extending the life span. However, its role in alcoholic liver injury remains unknown. The present study aimed to investigate the effects of MCP on early alcoholic liver injury in rats. Rats were administered with alcohol at a dose of 6 g/kg body weight intragastrically per d to induce early liver injury, which was then evaluated by serum markers and histopathological examination. Treatment with MCP could reverse the increased level of serum aminotransferase and reduce hepatic histological damage. In addition, MCP attenuated the alteration in serum superoxide dismutase and malondialdehyde levels. MCP also counteracted the increased levels of total cholesterol and TAG. However, no significant difference was observed in the contents of alcohol dehydrogenase both in liver and serum protein of rats. These findings suggest that MCP have a protective effect on early alcoholic liver injury in rats by their antioxidative activity and improving lipid metabolism.
Vitamin C and fibre consumption from fruits and vegetables improves oxidative stress markers in healthy young adults
Authors: Hermsdorff Helen Hermana M. , Barbosa Kiriaque B. F. , Volp Ana Carolina P. , Puchau Blanca , Bressan Josefina , Zulet M. Ángeles , Martínez J. Alfredo
Published: September 2011

The aim of the present cross-sectional study was to assess the potential relationships between fruit and vegetable (FV) consumption and some oxidative stress markers in young adults, with particular emphasis on fibre and vitamin C intake. The study enrolled 246 healthy subjects (eighty-eight men and 158 women), with a mean age of 22 (sd3) years and a mean BMI of 21·9 (sd2·8) kg/m2. Dietary intake, anthropometry, blood pressure, lifestyle features and blood biochemical data were assessed with validated procedures. Those subjects in the highest tertile (T) of FV consumption ( ≥ 705 g/d) had statistically lower oxidised LDL (ox-LDL) concentrations as well as higher plasma total antioxidant capacity (TAC) and glutathione peroxidase (GPx) activity (Pfor trend < 0·05), after adjusting for sex, age, energy intake, physical activity, smoking, BMI, vitamin supplement use and other confounding factors. Moreover, plasma ox-LDL concentrations showed a decreasing trend and TAC an increasing trend across tertiles of fibre (T3: ≥ 14 g/d) and vitamin C (T3: ≥ 150 mg/d) from FV intake, while GPx activity was positively associated with vitamin C intake (Pfor trend < 0·05). In conclusion, greater FV consumption was independently associated with reduced ox-LDL as well as increased TAC and GPx activity in healthy young adults, with dietary fibre and vitamin C from FV clearly being implicated in this beneficial relationship.
Prognostic role of epidermal growth factor-like domain 7 protein expression in laryngeal squamous cell carcinoma
Authors: Li J-J , Yang X-M , Wang S-H , Tang Q-L
Published: September 2011

Objective:

This study aimed to retrospectively analyse the expression of epidermal growth factor-like domain 7 protein in cases of laryngeal squamous cell carcinoma.

Methods:

We studied 116 patients retrospectively. Expression of epidermal growth factor-like domain 7 protein was determined in tumour and nontumour tissue samples, by immunohistochemistry.

Results:

Expression levels were significantly increased in 94 cases. Increased expression levels correlated well with tumour stage (p = 0.001) and lymph node metastasis (p = 0.002). Log-rank survival testing showed a significant difference between patients with marked versus limited expression levels (p = 0.03). Multivariable Cox regression analysis showed that epidermal growth factor-like domain 7 protein expression level was an independent predictor of laryngeal squamous cell carcinoma prognosis.

Conclusion:

These findings provide evidence that increased epidermal growth factor-like domain 7 protein expression is associated with laryngeal squamous cell carcinoma stage, lymph node metastasis and poor survival. This suggests that this protein may be a potential marker for laryngeal squamous cell carcinoma.
Face salient points and eyes tracking for robust drowsiness detection
Authors: Jimenez-Pinto J. , Torres-Torriti M.
Published: September 2011

Measuring a driver's level of attention and drowsiness is fundamental to reducing the number of traffic accidents that often involve bus and truck drivers, who must work for long periods of time under monotonous road conditions. Determining a driver's state of alert in a noninvasive way can be achieved using computer vision techniques. However, two main difficulties must be solved in order to measure drowsiness in a robust way: first, detecting the driver's face location despite variations in pose or illumination; secondly, recognizing the driver's facial cues, such as blinks, yawns, and eyebrow rising. To overcome these challenges, our approach combines the well-known Viola–Jones face detector with the motion analysis of Shi–Tomasi salient features within the face. The location of the eyes and blinking is important to refine the tracking of the driver's head and compute the so-called PERCLOS, which is the percentage of time the eyes are closed over a given time interval. The latter cue is essential for noninvasive driver's alert state estimation as it has a high correlation with drowsiness. To further improve the location of the eyes under different conditions of illumination, the proposed method takes advantage of the high reflectivity of the retina to near infrared illumination employing a camera with an 850 nm wavelength filter. The paper shows that motion analysis of the salient points, in particular cluster mass centers and spatial distributions, yields better head tracking results compared to the state-of-the-art and provides measures of the driver's alert state.
Establishing quantitative habitat targets for a ‘Critically Endangered’ Neotropical migrant (Golden-cheeked WarblerDendroica chrysoparia) during the non-breeding season
Authors: KING DAVID I. , CHANDLER CARLIN C. , RAPPOLE JOHN H. , CHANDLER RICHARD B. , MEHLMAN DAVID W.
Published: September 2011

The Golden-cheeked WarblerDendroica chrysopariais a federally endangered Neotropical migrant that inhabits montane pine-oak forests in Mexico and northern Central America during the non-breeding season. Although it is known that Golden-cheeked Warblers are closely associated with ‘encino’ oaks (evergreen or holm oak) such asQuercus sapotifolia,Q. elipticaandQ. elongata,which have shiny, narrow, elliptical, or oblong leaves, quantitative habitat targets are useful for effectively incorporating this information into conservation planning and forest management practices. We analysed data on wintering Golden-cheeked Warblers collected during the non-breeding season in Honduras from 1996 to 1998 to identify quantitative targets for habitat conditions for this species. Data on warbler abundance were collected using line transect surveys located in montane pine-oak forests in a stratified-random fashion. Habitat data were collected at five 0.04 ha plots on these same transects and the averaged values used as predictors of Golden-cheeked Warbler abundance. We found that Golden-cheeked Warblers were strongly associated with the basal area ofencinooaks and density of ‘roble’ oaks, such asQ. segoviensis,Q. purulhanaandQ. rugosa, which have large, lobed leaves. Density of Golden-cheeked Warblers peaked at ≈ 5.6 m2ha–1basal area ofencinoand ≈7robleoaks ha–1. These values can be used to identify quantitative habitat targets that can be directly incorporated into forest management practices to ensure that these activities maintain habitat conditions necessary for their use by Golden-cheeked Warblers.
The receptive–expressive gap in the vocabulary of young second-language learners: Robustness and possible mechanisms
Authors: GIBSON TODD A. , OLLER D. KIMBROUGH , JARMULOWICZ LINDA , ETHINGTON CORINNA A.
Published: September 2011

Adults and children learning a second language show difficulty accessing expressive vocabulary that appears accessible receptivelyin their first language(L1). We call this discrepancy the receptive–expressive gap. Kindergarten Spanish (L1) – English (L2) sequential bilinguals were given standardized tests of receptive and expressive vocabulary in both Spanish and English. We found a small receptive–expressive gap in English but a large receptive–expressive gap in Spanish. We categorized children as having had high or low levels of English exposure based on demographic variables and found that the receptive–expressive gap persisted across both levels of English exposure. Regression analyses revealed that variables predicting both receptive and expressive vocabulary scores failed to predict the receptive–expressive gap. The results suggest that the onset of the receptive–expressive gap in L1 may have been abrupt. We discuss possible mechanisms underlying the phenomenon.
It matters how much you talk: On the automaticity of affective connotations of first and second language words
Authors: DEGNER JULIANE , DOYCHEVA CVETA , WENTURA DIRK
Published: September 2011

We report the results of an affective priming study conducted with proficient sequential German and French bilinguals to assess automatic affective word processing in L1 and L2. Additionally, a semantic priming task was conducted in both languages. Whereas semantic priming effects occurred in L1 and L2, and significant affective priming effects were found in L1, affective priming effects in L2 were only found for participants with high levels of language immersion and frequency of L2 use. These results suggest that for sequential bilinguals the intensity of L2 use largely determines whether emotional words in L2 automatically activate their affective connotations.
A SENSELESS CONVERSATION
Authors: Barnett Zach
Published: September 2011

My name is Zach Barnett. Can machines think? Until what happened today, I thought that no human-made machine could ever think as a human does. I now know that I was wrong.
THREE CHEERS FOR SCIENCE AND PHILOSOPHY!
Authors: Kidd Ian James
Published: September 2011

Stephen Hawking recently caused controversy by suggesting that philosophy had become obsolete in the face of the advance of modern science. Hawking's The Grand Design is only the latest in a long series of premature notifications of the obsolescence of philosophy. A wide range of writers, including but not limited to scientists and philosophers, have suggested that philosophy, in part or in whole, has been superseded by the sciences in a way that, all things considered, justifies its abandonment. Some forty years ago, E.O. Wilson suggested that the province of ethics should be turned over to biology, forty years before that the logical positivists had drawn up plans for the formation of a ‘scientific philosophy’, and before that, in the nineteenth century, Comte had identified philosophy as the mere precursor to a modern, ‘positive’ stage of human culture. The list of examples could be extended, a fact which prompts the point that, if philosophy is dying, then it is putting up quite a fight.
PASCAL AND NIETZSCHE
Authors: Boyd Ryan
Published: September 2011

It is wonderful when you discover something which is really pleasing to hear about in an educational setting, let alone being able to investigate it for yourself – the something which you instinctively feel has something vital about it, which inspires you or ignites some cognitive flame. Blake, Shakespeare and Orwell have all done that for me, and now I can add two more to that list: Friedrich Nietzsche and Blaise Pascal.
THE CASE AGAINST THEISM
Authors: Williams Reginald
Published: September 2011

Many people claim that you can't prove or disprove God's existence. But why would anybody think you could? What's such a proof or disproof supposed to look like?
HOW DESTRUCTIVE OF TRADITIONAL CHRISTIAN BELIEFS IS HISTORICAL CRITICISM OF THE BIBLE TODAY CONCEDED TO BE?
Authors: Wells George A.
Published: September 2011

Many theologians accept that it is not plausible to dismiss what is called the ‘higher criticism’ altogether, but try to limit its efficacy. This article discusses a number of their ways of doing so.
Interannual variability of the Azores Current strength and eddy energy in relation to atmospheric forcing
Authors: Volkov Denis L. , Fu Lee‐Lueng
Published: September 2011

Spaceborne observations of sea surface topography have revealed a significant interannual variability of the Azores Current strength and eddy energy. The objective of this paper is to establish the relationship between these variations and atmospheric forcing over the subtropical North Atlantic. Based on satellite altimetry, hydrography, and atmospheric reanalysis products, it is demonstrated that the interannual variability of the Azores Current eastward velocity and eddy energy may be driven by the adjustment of the ocean to the strength of westerly and trade winds, modulated by the North Atlantic Oscillation. Surface intensification (frontogenesis), which is mainly due to the wind‐driven meridional Ekman current convergence, is found significant, but not sufficient to explain the observed interannual variability of the Azores Current strength.
Biomedical Resource Ontology
Authors: Whetzel Trish
Published: September 2011

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NCBO Overview and Biositemaps
Authors: Whetzel Patricia
Published: September 2011

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The statistics of contour fragments in natural scenes
Authors: Merel Josh , Tkacik Gasper , Gifford Adam , Prentice Jason , Balasubramanian Vijay
Published: September 2011

Summary: Recent electrophysiology recordings in macaque V4/IT suggest that single neuron response to synthetic closed contours can be largely captured by models which only consider a small number of contour fragments (Brincat and Connor 2004). Motivated by this experimental work, we sought firstly to characterize the statistics of contour fragments in natural scenes, and secondly to generate synthetic images which reflect the measured contour-fragment statistics.To detect contour fragments, we defined a set of feature detectors which respond only in the presence of two edges co-occurring at a fixed relative angle – implemented as a logical ‘AND’ of two Gabor-like, laplacian-of-gaussian linear filters. We then determined the pairwise correlations of these contour fragments in a natural image ensemble. If efficient coding extends to higher cortical centers and processing in the ventral visual stream can be modeled as a sequence of logical operations on linear shape features, then the pairwise statistics we measure should be informative about neural shape coding.Using these statistics directly, it is possible to produce a generative model of simple images which contain the measured statistics. We implemented a modified Ising model and solved the inverse problem of determining the optimal model parameters which satisfy the measured correlations. The resulting Ising-like model of the pairwise statistics can generate the probability of any arrangement of contour fragments as measured in the natural image ensemble.As a complementary approach to producing images with naturalistic contour fragment statistics, it is possible to start with a natural scene and isolate the target features. This is achieved by applying our contour fragment detection processing to the single scene and then separately visualizing the fragments detected. This second procedure lends itself to parametric randomization of the generated image.Narrative Elaboration: The central question guiding our study is how shapes are represented in inferotemporal cortex. To that end, we have investigated natural images in order to motivate experiments capable of targeting the extent to which neural processing of shapes involves representing shapes as combinations of key contour features. To simplify, we are focusing on black-and-white images and prioritizing contour features. This project suggests it is possible to generate synthetic images containing only a select set of contour statistics. Our subsequent goals include conducting collaborative macaque electrophysiology experiments with our generated images as visual stimuli.
Urban Tree Canopy Prioritization (UTC): Experience from Baltimore
Authors: Grove J. Morgan , Locke Dexter
Published: September 2011

The recently emerging shift in urban land management to an “all lands, all people” approach to achieve critical urban sustainability goals created the need to 1) characterize landcover at the unit of individual property units: i.e. property parcels, and 2) integrate social and ecological data corresponding to diverse, sustainability goals so that all neighborhoods and parcels can be prioritized. Currently, there are two types of UTC tools: 1) UTC Assessment and Monitoring tools are used to assess existing and potential urban tree canopy at a parcel level (2’ resolution) and regional extent; and 2) UTC Prioritization tools are used to identify where to increase urban tree canopy at watershed, neighborhood, and parcel levels based upon diverse stakeholders’ goals and preferences among goals. These goals may be ecological, social, and/or economic.In this presentation, we report on advances in our development of UTC Prioritization tools and their application in Baltimore, Maryland.
Catalytic and transport cycles of ABC exporters
Authors: Al-Shawi Marwan K.
Published: September 2011

ABC (ATP-binding cassette) transporters are arguably the most important family of ATP-driven transporters in biology. Despite considerable effort and advances in determining the structures and physiology of these transporters, their fundamental molecular mechanisms remain elusive and highly controversial. How does ATP hydrolysis by ABC transporters drive their transport function? Part of the problem in answering this question appears to be a perceived need to formulate a universal mechanism. Although it has been generally hoped and assumed that the whole superfamily of ABC transporters would exhibit similar conserved mechanisms, this is proving not to be the case. Structural considerations alone suggest that there are three overall types of coupling mechanisms related to ABC exporters, small ABC importers and large ABC importers. Biochemical and biophysical characterization leads us to the conclusion that, even within these three classes, the catalytic and transport mechanisms are not fully conserved, but continue to evolve. ABC transporters also exhibit unusual characteristics not observed in other primary transporters, such as uncoupled basal ATPase activity, that severely complicate mechanistic studies by established methods. In this chapter, I review these issues as related to ABC exporters in particular. A consensus view has emerged that ABC exporters follow alternating-access switch transport mechanisms. However, some biochemical data suggest that alternating catalytic site transport mechanisms are more appropriate for fully symmetrical ABC exporters. Heterodimeric and asymmetrical ABC exporters appear to conform to simple alternating-access-type mechanisms.
ABC solute importers in bacteria
Authors: Cui Jinming , Davidson Amy L.
Published: September 2011

The bacterial ABC (ATP-binding cassette) importers mediate nutrient uptake and some are essential for survival in environments where nutrients are limited, such as in the human body. Although ABC importers exhibit remarkable versatility in the substrates that they can transport, they appear to share a similar multisubunit architecture and mechanism of energization by ATP hydrolysis. This chapter will provide both basic understanding and up-to-date information on the structure, mechanism and regulation of this important family of proteins.