bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC‐MS/MS. 1. Preparation of more than 4000 native protein maps
Authors: Jin Ya , Zhang Jun , Yuan Qi , Manabe Takashi , Tan Wen
Published: April 2015

Soluble proteins of human bronchial smooth muscle cells (HBSMC) were separated by nondenaturing micro 2DE and a 30 mm × 40 mm area of the CBB‐stained slab gel (1.0 mm thick) was cut into 1.1 mm × 1.1 mm squares, then the proteins in the 972 gel pieces (squares) were applied to quantitative LC‐MS/MS. Grid‐cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC‐MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data [1]. Totally 4323 proteins were identified in successfully analyzed 967 squares and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The quantity of the proteins distributed from 3.6% to 1 × 10−5% of the total protein quantity in the grid area. Each protein map was characterized by several features, including the position of quantity peak square, number of detected squares, and degree of concentration (focused or dispersed). About 4% of the proteins were detected in 100 or more squares, suggesting that they might be ubiquitous and interacting with other proteins. In contrast, many proteins showed more concentrated quantity distribution and the quantity peak positions of 565 proteins with a defined degree of concentration were summarized into a quantity peak map. These results for the first time visualized the distribution patterns of cellular proteins on a nondenaturing 2D gel.
Comparative proteomic analysis of oil palm leaves infected with Ganoderma boninense revealed changes in proteins involved in photosynthesis, carbohydrate metabolism, and immunity and defense
Authors: Jeffery Daim Leona Daniela , Ooi Tony Eng Keong , Ithnin Nalisha , Mohd Yusof Hirzun , Kulaveerasingam Harikrishna , Abdul Majid Nazia , Karsani Saiful Anuar
Published: April 2015

The basidiomycete fungal pathogen Ganoderma boninense is the causative agent for the incurable basal stem rot (BSR) disease in oil palm. This disease causes significant annual crop losses in the oil palm industry. Currently, there is no effective method for disease control and elimination, nor is any molecular marker for early detection of the disease available. An understanding of how BSR affects protein expression in plants may help identify and/or assist in the development of an early detection protocol. Although the mode of infection of BSR disease is primarily via the root system, defense‐related genes have been shown to be expressed in both the root and leafs. Thus, to provide an insight into the changes in the global protein expression profile in infected plants, comparative 2DE was performed on leaf tissues sampled from palms with and without artificial inoculation of the Ganoderma fungus. Comparative 2DE revealed that 54 protein spots changed in abundance. A total of 51 protein spots were successfully identified by LC‐QTOF MS/MS. The majority of these proteins were those involved in photosynthesis, carbohydrate metabolism as well as immunity and defense.
Selective detection and quantification of carbon nanotubes in soil
Authors: Jeong Junhoe , Lee Yong-ju , Hwang Yu sik , Hong In Seok
Published: April 2015

Carbon nanotubes (CNTs) have been widely applied in many industrial fields. As world production of CNTs increases, the risk of environmental exposure to CNTs also increases. Therefore, to evaluate the impact on the environment, many cell and animal studies have reported on the toxicity of CNTs. It is important to determine the degree of contamination of CNTs in soil and to find the pollution pathways for assessment of the environmental toxicity of CNTs. However, selective detection methods for CNTs in soil or water have rarely been reported. In the present study, a novel technique was developed to quantify the amount of CNTs in soil mixtures using fluorescent SYBR Green I dye after isolation of the CNTs with specific DNA oligomers. As a result, a limit of detection of CNTs in soil was obtained in the range of 250 ppb. This limit can easily be extended to the level of 10 ppb using magnetic well plates with a greater capacity. This method also worked well in the presence of graphene oxide and could be applied to the detection of CNTs in a variety of surroundings (e.g., fish and other tissues). Environ Toxicol Chem 2015;34:1969–1974. © 2015 SETAC
Development of cereal‐based functional food using cereal‐mix substrate fermented with probiotic strain – Pichia kudriavzevii OG32
Authors: Ogunremi Omotade R. , Agrawal Renu , Sanni Abiodun I.
Published: April 2015

Probiotic strains contribute to the functionality of foods during fermentation. In this present work, cereal‐mix was fermented with probiotic Pichia kudriavzevii OG32. Selected fermentation parameters and functional properties of the product were determined. The growth of Pichia kudriavzevii OG32 was supported by the cereal‐mix containing 1% salt and 0.2% red chili powder to counts of between 7.46 and 8.22 Log10 cfu/mL within 24 h. Pichia kudriavzevii OG32 increased the viscosity of cereal‐mix with the highest inoculum size (1.84x105cfu/ml) giving the highest viscosity of 1793.6 mPa.S. An inoculum size of 1.98 × 104 cfu/mL gave the most acceptable product based on the sensory evaluation by the panelist. Forty volatile compounds were identified in the fermented product, while acids (32.21%) and esters (32.37%) accounted for the largest proportions. The cereal‐based fermented product scavenged DPPH from 200 μmol/L methanolic solution by 55.71%. Probiotic yeast improved the sensory and some functional properties of cereal‐based substrate during fermentation. This is one of the first reports on the volatile composition of cereal‐based functional food produced with probiotic yeast.
mRNAs and miRNAs in whole blood associated with lung hyperplasia, fibrosis, and bronchiolo‐alveolar adenoma and adenocarcinoma after multi‐walled carbon nanotube inhalation exposure in mice
Authors: Snyder‐Talkington Brandi N. , Dong Chunlin , Sargent Linda M. , Porter Dale W. , Staska Lauren M. , Hubbs Ann F. , Raese Rebecca , McKinney Walter , Chen Bean T. , Battelli Lori , Lowry David T. , Reynolds Steven H. , Castranova Vincent , Qian Yong , Guo Nancy L.
Published: April 2015

Inhalation exposure to multi‐walled carbon nanotubes (MWCNT) in mice results in inflammation, fibrosis and the promotion of lung adenocarcinoma; however, the molecular basis behind these pathologies is unknown. This study determined global mRNA and miRNA profiles in whole blood from mice exposed by inhalation to MWCNT that correlated with the presence of lung hyperplasia, fibrosis, and bronchiolo‐alveolar adenoma and adenocarcinoma. Six‐week‐old, male, B6C3F1 mice received a single intraperitoneal injection of either the DNA‐damaging agent methylcholanthrene (MCA, 10 µg g−1 body weight) or vehicle (corn oil). One week after injections, mice were exposed by inhalation to MWCNT (5 mg m−3, 5 hours per day, 5 days per week) or filtered air (control) for a total of 15 days. At 17 months post‐exposure, mice were euthanized and examined for the development of pathological changes in the lung, and whole blood was collected and analyzed using microarray analysis for global mRNA and miRNA expression. Numerous mRNAs and miRNAs in the blood were significantly up‐ or down‐regulated in animals developing pathological changes in the lung after MCA/corn oil administration followed by MWCNT/air inhalation, including fcrl5 and miR‐122‐5p in the presence of hyperplasia, mthfd2 and miR‐206‐3p in the presence of fibrosis, fam178a and miR‐130a‐3p in the presence of bronchiolo‐alveolar adenoma, and il7r and miR‐210‐3p in the presence of bronchiolo‐alveolar adenocarcinoma, among others. The changes in miRNA and mRNA expression, and their respective regulatory networks, identified in this study may potentially serve as blood biomarkers for MWCNT‐induced lung pathological changes. Copyright © 2015 John Wiley & Sons, Ltd.
Small‐molecule compounds exhibiting target‐mediated drug disposition — A case example of ABT‐384
Authors: An Guohua , Liu Wei , Dutta Sandeep
Published: April 2015

Nonlinearities are frequently encountered in pharmacokinetics, and they can occur when 1 or more processes of absorption, distribution, metabolism, and excretion are saturable. One special source of nonlinearity that has been noticed recently is the saturable binding of the drug to a high‐affinity–low‐capacity target, a phenomenon known as target‐mediated drug disposition (TMDD). Although TMDD can occur in both small‐molecule compounds and large‐molecule compounds, the latter has received much more attention because of its high prevalence. With the development of more potent small‐molecule drugs acting on highly specific targets and the availability of increasingly sensitive analytical techniques, small‐molecule compounds exhibiting TMDD have been increasingly reported in the past several years. ABT‐384 is a small‐molecule drug candidate that exhibited significant nonlinear pharmacokinetics, potentially imparted by TMDD, in a first‐in‐human clinical trial conducted in healthy volunteers. Compared with published small‐molecule compounds exhibiting TMDD, ABT‐384 pharmacokinetic characteristics are more consistent with TMDD. To expand current knowledge of TMDD of small‐molecule compounds and increase awareness of this interesting and clinically important phenomenon, in this review the general features of small‐molecule compounds exhibiting TMDD are highlighted, with ABT‐384 provided as an example.
SEFE without Mapping via Large Induced Outerplane Graphs in Plane Graphs
Authors: Angelini Patrizio , Evans William , Frati Fabrizio , Gudmundsson Joachim
Published: April 2015

We show that every n‐vertex planar graph admits a simultaneous embedding without mapping and with fixed edges with any ‐vertex planar graph. In order to achieve this result, we prove that every n‐vertex plane graph has an induced outerplane subgraph containing at least vertices. Also, we show that every n‐vertex planar graph and every n‐vertex planar partial 3‐tree admit a simultaneous embedding without mapping and with fixed edges.
Isoxazolopyrimidinethione and Isoxazolopyridopyrimidinethione Derivatives: Key Intermediates for Synthesis of Novel Fused Triazoles as Potent 5α‐Reductase Inhibitors and Anti‐Prostate Cancer
Authors: Gomha Sobhi M. , Badry Mohamed G. , Abdalla Mohamed M.
Published: April 2015

The arylideneisoxazolone derivative 1 is used for preparation of two different pyrimidinethiones 3 and 5 through interaction with thiourea and thiouracil, respectively. Compounds 3 and 5 were subjected to reaction with different hydrazonyl halides in basic medium to afford different triazolopyrimidines 9a, 9b, 9c, 9d, 9e, 9f, 9g, 9h and 13a, 13b, 13c, 13d, 13e, 13f, the structures were confirmed by their spectral and elemental analysis. All the newly synthesized products were screened against 5α‐reductase. Some of the newly synthesized compounds showed potent 5α‐reductase inhibition activities with good ED50.
Mutations in the RAS and PI3K pathways are associated with metastatic location in colorectal cancers
Authors: Lan Yuan‐Tzu , Jen‐Kou Lin , Lin Chien‐Hsing , Yang Shung‐Haur , Lin Chun‐Chi , Wang Huann‐Sheng , Chen Wei‐Shone , Lin Tzu‐Chen , Jiang Jeng‐Kai , Chang Shih‐Ching
Published: April 2015

Background and objectives

Identification of mutations in the downstream epidermal growth factor receptor (EGFR) signaling pathway could provide important insights of EGFR‐targeted therapies in colorectal cancers. We analyzed the mutation spectra of the PI3K/PTEN/AKT and RAS/RAF/MAPK pathways in colorectal cancers and the associations of these mutations with sites of metastases or recurrence.

Methods

The study population comprised 1,492 retrospectively collected stages I–IV colorectal cancer specimens. Tissue was obtained between 2000 and 2010 at a single hospital. We analyzed 61 hot spots using MALDI–TOF mass spectrometry for nucleic acid analysis.

Results

Mutations were found in the RAS pathway in 47.3% of patients and in the PI3K pathway in 14.3% of patients, with 9.2% of patients carrying mutations in both pathways. Both the RAS and PI3K pathway mutations were significantly associated with proximal tumors, mucinous tumors, and microsatellite instability. Tumors carrying a RAS pathway mutation exhibited a higher frequency of lung and peritoneal metastasis than did tumors with a wild‐type gene (P = 0.025 and 0.009, respectively). NRAS gene mutation was significantly associated with lung metastasis (P = 0.001).

Conclusions

Somatic mutations in the RAS pathway of the primary tumor in colorectal cancer can influence patterns of metastasis and recurrence. J. Surg. Oncol. 2015 111:905–910. © 2014 Wiley Periodicals, Inc.
Leiomyosarcoma: One disease or distinct biologic entities based on site of origin?
Authors: Worhunsky David J. , Gupta Mihir , Gholami Sepideh , Tran Thuy B. , Ganjoo Kristen N. , van de Rijn Matt , Visser Brendan C. , Norton Jeffrey A. , Poultsides George A.
Published: April 2015

Background

Leiomyosarcoma (LMS) can originate from the retroperitoneum, uterus, extremity, and trunk. It is unclear whether tumors of different origin represent discrete entities. We compared clinicopathologic features and outcomes following surgical resection of LMS stratified by site of origin.

Methods

: Patients with LMS undergoing resection at a single institution were retrospectively reviewed. Clinicopathologic variables were compared across sites. Survival was calculated using the Kaplan–Meier method and compared using log‐rank and Cox regression analyses.

Results

From 1983 to 2011, 138 patients underwent surgical resection for LMS. Retroperitoneal and uterine LMS were larger, higher grade, and more commonly associated with synchronous metastases. However, disease‐specific survival, recurrence‐free survival, and recurrence patterns were not significantly different across the four sites. Synchronous metastases (HR 3.20, P < 0.001), but not site of origin, size, grade, or margin status, were independently associated with worse DSS. A significant number of recurrences and disease‐related deaths were noted beyond 5 years.

Conclusions

Although larger and higher grade, retroperitoneal and uterine LMS share similar survival and recurrence patterns with their trunk and extremity counterparts. LMS of various anatomic sites may not represent distinct disease processes based on clinical outcomes. The presence of metastatic disease remains the most important prognostic factor for LMS. J. Surg. Oncol. 2015 111:808–812. © 2014 Wiley Periodicals, Inc.
Development of a low‐density‐solvent dispersive liquid–liquid microextraction with gas chromatography and mass spectrometry method for the quantitation of tetrabromobisphenol‐A from dust
Authors: Barrett Christopher A. , Orban David A. , Seebeck Shannon E. , Lowe Luis E. , Owens Janel E.
Published: April 2015

The development of an alternative dispersive liquid–liquid microextraction protocol utilizing a low‐density extraction solvent, toluene, is described here for the extraction of the brominated flame retardant, tetrabromobisphenol‐A, from dust prior to selected ion monitoring analysis by gas chromatography with mass spectrometry. Method parameters of dispersive solvent type and extraction solvent type were optimized. Excellent recovery (88.9%; n = 5 spike replicates) with good precision was achieved in a spike and recovery study. This developed method was utilized to survey tetrabromobisphenol‐A concentrations in dust sampled from a local electronics recycling facility from the ambient environment and 20 computer towers undergoing recycling. Concentrations of tetrabromobisphenol‐A from dust in computer towers ranged from not detected (n = 2) up to 64 μg/g with a mean value of 11 μg/g and median of 4.1 μg/g tetrabromobisphenol‐A. A composite sample of dust collected from the ambient indoor environment was analyzed with a resulting concentration of 36 μg/g. This is the first application of this novel green method for pre‐concentrating flame retardants from dust and the first report of tetrabromobisphenol‐A concentrations at a U.S.‐based electronics recycling facility.
Physiological relevance of food grade microcapsules: Impact of milk protein based microcapsules on inflammation in mouse models for inflammatory bowel diseases
Authors: Würth Rebecca , Lagkouvardos Ilias , Clavel Thomas , Wilke Julia , Foerst Petra , Kulozik Ulrich , Haller Dirk , Hörmannsperger Gabriele
Published: April 2015

In order to increase beneficial effects of bioactive compounds in functional food and dietary supplements, enormous efforts are put in the technological development of microcapsules. Although these products are often tailor‐made for disease susceptible consumer, the physiological impact of microcapsule uptake on the respective target consumer has never been addressed. The present study aimed to assess the relevance of this aspect by analyzing the impact of milk protein based microcapsules on experimental inflammatory bowel disease. Long‐term feeding of sodium caseinate or rennet gel microcapsules resulted in significant alterations in the intestinal microbiota of healthy mice. In TNFΔARE/wt mice, a model for chronic ileal inflammation, rennet gel microcapsules resulted in further increased splenomegaly, whereas ileal inflammation was unchanged. In IL10−/− mice, a model for chronic colitis, both types of microcapsules induced a local increase of the intestinal inflammation. The present study is the first to demonstrate that, independent of their cargo, microcapsules have the potential to affect the intestinal microbiota and to exert unprecedented detrimental effects on disease‐susceptible individuals. In conclusion, the impact of microcapsule uptake on the respective target consumer groups should be thoroughly investigated in advance to their commercial use in functional food or dietary supplements.
l‐Cysteine metabolism and its nutritional implications
Authors: Yin Jie , Ren Wenkai , Yang Guan , Duan Jielin , Huang Xingguo , Fang Rejun , Li Chongyong , Li Tiejun , Yin Yulong , Hou Yongqing , Kim Sung Woo , Wu Guoyao
Published: April 2015

l‐Cysteine is a nutritionally semiessential amino acid and is present mainly in the form of l‐cystine in the extracellular space. With the help of a transport system, extracellular l‐cystine crosses the plasma membrane and is reduced to l‐cysteine within cells by thioredoxin and reduced glutathione (GSH). Intracellular l‐cysteine plays an important role in cellular homeostasis as a precursor for protein synthesis, and for production of GSH, hydrogen sulfide (H2S), and taurine. l‐Cysteine‐dependent synthesis of GSH has been investigated in many pathological conditions, while the pathway for l‐cysteine metabolism to form H2S has received little attention with regard to prevention and treatment of disease in humans. The main objective of this review is to highlight the metabolic pathways of l‐cysteine catabolism to GSH, H2S, and taurine, with special emphasis on therapeutic and nutritional use of l‐cysteine to improve the health and well‐being of animals and humans.
Fixierte Konstanten
Authors: Stohner Jürgen , Quack Martin
Published: April 2015

Das Mol, die Masseneinheit und die Avogadrosche Konstante stehen vor einer Neudefinition. Welche Auswirkungen hat das auf die Chemie?
Fukushima Daiichi: Eintrag radioaktiver Stoffe ins Meer
Authors: Nies Hartmut
Published: April 2015

Vor vier Jahren kam es im japanischen Kernkraftwerk Fukushima Daiichi infolge eines katastrophalen Tsunamis zu einem schweren Unfall. Große Mengen radioaktiver Stoffe gelangten in den pazifischen Ozean. Welche Folgen hatte die Kontamination des Meeres und was sind die längerfristigen Auswirkungen?
The role of the Bézier extraction operator for T‐splines of arbitrary degree: linear dependencies, partition of unity property, nesting behaviour and local refinement
Authors: May Stefan , Vignollet Julien , de Borst René
Published: April 2015

We determine linear dependencies and the partition of unity property of T‐spline meshes of arbitrary degree using the Bézier extraction operator. Local refinement strategies for standard, semi‐standard and non‐standard T‐splines – also by making use of the Bézier extraction operator – are presented for meshes of even and odd polynomial degrees. A technique is presented to determine the nesting between two T‐spline meshes, again exploiting the Bézier extraction operator. Finally, the hierarchical refinement of standard, semi‐standard and non‐standard T‐spline meshes is discussed. This technique utilises the reconstruction operator, which is the inverse of the Bézier extraction operator. Copyright © 2015 John Wiley & Sons, Ltd.
Novel Carbazole (Cbz)‐Based Carboxylated Functional Monomers: Design, Synthesis, and Characterization
Authors: Mondal Ejabul , Lellouche Jean‐Paul , Naddaka Maria
Published: April 2015

A series of novel functional carbazole (Cbz)‐based carboxylated monomers were synthesized and characterized. A Clauson‐Kaas procedure, a deprotection step, amide coupling, and hydrolysis were utilized as key chemical reactions towards the multistep synthesis of monomers in good to excellent isolated yields. The design strategy was further extended to complex carbazole‐COOH monomers incorporated arylazo groups as photoreactive moieties. In addition, photoreactive hybrid carbazole (Cbz)‐pyrrole (Pyr)‐based carboxylated monomers, comprising a pyrrole core linking a carbazole and a photoreactive phenylazide or benzophenone moiety through an amide spacer in the molecular structure, were also synthesized. The latter can be utilized for surface modification of polymeric films in their monomeric form or as polymeric microparticles (MPs).
Forensic comparison of synthetic fibers
Authors: Farah Shady , Kunduru Konda Reddy , Tsach Tsadok , Bentolila Alfonso , Domb Abraham J.
Published: April 2015

Polymeric fibers are one kind of trace evidence found in the crime scenes, and they play a crucial role in criminal investigation. Identification and comparison of polymeric fibers are a direct result of professional analysis. When performed properly, the analytical method used in differentiating fibers of different origins can be of high evidential value. Regular forensic examinations of synthetic fibers to determine type and subtype are based on microscopy, spectroscopy, chromatographic, and mass spectrometry. This review covers different analytical methods used in the forensic analysis and comparison of synthetic fibers. Copyright © 2015 John Wiley & Sons, Ltd.
A type I interferon signature characterizes chronic antibody‐mediated rejection in kidney transplantation
Authors: Rascio Federica , Pontrelli Paola , Accetturo Matteo , Oranger Annarita , Gigante Margherita , Castellano Giuseppe , Gigante Maddalena , Zito Anna , Zaza Gianluigi , Lupo Antonio , Ranieri Elena , Stallone Giovanni , Gesualdo Loreto , Grandaliano Giuseppe
Published: April 2015

Chronic antibody‐mediated rejection (CAMR) represents the main cause of kidney graft loss. To uncover the molecular mechanisms underlying this condition, we characterized the molecular signature of peripheral blood mononuclear cells (PBMCs) and, separately, of CD4+ T lymphocytes isolated from CAMR patients, compared to kidney transplant recipients with normal graft function and histology. We enrolled 29 patients with biopsy‐proven CAMR, 29 stable transplant recipients (controls), and 8 transplant recipients with clinical and histological evidence of interstitial fibrosis/tubular atrophy. Messenger RNA and microRNA profiling of PBMCs and CD4+ T lymphocytes was performed using Agilent microarrays in eight randomly selected patients per group from CAMR and control subjects. Results were evaluated statistically and by functional pathway analysis (Ingenuity Pathway Analysis) and validated in the remaining subjects. In PBMCs, 45 genes were differentially expressed between the two groups, most of which were up‐regulated in CAMR and were involved in type I interferon signalling. In the same patients, 16 microRNAs were down‐regulated in CAMR subjects compared to controls: four were predicted modulators of six mRNAs identified in the transcriptional analysis. In silico functional analysis supported the involvement of type I interferon signalling. To further confirm this result, we investigated the transcriptomic profiles of CD4+ T lymphocytes in an independent group of patients, observing that the activation of type I interferon signalling was a specific hallmark of CAMR. In addition, in CAMR patients, we detected a reduction of circulating BDCA2+ dendritic cells, the natural type I interferon‐producing cells, and their recruitment into the graft along with increased expression of MXA, a type I interferon‐induced protein, at the tubulointerstitial and vascular level. Finally, interferon alpha mRNA expression was significantly increased in CAMR compared to control biopsies. We conclude that type I interferon signalling may represent the molecular signature of CAMR. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Mechanical behaviors of four‐step 1 × 1 braided carbon/epoxy three‐dimensional composite tubes under axial compression loading
Authors: Gideon Rotich K. , Sun Baozhong , Gu Bohong
Published: April 2015

This article focuses on the quasistatic axial compression behavior and the consequent energy absorption of three different types of carbon/epoxy braided composite tubes. The focus is to evaluate the effect of sample length and braiding angle on the energy absorption and failure mechanism of the braided composite tubes. All tubes were manufactured with carbon fiber through four‐step 1 × 1 braiding process and epoxy resin. Quasistatic axial compression tests were carried out to comprehend the failure mechanism and the corresponding compressive load–displacement characteristics of each braided composite tube. The quasistatic compression test parameters such as the compression peak load and the energy absorption of all these composite tubes were compared. It was found that as the length of the sample increased, the peak load reduced and the energy absorption of the braided tubes at 45° braiding angle was considerably higher than that of other braiding angles of 25° and 35°. The failure modes included matrix crack along the braiding angle, fiber breakage, bulging and debonding between yarns. POLYM. COMPOS., 37:3210–3218, 2016. © 2015 Society of Plastics Engineers
Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling
Authors: Nilse Lars , Sigloch Florian Christoph , Biniossek Martin L. , Schilling Oliver
Published: April 2015

Reliable detection of peptides in LC‐MS data is a key algorithmic step in the analysis of quantitative proteomics experiments. While highly abundant peptides can be detected reliably by most modern software tools, there is much less agreement on medium and low‐intensity peptides in a sample. The choice of software tools can have a big impact on the quantification of proteins, especially for proteins that appear in lower concentrations. However, in many experiments, it is precisely this region of less abundant but substantially regulated proteins that holds the biggest potential for discoveries. This is particularly true for discovery proteomics in the pharmacological sector with a specific interest in key regulatory proteins. In this viewpoint article, we discuss how the development of novel software algorithms allows us to study this region of the proteome with increased confidence. Reliable results are one of many aspects to be considered when deciding on a bioinformatics software platform. Deployment into existing IT infrastructures, compatibility with other software packages, scalability, automation, flexibility, and support need to be considered and are briefly addressed in this viewpoint article.
Body mass index and mortality in men with prostate cancer
Authors: Cantarutti Anna , Bonn Stephanie E. , Adami Hans‐Olov , Grönberg Henrik , Bellocco Rino , Bälter Katarina
Published: April 2015

BACKGROUND

Body Mass index (BMI) has been shown to affect risk and mortality of several cancers. Prostate cancer and obesity are major public health concerns for middle‐aged and older men. Previous studies of pre‐diagnostic BMI have found an increased risk of prostate cancer mortality in obese patients.

OBJECTIVE

To study the associations between BMI at time of prostate cancer diagnosis and prostate cancer specific and overall mortality.

METHODS

BMI was analyzed both as a continuous variable and categorized into four groups based on the observed distribution in the cohort (BMI < 22.5, 22.5 < 25, 25 < 27.5 and ≥27.5 kg/m2). The association between BMI and mortality was assessed using stratified Cox proportional hazards models and by fitting regression splines for dose response analysis in 3,161 men diagnosed with prostate cancer. After 11 years of follow up via linkage to the population‐based cause of death registry, we identified 1,161 (37%) deaths off which 690 (59%) were due to prostate cancer.

RESULTS

High BMI (BMI ≥ 27.5 kg/m2) was associated with a statistically significant increased risk of prostate cancer specific mortality (HR:1.44, 95%CI: 1.09–1.90) and overall mortality (HR:1.33, 95%CI: 1.09–1.63) compared to the reference group (BMI 22.5 < 25 kg/m2). Additionally, men with a low BMI (<22.5 kg/m2), had a statistically significant increased risk of prostate cancer specific mortality (HR:1.33, 95%CI: 1.02–1.74) and overall mortality (HR:1.36, 95%CI: 1.11–1.67) compared to the reference. However, this effect disappeared when men who died within the first two years of follow‐up were excluded from the analyses while the increased risk of prostate cancer specific mortality and overall mortality remained statistically significant for men with a BMI ≥ 27.5 kg/m2 (HR:1.44, 95%CI: 1.09–1.90 and HR: 1.33, 95%CI: 1.09–1.63, respectively).

CONCLUSION

This study showed that a high BMI at time of prostate cancer diagnosis was associated with increased overall mortality. Prostate 75: 1129–1136, 2015. © 2015 Wiley Periodicals, Inc.
The Performance of Variable Sample Size Chart with Measurement Errors
Authors: Hu XueLong , Castagliola Philippe , Sun Jinsheng , Khoo Michael B.C.
Published: April 2015

The variable sample size (VSS)
chart has been investigated by several researchers under the assumption of no measurement error. However, in practice, measurement errors may exist in quality control applications. In this paper, the overall performance of the VSS
chart is investigated when measurement errors exist using a linearly covariate error model, and a methodology is proposed for choosing optimal parameters by considering measurement errors. It is shown that the overall performance of the VSS
chart is significantly affected by the presence of measurement errors. The effect of taking multiple measurements for each item in a subgroup on the performance of VSS
chart is also investigated in this paper. An example is provided to illustrate the application of the VSS
chart with measurement errors. Copyright © 2015 John Wiley & Sons, Ltd.
Variables Sampling Plan for Resubmitted Lots in a Process with Linear Profiles
Authors: Wang Fu‐Kwun
Published: April 2015

Acceptance sampling plans include a sampling scheme and a set of rules for determining whether an inspection lot from a supplier should be accepted or rejected. In some circumstances, the supplier is allowed to resubmit lots for further inspection when the original inspection result is unacceptable. In this study, two variables sampling plans based on the process‐yield index for a process with linear profiles are proposed to deal with lot sentencing. The single sampling plan is a special case of the resubmitted lots sampling plan. The plan parameters are determined using a nonlinear optimization method under the given values of producer's risk, consumer's risk, acceptable quality level, and lot tolerance percent defective. Numerous tables are provided to determine the plan parameters. One real example is used to illustrate our proposed method. Copyright © 2015 John Wiley & Sons, Ltd.
Active space and basis set effects in CASPT2 models of the 1,3‐butadiene‐ethene cycloaddition and the 1,3‐butadiene dimerization
Authors: Scarborough David L. A. , Kobayashi Rika , Thompson Christopher D. , Izgorodina Ekaterina I.
Published: April 2015

The first step of the asynchronous biradical, stepwise biradical, and concerted mechanisms of the 1,3‐butadiene Diels–Alder reactions with both ethene and itself was studied using CASPT2 to determine the influence of basis set and active space on reaction barriers. CASPT2(6,6) with the cc‐pVDZ, 6‐311+G(3df,2p) and cc‐pVTZ basis sets provided the best results with average errors below 3.1 kJ mol−1 with respect to the experimental result. Increasing the active space size also had little effect on the calculated reaction barriers. With respect to experimental results, uncontracted multireference averaged quadratic coupled cluster (MRAQCC) produced superior barriers than internally contracted MRAQCC by 16.1–39.3 kJ mol−1. The inability of CASSCF to locate transition states for some of the cycloadditions across the butadiene‐ethene and butadiene dimerization reactions is also rationalized. CASPT2 suggests a preference for the concerted mechanism of the butadiene‐ethene reaction, however, no basis set yielded a preference for any of the butadiene dimerization pathways. © 2015 Wiley Periodicals, Inc.
Effect of gaseous ozone and light‐activated disinfection on the surface hardness of resin‐based root canal sealers
Authors: Tuncay Öznur , Er Özgür , Demirbuga Sezer , Zorba Yahya Orçun , Topçuoğlu Hüseyin Sinan
Published: April 2015

Although root canal instruments remove most of the content from the main root canal space, disinfection or irrigation plays an indispensable role in all areas of the root canal system, especially in parts that are inaccessible by instruments. The originality of this study was to investigate the effect of two novel disinfection techniques on the surface hardness of resin‐based endodontic sealers using atomic force microscopy (AFM). Forty extracted single‐rooted maxillary central human teeth were prepared and divided into four groups according to treatment methods. The first group was irrigated with saline and served as a control, other groups irrigated with sodium hypochlorite (NaClO); gaseous ozone; and light‐activated disinfection (LAD). The groups were divided into two subgroups, according to the obturation method used: subgroup A: gutta‐percha and AH plus; and subgroup B: EndoREZ/resin‐coated cones. After obturation, atomic force microscopy (AFM) measurement was performed to analyze the surface hardness of the sealers. There was a significant difference between group 1A and group 3A (p < 0.05). Group 3B had the highest surface hardness values that were statistically different (p < 0.05). When disregarding the sealers, the ozone possessed statistically higher surface hardness values than the other groups in all root thirds (p < 0.05). The use of ozone and LAD may alter the surface hardness of resin‐based sealers. The use of AFM can be considered an alternative hardness test techonology for sealing material. SCANNING 38:141–147, 2016. © 2015 Wiley Periodicals, Inc.
A Bayesian mixture of semiparametric mixed‐effects joint models for skewed‐longitudinal and time‐to‐event data
Authors: Chen Jiaqing , Huang Yangxin
Published: April 2015

In longitudinal studies, it is of interest to investigate how repeatedly measured markers in time are associated with a time to an event of interest, and in the mean time, the repeated measurements are often observed with the features of a heterogeneous population, non‐normality, and covariate measured with error because of longitudinal nature. Statistical analysis may complicate dramatically when one analyzes longitudinal–survival data with these features together. Recently, a mixture of skewed distributions has received increasing attention in the treatment of heterogeneous data involving asymmetric behaviors across subclasses, but there are relatively few studies accommodating heterogeneity, non‐normality, and measurement error in covariate simultaneously arose in longitudinal–survival data setting. Under the umbrella of Bayesian inference, this article explores a finite mixture of semiparametric mixed‐effects joint models with skewed distributions for longitudinal measures with an attempt to mediate homogeneous characteristics, adjust departures from normality, and tailor accuracy from measurement error in covariate as well as overcome shortages of confidence in specifying a time‐to‐event model. The Bayesian mixture of joint modeling offers an appropriate avenue to estimate not only all parameters of mixture joint models but also probabilities of class membership. Simulation studies are conducted to assess the performance of the proposed method, and a real example is analyzed to demonstrate the methodology. The results are reported by comparing potential models with various scenarios. Copyright © 2015 John Wiley & Sons, Ltd.
Humor in Children's Picture Books
Authors: Serafini Frank , Coles Richard
Published: April 2015

Humorous literature for children has been around since Randolph Caldecott first started writing and illustrating picturebooks. In the article, the authors try to understand what makes picturebooks funny and discuss ways to use humor in the classroom. Many examples of humorous picturebooks are cited to provide teachers with resources for their classrooms.
An indoor radio propagation model considering angles for WLAN infrastructures
Authors: Han Shuai , Gong Zijun , Meng Weixiao , Li Cheng
Published: April 2015

Wireless local area network fingerprint‐based indoor location system is a hot topic these years because it needs no extra hardware and is very easy to deploy. However, it demands a database containing the distribution of received signal strength (RSS) of the area of interest,called radio map. Conventionally, we need to grid the area densely and manually measure RSS values on intersections, which will consume a lot of time and human resources. What is worse, change of the environment may render this database totally useless. Our consideration is to measure RSS on a small amount of these intersections and use them to build a radio propagation model. Then, this model can be deployed to predict RSS values of other intersections and reconstruct the radio map. In other words, we only need to collect a very small part the radio map and utilize the radio propagation model to recover the whole one. So far, many models have been proposed, among which the one suggested by Seidel, named floor attenuation factor propagation model, achieves great balance between computational request and accuracy. But it is not compatible with environments in some scenarios. So as to compensate for this deficiency, we take into account the angles formed by signal and surfaces of obstacles, and the results show better compatibility. The proposed model has four parameters that are related to the environments, and our second contribution in this paper is to propose a method to determine them. In fact, after collecting a small part of the radio map, we can estimate these parameters with least square method. Then, these parameters can be used to predict the signal strength at any other points in the same environment, and the whole radio map is rebuilt. According to practical experiments, performance of the radio map built by the proposed model is not as good as the manually collected one, but 80% of collecting labor is saved. Copyright © 2015 John Wiley & Sons, Ltd.
Systems biology of host–microbe metabolomics
Authors: Heinken Almut , Thiele Ines
Published: April 2015

The human gut microbiota performs essential functions for host and well‐being, but has also been linked to a variety of disease states, e.g., obesity and type 2 diabetes. The mammalian body fluid and tissue metabolomes are greatly influenced by the microbiota, with many health‐relevant metabolites being considered ‘mammalian–microbial co‐metabolites’. To systematically investigate this complex host–microbial co‐metabolism, a systems biology approach integrating high‐throughput data and computational network models is required. Here, we review established top‐down and bottom‐up systems biology approaches that have successfully elucidated relationships between gut microbiota‐derived metabolites and host health and disease. We focus particularly on the constraint‐based modeling and analysis approach, which enables the prediction of mechanisms behind metabolic host–microbe interactions on the molecular level. We illustrate that constraint‐based models are a useful tool for the contextualization of metabolomic measurements and can further our insight into host–microbe interactions, yielding, e.g., in potential novel drugs and biomarkers. WIREs Syst Biol Med 2015, 7:195–219. doi: 10.1002/wsbm.1301

This article is categorized under:

Models of Systems Properties and Processes > Mechanistic Models

Biological Mechanisms > Metabolism

Laboratory Methods and Technologies > Metabolomics
“Suddenly Having two Positive People who are Carriers is a Whole New Thing”‐ Experiences of Couples Both Identified as Carriers of Cystic Fibrosis Through a Population‐Based Carrier Screening Program in Australia
Authors: Ioannou Liane , Delatycki Martin B. , Massie John , Hodgson Jan , Lewis Sharon
Published: April 2015

A population‐based CF carrier screening program was implemented in Victoria, Australia in 2006. This study explored the experiences of couples when both partners were identified as CF carriers. Between January 2006 and December 2010, 10 carrier couples were identified and invited to undertake a semi‐structured interview. Nine interviews were conducted, seven couple interviews and two individual interviews. One couple declined to participate due to the recent termination of an affected pregnancy. Interviews were analyzed using inductive content analysis. All couples experienced surprise on learning their carrier couple result. The couples who were pregnant at the time of screening chose to have prenatal diagnosis, with the majority considering it to be the “next step.” The two couples who had an affected pregnancy reported feelings of devastation and grief upon receiving their prenatal diagnosis result and terminated the pregnancy. All carrier couples were offered free genetic counseling, with only one couple declining the offer. Couples were unprepared for a positive carrier couple result. However, all the couples changed their reproductive behavior as a result of their carrier status. The results of this study have been used to inform the program and service offered to CF carrier couples particularly with respect to genetic counseling for reproductive decision making.
Extraction, Composition and Functional Properties of Pennycress (Thlaspi arvense L.) Press Cake Protein
Authors: Hojilla‐Evangelista Mila P. , Selling Gordon W. , Berhow Mark A. , Evangelista Roque L.
Published: April 2015

This study compared two methods for extracting the protein in pennycress (Thlaspi arvense L.) press cake and determined the composition and functional properties of the protein products. Proteins in pennycress press cake were extracted by using the conventional alkali‐solubilization–acid‐precipitation (AP) method or saline‐based (SE) procedure (0.1 M NaCl at 50 °C). The extraction method has a major influence on the purity and functional properties of press cake protein products. AP had a lower protein yield (23 %) but much higher purity (90 % crude protein) compared with SE (45 % yield, 67 % crude protein). AP protein isolate had high foam capacity (120 ml), high foam stability (96 % foam volume retention) and high emulsion stability (24–35 min), and it was resistant to heat denaturation (3 % loss of solubility at pH 2 and pH 10). On the other hand, SE protein concentrate showed remarkably high solubility (>76 %) between pH 2 and 10 and exceptional emulsifying activity (226–412 m2/g protein), but was more susceptible to heat denaturation at pH 7 and pH 10 (65–78 % loss of solubility). These results strongly demonstrate that higher purity pennycress press cake protein can be produced by either saline extraction or acid precipitation and have functional properties that are desirable for non‐food uses.
Amebic and cytomegalovirus colitis mimic ulcerative colitis
Authors: Weng Meng‐Tzu , Wei Shu‐Chen , Leong Yew‐Loong , Tung Chien‐Chih , Shun Chia‐Tung , Wong Jau‐Min
Published: April 2015

Here we present a 50‐year‐old man who suffered from progressively bloody diarrhea for 2 months. A colonoscopy revealed pancolonic mucosal inflammation, ulceration, and spontaneous bleeding. Ulcerative colitis was initially diagnosed and sulfasalazine was prescribed. Hypoalbuminemia and renal function deterioration developed 1 year later. Steroids were prescribed for suspected nephrotic syndrome. His bloody diarrhea and abdominal symptoms worsened after steroid use. Progressive sepsis and acute renal function deterioration also developed. Positive human immunodeficiency virus (HIV) antibody was found during routine hemodialysis screening. An episode of colon perforation occurred and surgery was performed. The resected colon showed amoeba, cytomegalovirus, and fungal infection. The patient died of sepsis. In this report, we discuss how to diagnose ulcerative colitis. It is important to exclude infection before using an immunosuppressive agent.
Adolescent Performance on The Awareness of Social Inference Test: TASIT
Authors: McDonald Skye , Fisher Alana , Togher Leanne , Tate Robyn , Rushby Jacqueline , English Therese , Kelly Michelle , Mathersul Danielle , Froreich Francesca , Francis Heather
Published: April 2015

Primary objective: Social cognition underlies social skills and can be disrupted in numerous developmental and acquired brain disorders during childhood and adolescence. Despite this, there are few tools to assess social cognition clinically in this age group. This study examined adolescent performance on The Awareness of Social Inference Test (TASIT), a valid measure of social cognition in adults.

Design: Cross-sectional design examining performance on Parts 1, 2 and 3 of TASIT (and alternate forms) in Australian girls and boys with varying levels of English familiarity.

Methods: 665 schoolchildren from private and government schools were administered TASIT subtests. Of these, 464 students aged 13–15 were selected to provide normative data. Scores from a further 97 provided information about the effects of lack of English familiarity.

Results: The two Forms of TASIT were statistically equivalent for two of the three parts. Adolescents performed lower than adults, although the differences were not large. Some incremental effects were seen for chronological age. Gender effects were apparent on all subtests. Lack of English familiarity (i.e., English not spoken at home) reduced scores a further 6–13% relative to high English proficiency.

Conclusions: TASIT appears to be suitable for adolescents. Norms are best aggregated across ages in adolescence and stratified according to gender.