bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA stable pentaploid H1 (ES) cells obtained from an octaploid cell induced from tetraploid cells polyploidized using demecolcine
Authors: Fujikawa‐Yamamoto Kohzaburo , Luo Xianwen , Miyagoshi Minoru , Yamagishi Hiroko
Published: January 2010

Pentaploid H1 (ES) cells (5H1 cells) were accidentally obtained through one‐cell cloning of octaploid H1 (ES) cells (8H1 cells) that were established from tetraploid H1 (ES) cells (4H1 cells) polyploidized using demecolcine. The number of chromosomes of 5H1 cells was 100, unlike the 40 of diploid H1 (ES) cells (2H1 cells), 80 of 4H1, and 160 of 8H1 cells. The durations of G1, S, and G2/M phases of 5H1 cells were 3, 7, and 6 h, respectively, almost the same as those of 2H1, 4H1, and 8H1 cells. The cell volume of 5H1 cells was half of that of 8H1 cells, suggesting that 5H1 cells were created through abnormal cell divisions of 8H1 cells. The morphology of growing 5H1 cells was a spherical cluster similar to that of 2H1 cells and differing from the flagstone‐like shape of 4H1 and 8H1 cells. Pentaploid solid tumors were formed from 5H1 cells after interperitoneal injection into the mouse abdomen, and they contained endodermal, mesodermal, and ectodermal cells as well as undifferentiated cells, suggesting both that the DNA content of 5H1 cells was retained during tumor formation and that the 5H1 cells were pluripotent. The DNA content of 5H1 cells was stable in long‐term culturing as 2H1 cells, meaning that 5H1 and 2H1 cells shared similarities in DNA structure. The excellent stability of the DNA content of 5H1 cells was explained using a hypothesis for the DNA structure of polyploid cells because the pairing of homologous chromosomes in 5H1 cells is spatially forbidden. J. Cell. Physiol. 223: 369–375, 2010. © 2010 Wiley‐Liss, Inc.
Highly efficient gene transfer system using a laminin–DNA–apatite composite layer
Authors: Oyane Ayako , Tsurushima Hideo , Ito Atsuo
Published: January 2010

Background

We have recently developed a safe and efficient gene transfer system using a laminin–DNA–apatite composite layer. The objectives of the present study were to fully characterize and optimize the laminin–DNA–apatite composite layer in relation to the efficiency of gene transfer and to demonstrate the feasibility of the composite layer in the induction of cell differentiation.

Methods

The laminin–DNA–apatite composite layer was prepared under various conditions. The efficiency of gene transfer on the resulting composite layer was evaluated using luciferase and ß‐galactosidase gene expression assay systems. A laminin–DNA–apatite composite layer, prepared under the optimized condition using a plasmid including cDNA of nerve growth factor (NGF), was then applied to the neuron‐like differentiation of PC12 cells.

Results

The laminin content of the laminin–DNA–apatite composite layer was found to be a dominant factor improving the efficiency of gene transfer rather than the DNA content. The cell adhesion property of laminin in the composite layer should be responsible for the improvement in efficiency of gene transfer because the immobilization of albumin without the cell adhesion property in a DNA–apatite composite layer had no effect on the efficiency of gene transfer. A laminin–DNA–apatite composite layer, prepared under the optimized condition using a plasmid including cDNA of NGF, successfully induced the neuron‐like differentiation of PC12 cells.

Conclusions

The present gene transfer system, with the potential to control cell differentiation and having features of safety and relatively high and controllable efficiency, would be a useful tool for tissue engineering applications and the production of transfection microarrays. Copyright © 2010 John Wiley & Sons, Ltd.
Infinite families of crossing‐critical graphs with prescribed average degree and crossing number
Authors: Bokal Drago
Published: January 2010

Širáň constructed infinite families of k‐crossing‐critical graphs for every k⩾3 and Kochol constructed such families of simple graphs for every k⩾2. Richter and Thomassen argued that, for any given k⩾1 and r⩾6, there are only finitely many simple k‐crossing‐critical graphs with minimum degree r. Salazar observed that the same argument implies such a conclusion for simple k‐crossing‐critical graphs of prescribed average degree r>6. He established the existence of infinite families of simple k‐crossing‐critical graphs with any prescribed rational average degree r∈[4, 6) for infinitely many k and asked about their existence for r∈(3, 4). The question was partially settled by Pinontoan and Richter, who answered
it positively for \documentclass{article}\usepackage{amssymb}\usepackage{amsbsy}\usepackage[mathscr]{euscript}\footskip=0pc\pagestyle{empty}\begin{document}$r\in(3\frac{1}{2},4)$\end{document}.

The present contribution uses two new constructions of crossing‐critical simple graphs along with the one developed by Pinontoan and Richter to unify these results and to answer Salazar's question by the following statement: there exist infinite families of simple k‐crossing‐critical graphs with any prescribed average degree r∈(3, 6), for any k greater than some lower bound Nr. Moreover, a universal lower bound NI on k applies for rational numbers in any closed interval I⊂(3, 6). © 2010 Wiley Periodicals, Inc. J Graph Theory 65: 139–162, 2010
Simple and accurate approaches to implement the complex trans‐conductance suited for time‐domain simulators for small‐signal and large‐signal table‐based models
Authors: Homayouni Seyed Majid , Schreurs Dominique , Nauwelaers Bart
Published: January 2010

This paper focuses on the implementation of table‐based models of high‐frequency transistors for time‐domain simulators at microwave and mm‐wave frequencies. In this frequency range, the channel is not capable of responding to the excitation instantaneously therefore, a delay‐time exists between the channel response and the channel excitation. This delay is represented by a complex trans‐conductance in terms of circuit elements. The high‐frequency models of transistors are required to have the implementation of complex trans‐conductance, where the complex part accounts mathematically for the delay‐time between the channel response and the channel excitation. This paper presents simple and accurate approaches to incorporate the complex trans‐conductance in both small‐signal and large‐signal table‐based models for time‐domain simulators (MOS‐AK International Meeting. Eindhoven, Netherlands, April 2008). Implementation approach for each model, small‐signal and large‐signal, is presented in separated sections. In the first step, the delay is realized by the introduction of an ideal transmission line between the channel excitation and the channel response. As transmission lines are not generally suitable for time‐domain simulations, a lumped element equivalent network is introduced in the second step. The latter approach is fully compatible with time‐domain simulators but frequency limitation, determined by the delay‐time value itself, is introduced. Then the implementation of the complex trans‐conductance in large‐signal model is introduced. In terms of large‐signal behavior, delay‐time is important to achieve a non‐quasi static model. Yet again there is limitation in terms of the frequency range that is determined by the delay value itself. The methodology is illustrated on the small‐signal and the large‐signal equivalent circuit of a Multi‐Fin MOSFET transistor. Simulations are carried out by Cadence Spectre and Agilent ADS simulators, and comparisons are carried out between the simulation results and the measurements. Copyright © 2010 John Wiley & Sons, Ltd.
Molecular investigation of a gene encoding organic solvent‐tolerant alkaline protease from Pseudomonas aeruginosa strain K
Authors: Abd. Rahman Raja Noor Zaliha Raja , Geok Lee Poh , Wong Chee Fah , Basri Mahiran , Salleh Abu Bakar
Published: January 2010

A gene encoding an organic solvent‐stable protease was amplified from Pseudomonas aeruginosa strain K by polymerase chain reaction using consensus primers based on multiple sequence alignment of alkaline and metalloprotease genes from Pseudomonas species. The gene, which consisted of 1440 bp nucleotides and deduced 479 amino acid residues, was successfully expressed in pGEX‐4T‐1 expression system in the presence of 1.0 mM IPTG, after an incubation of 6 h at 37 °C. Under these conditions, the recombinant strain K protease was, subsequently, released into the periplasm of E. coli BL21 (DE3) with an optimum proteolytic activity detected at 1.0112 U/ml. To date, this is the first reported expression of alkaline protease (aprA) with such remarkable property in Escherichia coli. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optimization of media components for laccase production by litter dwelling fungal isolate Fusarium incarnatum LD‐3
Authors: Chhaya Urvish , Gupte Akshaya
Published: January 2010

Laccase production by solid state fermentation (SSF) using an indigenously isolated litter dwelling fungus Fusarium incarnatum LD‐3 was optimized. Fourteen medium components were screened by the initial screening method of Plackett‐Burman. Each of the components was screened on the basis of ‘p’ (probability value) which was above 95% confidence level. Ortho‐dianisidine, thiamine HCl and CuSO4 · 5 H2O were identified as significant components for laccase production. The Central Composite Design response surface methodology was then applied to further optimize the laccase production. The optimal concentration of these three medium components for higher laccase production were (g/l): CuSO4 · 5 H2O, 0.01; thiamine HCl, 0.0136 and ortho‐dianisidine, 0.388 mM served as an inducer. Wheat straw, 5.0 g was used as a solid substrate. Using this statistical optimization method the laccase production was found to increase from 40 U/g to 650 U/g of wheat straw, which was sixteen times higher than non optimized medium. This is the first report on statistical optimization of laccase production from Fusarium incarnatum LD‐3. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
GC – MS analysis reveals production of 2 – Phenylethanol from Aspergillus niger endophytic in rose
Authors: Wani Masood Ahmed , Sanjana Kaul , Kumar Dhar Manoj , Lal Dhar Kanahya
Published: January 2010

Endophytes include all organisms that during a variable period of their life, colonize the living internal tissues of their hosts without causing detectable symptoms. Several fungal endophytes have been isolated from a variety of plant species which have proved themselves as a rich source of secondary metabolites. The reported natural products from endophytes include antibiotics, immunosuppresants, anticancer compounds, antioxidant agents, etc. For the first time Rosa damacaena (rose) has been explored for its endophytes. The rose oil industry is the major identified deligence for its application in perfumery, flavouring, ointments, and pharmaceuticals including various herbal products. During the present investigation fungal endophytes were isolated from Rosa damacaena. A total of fifty four isolates were isolated out of which sixteen isolates were screened for the production of secondary metabolites. GCMS analysis reveals the production of 2‐phenylethanol by one of the isolates JUBT 3M which was identified as Aspergillus niger. This is the first report of production of 2‐phenylethanol from endophytic A. niger. 2‐phenylethanol is an important constituent of rose oil constituting about 4.06% of rose oil. Presence of 2‐phenylethanol indicates that the endophyte of rose may duplicate the biosynthesis of phenyl propanoids by rose plant. Besides this, the other commercial applications of phenylethanol include its use in antiseptics, disinfectants, anti‐microbials and preservative in pharmaceuticals. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Development of a breast reconstruction satisfaction questionnaire (BRECON): Dimensionality and clinical importance of breast symptoms, donor site issues, patient expectations, and relationships
Authors: Temple Claire L.F. , Cook E. Francis , Ross Douglas C. , Bettger‐Hahn Margo , MacDermid Joy
Published: January 2010

Objectives

To develop a valid, reliable and responsive, self‐administered questionnaire to assess women's satisfaction with breast reconstruction.

Methods

Item generation: Three sources for item inventory were utilized: focus groups, expert panel, and literature review.

Item reduction: Item impact scores were derived from patients and experts each ranking the importance and frequency of each item. Correlation between patient and expert scores was calculated. The highest impact questions were maintained.

Results

Four focus groups comprising 20 women generated 515 items, 10 experts developed 171 items, and literature review produced 227 items. These 913 potential items were reduced to 183 by combining redundancy. The 183 items underwent formal reduction by assessing importance and frequency of each item. Thirty‐two of 40 reconstructed women and 19 of 19 experts responded to the mail‐out. Seventy‐seven items of the women's top 100 also made the experts' top 100 list. Intraclass correlation between patients and experts was 0.71 [0.62 0.77], indicating “good” but not “excellent” agreement, reinforcing the importance of patient involvement in questionnaire development. Women rated abdominal donor site issues higher than experts, and experts rated breast softness and symmetry higher than women.

Conclusions

A 100‐item pilot questionnaire for breast reconstruction satisfaction was developed for psychometric testing. J. Surg. Oncol. 2010; 101:209–216. © 2010 Wiley‐Liss, Inc.
Pretransplant predictors of recovery of renal function after liver transplantation
Authors: Northup Patrick G. , Argo Curtis K. , Bakhru Mihir R. , Schmitt Timothy M. , Berg Carl L. , Rosner Mitchell H.
Published: January 2010

The Model for End-Stage Liver Disease system has given priority on the liver transplant waiting list to candidates with renal failure. This study determined the predictors of spontaneous recovery of renal function after transplantation in 1041 liver transplant recipients on renal replacement therapy (RRT) at the time of transplant (from February 2002 to January 2007). Data from these patients were obtained from the US Organ Procurement and Transplantation Network and US Renal Data System databases. Univariate and multivariate survival models were constructed along with multivariate logistic regression models to find independent predictors of spontaneous renal recovery. Seven hundred seven recipients (67.9%) had spontaneous recovery of renal function after liver transplantation. Those recovering spontaneously had a significantly shorter course of RRT in the pretransplant time period (15.6 versus 36.6 days, P < 0.001). Recovery of renal function was observed in 70.8% and 11.5% of recipients on RRT for less than 30 days and more than 90 days, respectively. Other statistically significant pretransplant variables independently associated with recovery of renal function included recipient age, recipient pretransplant diabetes, and donor age. In conclusion, the duration of pretransplant RRT is highly predictive of spontaneous renal recovery post-transplant. Liver transplant candidates requiring less than 30 days of pretransplant RRT are likely to spontaneously recover renal function after liver transplantation, whereas those on RRT for more than 90 days are not.
Perioperative coagulation profile in living liver donors as assessed by rotational thromboelastometry
Authors: Gouvêa Glauber , Diaz Rodrigo , Auler Lúcio , Toledo Renato , Soluri André , Haack Alfredo G. , de Oliveira Mariana M. , Vilanova Bruno , Machado Virgínia R. , Martinho José Manoel
Published: January 2010

Transient postoperative coagulation abnormalities frequently occur in living liver donors, particularly after right liver resection. Usually, this coagulopathy is diagnosed by alterations in conventional coagulation tests (CCTs) such as the international normalized ratio (INR) of the prothrombin time. However, recent studies using other methods of coagulation monitoring have suggested that postoperative hypercoagulability may also occur in living donors. The rotational thromboelastometry (ROTEM) system is a coagulation monitor based on the viscoelastic properties of blood. The use of ROTEM for perioperative coagulation monitoring in the setting of living liver donors has not been reported. We evaluated the perioperative coagulation profile as assessed by ROTEM in 16 consecutive donors who underwent either right or left liver resection at our institution. ROTEM analysis and CCTs were performed at the baseline (before skin incision) and on postoperative days 1 and 3. According to the CCTs, hypocoagulability was revealed in all but 1 (left liver) donor. The INR was highest on postoperative day 1 [median = 1.67 (interquartile range = 1.37-1.8)]. In contrast, all donors had a normal coagulation profile as assessed by the ROTEM system throughout the study period. In conclusion, this study showed the disagreement between the CCTs and the ROTEM system, as no significant coagulation abnormalities could be revealed with the latter method during the study period. Further studies are needed to confirm the role of the ROTEM system as a perioperative coagulation monitor in this setting and ultimately its influence on the outcome of living donors. Liver Transpl 16:387–392, 2010. © 2010 AASLD.
Severe novel H1N1 influenza A infection in the immediate postoperative period of a liver transplant patient
Authors: Zapata Rodrigo , Uribe Mario , Martínez Waldo , Andrade Alejandro , Leal José Luis , Gomez Fernando
Published: January 2010

In 2009, the World Health Organization recognized the novel H1N1 influenza A virus as a pandemic infection. Since April 2009, thousands of cases of novel H1N1 influenza A infection have been reported worldwide, and they have resulted in thousands of deaths. South American countries were affected by this infection during their winter season, and Chile presented one of the highest incidence rates. We have recently managed a liver transplant patient who presented with a severe novel H1N1 influenza A infection in the early postoperative period and required prolonged mechanical ventilation. The early suspicion of this infection during the current pandemic influenza in Chile made possible a timely treatment with oseltamivir. We decided to report this case because no other cases of liver transplant patients affected by H1N1 influenza A have been reported so far. We intend to alert clinicians about this potentially devastating viral infection in view of the current pandemic scenario, and here we review some of the recommendations for its prevention, diagnosis, therapy, and possible complications.
Forms of the Pasch axiom in ordered geometry
Authors: Pambuccian Victor
Published: January 2010

We prove that, in the framework of ordered geometry, the inner form of the Pasch axiom (IP) does not imply its outer form (OP). We also show that OP can be properly split into IP and the weak Pasch axiom (WP) (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On pseudolinearity and generic pairs
Authors: Vassiliev Evgueni
Published: January 2010

We continue the study of the connection between the “geometric” properties of SU ‐rank 1 structures and the properties of “generic” pairs of such structures, started in [8]. In particular, we show that the SU‐rank of the (complete) theory of generic pairs of models of an SU ‐rank 1 theory T can only take values 1 (if and only if T is trivial), 2 (if and only if T is linear) or ω, generalizing the corresponding results for a strongly minimal T in [3]. We also use pairs to derive the implication from pseudolinearity to linearity for ω ‐categorical SU ‐rank 1 structures, established in [7], from the conjecture that an ω ‐categorical supersimple theory has finite SU ‐rank, and find a condition on generic pairs, equivalent to pseudolinearity in the general case (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Łoś type theorem for linear metric formulas
Authors: Bagheri Seyed‐Mohammad
Published: January 2010

We define an ultraproduct of metric structures based on a maximal probability charge and prove a variant of Łoś theorem for linear metric formulas. We also consider iterated ultraproducts (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tallness and level by level equivalence and inequivalence
Authors: Apter Arthur W.
Published: January 2010

We construct two models containing exactly one supercompact cardinal in which all non‐supercompact measurable cardinals are strictly taller than they are either strongly compact or supercompact. In the first of these models, level by level equivalence between strong compactness and supercompactness holds. In the other, level by level inequivalence between strong compactness and supercompactness holds. Each universe has only one strongly compact cardinal and contains relatively few large cardinals (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Loss of syndecan‐1 is associated with malignant conversion in skin carcinogenesis
Authors: Stepp Mary Ann , Pal‐Ghosh Sonali , Tadvalkar Gauri , Rajjoub Lamise , Jurjus Rosalyn A. , Gerdes Michael , Ryscavage Andrew , Cataisson Christophe , Shukla Anjali , Yuspa Stuart H.
Published: January 2010

Syndecan‐1 (sdc‐1) is a cell surface proteoglycan that mediates the interaction of cells with their matrix, influencing attachment, migration, and response to growth factors. In keratinocytes, loss of sdc‐1 delays wound healing, reduces migration, and increases Transforming growth factor β (TGFβ) 1 expression. In this study we show that sdc‐1 expression is significantly reduced in basal cell, squamous cell, and metastatic human skin cancers compared to normal human skin. In experimental mouse skin tumor induction, compared to wildtype (wt) BALB/c mice, papilloma formation in sdc‐1 null mice was reduced by 50% and the percent of papillomas converting to squamous cell carcinoma (SCC) was enhanced. sdc‐1 expression on wt mouse papillomas decreased as they converted to SCC. Furthermore, papillomas forming on sdc‐1 null mice expressed suprabasal α3 and β4 integrins; suprabasal β4 integrin is a marker of a high risk for progression. While the proliferative response to phorbol‐12‐myristate‐13‐acetate (TPA) did not differ among the genotypes, sdc‐1 null mice had an enhanced inflammatory response and retained higher levels of total TGFβ1 within their skin after TPA treatment. sdc‐1 null keratinocytes, transduced in vitro by oncogenic rasHa, expressed higher levels of β4 integrin and had enhanced pSmad2 signaling and reduced senescence when compared to wt rasHa‐transduced keratinocytes. When rasHa‐transduced cells of both genotypes were grafted onto nude mice, null tumors converted to SCC with higher frequency confirming the skin painting experiments. These data indicate that sdc‐1 is important both early in the development of skin tumors and in progression of skin cancers suggesting that reduced expression of sdc‐1 could be a useful marker for progression in neoplastic skin lesions. © 2010 Wiley‐Liss, Inc.
Leucine attenuates skeletal muscle wasting via inhibition of ubiquitin ligases
Authors: Baptista Igor L. , Leal Marcelo L. , Artioli Guilherme G. , Aoki Marcelo S. , Fiamoncini Jarlei , Turri Antonio O. , Curi Rui , Miyabara Elen H. , Moriscot Anselmo S.
Published: January 2010

The aim of this study was to assess the effect of leucine supplementation on elements of the ubiquitin–proteasome system (UPS) in rat skeletal muscle during immobilization. This effect was evaluated by submitting the animals to a leucine supplementation protocol during hindlimb immobilization, after which different parameters were determined, including: muscle mass; cross‐sectional area (CSA); gene expression of E3 ligases/deubiquitinating enzymes; content of ubiquitinated proteins; and rate of protein synthesis. Our results show that leucine supplementation attenuates soleus muscle mass loss driven by immobilization. In addition, the marked decrease in the CSA in soleus muscle type I fibers, but not type II fibers, induced by immobilization was minimized by leucine feeding. Interestingly, leucine supplementation severely minimized the early transient increase in E3 ligase [muscle ring finger 1 (MuRF1) and muscle atrophy F‐box (MAFbx)/atrogin‐1] gene expression observed during immobilization. The reduced peak of E3 ligase gene expression was paralleled by a decreased content of ubiquitinated proteins during leucine feeding. The protein synthesis rate decreased by immobilization and was not affected by leucine supplementation. Our results strongly suggest that leucine supplementation attenuates muscle wasting induced by immobilization via minimizing gene expression of E3 ligases, which consequently could downregulate UPS‐driven protein degradation. It is notable that leucine supplementation does not restore decreased protein synthesis driven by immobilization. Muscle Nerve, 2010
L1 radiculopathy mimicking meralgia paresthetica: A case report
Authors: Yang Seung Nam , Kim Dong Hwee
Published: January 2010

L1 radiculopathy is very rare and difficult to diagnose with needle electromyography. A patient presented with pain and hypesthesia on the anterolateral aspect of the left thigh. Nerve conduction studies and needle electromyography were normal, except for the quadratus lumborum and iliopsoas muscles, which showed abnormal spontaneous activity and polyphasic motor unit potentials with reduced recruitment patterns. Magnetic resonance imaging of the lumbar spine showed disc extrusion of the L1–2 intervertebral space with upward migration. This case demonstrates the usefulness of examination of the quadratus lumborum in the diagnosis of L1 radiculopathy. Muscle Nerve 41: 566–568, 2010
Specifying and provisioning virtual infrastructures with HIPerNET
Authors: Anhalt Fabienne , Koslovski Guilherme , Primet Pascale Vicat‐Blanc
Published: January 2010

With the expansion and convergence of communication and computing, dynamic provisioning of customized networking and processing infrastructures, as well as resource virtualization, are appealing concepts and technologies. Therefore, new models and tools are needed to allow users to create, trust and enjoy such on‐demand virtual infrastructures within a wide area context. This paper presents the HIPerNET framework we are designing and developing for creating, managing and controlling virtual infrastructures in the context of high‐speed Internet. The key idea of this proposal is the combination of network‐ and system‐virtualization associated with controlled resource reservation to provide fully isolated environments. HIPerNET's motivations and design principles are presented. Then we examine specifically how this framework handles the virtual infrastructures, called Virtual Private eXecution Infrastructures (VPXI). To help specifying customized isolated infrastructures, HIPerNET relies on VXDL, a language for VPXI description and modeling which considers end‐host resource as well as the virtual network topology interconnecting them, including virtual routers. After the specification, allocation and scheduling phases, HIPerNET helps in provisioning, deploying and configuring virtual private execution infrastructures. This means, it triggers the dynamic configuration of all the equipments involved. In this paper we concentrate on network configuration, particularly to achieve network performance isolation. We also study and evaluate mechanisms to implement and configure virtual‐link control. Experimental results obtained within the Grid'5000 testbed are presented and analyzed. Copyright © 2009 John Wiley & Sons, Ltd.
Data maximization by multipass analysis of protein mass spectra
Authors: Tharakan Ravi , Edwards Nathan , Graham David R. M.
Published: January 2010

With the proliferation of search engines for the analysis of MS data, multisearch techniques aimed at boosting the discriminating power of the search engines' score functions have recently become popular. Much statistical and algorithmic work has been done, therefore, in order to be able to combine and parse multiple search streams. However, multisearch techniques suffer from long run times, and may have little impact on false negatives because of similar peptide filtering heuristics between searches. This review focuses, rather, on multipass techniques, which use the results of one search to guide the selection of spectra, parameters and sequences in subsequent searches. This reduces the number of false‐negative peptide identifications due to peptide candidate filtering while preserving statistical significance of existing (correct) identifications. Furthermore, this technique avoids substantial increases in running time and, by limiting the search space, does not reduce the statistical significance of correct identifications or introduce a statistically significant number of false‐positive identifications. However, we argue that the existing combiner tools are not reliably applicable to these multipass situations, because of algorithmic assumptions about search space and statistical assumptions about the rate of true positives. Here we provide an overview of the advantages of and issues in multipass analysis techniques, the existing methods and workflows available to proteomic researchers, and the unsolved statistical and algorithmic issues amenable to future research.
A fatal case of cough
Authors: Bossley C.J. , Hogg C. , Stoneham S. , Jacques T.S. , Bush A.
Published: January 2010

Dysfunctional swallowing is an uncommon, but important cause of bronchiectasis. We describe a child with a brainstem tumor, who developed bronchiectasis caused by chronic aspiration secondary to a dysfunctional swallow. The case highlights the importance of thorough and repeated evaluation before a diagnosis of idiopathic bronchiectasis is made. If dysfunctional swallow is found further investigation to ascertain the cause is indicated. Pediatr Pulmonol. 2010; 45:205–207. © 2010 Wiley‐Liss, Inc.
Cystic fibrosis lung disease starts in the small airways: Can we treat it more effectively?
Authors: Tiddens Harm A.W.M. , Donaldson Scott H. , Rosenfeld Margaret , Paré Peter D.
Published: January 2010

The aims of this article are to summarize existing knowledge regarding the pathophysiology of small airways disease in cystic fibrosis (CF), to speculate about additional mechanisms that might play a role, and to consider the available or potential options to treat it. In the first section, we review the evidence provided by pathologic, physiologic, and imaging studies suggesting that obstruction of small airways begins early in life and is progressive. In the second section we discuss how the relationships between CF transmembrane conductance regulator (CFTR), ion transport, the volume of the periciliary liquid layer and airway mucus might lead to defective mucociliary clearance in small airways. In addition, we discuss how chronic endobronchial bacterial infection and a chronic neutrophilic inflammatory response increase the viscosity of CF secretions and exacerbate the clearance problem. Next, we discuss how the mechanical properties of small airways could be altered early in the disease process and how remodeling can contribute to small airways disease. In the final section, we discuss how established therapies impact small airways disease and new directions that may lead to improvement in the treatment of small airways disease. We conclude that there are many reasons to believe that small airways play an important role in the pathophysiology of (early) CF lung disease. Therapy should be aimed to target the small airways more efficiently, especially with drugs that can correct the basic defect at an early stage of disease. Pediatr Pulmonol. 2010; 45:107–117. © 2010 Wiley‐Liss, Inc.
Crystallographically oriented high resolution lithography of graphene nanoribbons by STM lithography
Authors: Dobrik G. , Tapasztó L. , Nemes‐Incze P. , Lambin Ph. , Biró L. P.
Published: January 2010

Due to its exciting physical properties and sheet‐like geometry graphene is in the focus of attention both from the point of view of basic science and of potential applications. In order to fully exploit the advantage of the sheet‐like geometry very high resolution, crystallographicaly controlled lithography has to be used. Graphene is a zero gap semiconductor, so that a field effect transistor (FET) will not have an “off” state unless a forbidden gap is created. Such a gap can be produced confining the electronic wave functions by etching narrow graphene nanoribbons (GNRs) typically of a few nanometers in width and with well defined crystallographic orientation. We developed the first lithographic method able to achieve GNRs that have both nanometer widths and well defined crystallographic orientation. The lithographic process is carried out by the local oxidation of the sample surface under the tip of a scanning tunneling microscopy (STM). Crystallographic orientation is defined by acquiring atomic resolution images of the surface to be patterned. The cutting of trenches with controlled depth and of a few nanometer in width, folding and manipulation of single graphene layers is demonstrated. The narrowest GNR cut by our method is of 2.5 nm width, scanning tunneling spectroscopy (STS) showed that it has a gap of 0.5 eV, comparable to that of germanium, which allows room temperature operation of graphene nanodevices.
Role of the growth parameters on the structural order of MWCNTs produced by arc discharge in liquid nitrogen
Authors: Bagiante Salvatore , Scalese Silvia , Scuderi Viviana , D'Urso Luisa , Messina Elena , Compagnini Giuseppe , Privitera Vittorio
Published: January 2010

We report a systematic study of the synthesis of multiwall carbon nanotubes (MWCNTs) by arc‐discharge in liquid nitrogen (LN2). The effect of the variation of the experimental parameters, such as size of electrodes and discharge current, on the formation of nanostructures has been investigated by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Raman spectroscopy. We found that an increase in the electrode size and/or in the discharge current determines a better quality of the nanotubes, as shown by the reduction of the ID/IG ratio in the Raman spectra. In some experimental conditions radial breathing modes (RBMs) have been observed and attributed to nanotubes with small innermost tube diameters.
Characterizations of nanostructured silicon‐carbon films deposited on p‐layer by PECVD
Authors: Coscia U. , Ambrosone G. , Basa D. K. , Ferrero S. , Veneri P. Delli , Mercaldo L. V. , Usatii I. , Tucci M.
Published: January 2010

Nanostructured silicon carbon films composed of silicon nanocrystallites embedded in the amorphous silicon carbon matrix are prepared by a rf‐PECVD system at 250 °C from silane and methane gas mixture highly diluted in hydrogen onto 7059 Corning glass and p‐layer deposited on tin oxide substrates by varying rf power from 25 to 65 W. The structural and compositional properties of the films have been investigated. The study demonstrates that rf power controls the crystalline fraction as well as the silicon crystallite size and that p‐layer/tin oxide structure enhances the nucleation of silicon grains as compared to Corning glass (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigation of structural properties of high‐rate deposited SiNx films prepared at low temperatures (100–300 °C) by atmospheric‐pressure plasma CVD
Authors: Yamaguchi Y. , Nakamura K. , Ohmi H. , Kakiuchi H. , Yasutake K.
Published: January 2010

We have investigated the structural properties of silicon nitride (SiNx) films deposited at low temperatures (100–300 °C with very high rates (>50 nm/s) in atmospheric‐pressure He/H2/SiH4/NH3 plasma excited by a 150 MHz very high‐frequency (VHF) power using a cylindrical rotary electrode. For this purpose, SiNx films are prepared on Si(001) wafers varying NH3/SiH4 ratio, H2 concentration in the plasma and substrate temperature (Tsub). Infrared absorption spectroscopy is used to analyze the bonding configurations of Si, N and H atoms in the films. It is shown that by decreasing NH3/SiH4 ratio or increasing H2 concentration, Si–N and Si–H bond densities increase, while N–H bond density decreases. A reasonably good‐quality film showing a BHF etching rate of 28 nm/min and a refractive index of 1.81 is obtained at Tsub = 300 °C despite the very high deposition rate of 166 nm/s. However, it is found that the decrease in Tsub causes the deterioration of film quality. Further surface excitation by increasing VHF power and/or H2 concentration together with the optimization of other deposition parameters will be needed to form high‐quality SiNx films with high rates at lower temperatures (Tsub ≤ 100 °C). (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Balanced dynamics in the Tropics
Authors: Verkley W.T.M. , van der Velde I.R.
Published: January 2010

For the shallow‐water equations on an equatorial beta plane, the properties of low‐frequency Rossby waves and (mixed) Rossby–gravity waves are investigated. It is shown that in the low‐frequency limit the horizontal divergence of these solutions is zero and their geopotential satisfies φ = fψ, where f = βy is the Coriolis parameter and ψ is the stream function of the non‐divergent velocity field. This type of balance is rather different from the geostrophic balance satisfied by Kelvin waves. It can be used to formulate a balanced potential vorticity equation in the single variable ψ that, while filtering out Kelvin waves and inertia–gravity waves, exactly reproduces Rossby waves and Rossby–gravity waves in the low‐frequency limit. Copyright © 2010 Royal Meteorological Society
The onset of precipitation in warm cumulus clouds: An observational case‐study
Authors: Burnet Frédéric , Brenguier Jean‐Louis
Published: January 2010

Data collected with a ground radar and an instrumented aircraft during the Small Cumulus Microphysics Study (SCMS) are analysed to examine the physical processes that control the onset of precipitation. On 10 August 1995, the Météo‐France Merlin‐IV successively sampled the core of the top cell in three convective clouds, following the cells from their initial stage of young vigorous ascending turrets up to their decaying stage. Simultaneous range–height indicator (RHI) scans were also performed by the National Center for Atmospheric Research CP2 radar.

Although the three clouds showed similar values of the droplet number concentrations and were able to generate precipitation embryos, the first two collapsed after reaching an altitude of 3 km above sea level, without producing any precipitation, while the third one reached a higher level of 4 km and produced significant precipitation. This case‐study illustrates how sensitive the onset of precipitation is to cloud dynamics, revealing that in a conditionally unstable atmosphere hardly noticeable changes in cloud thermodynamics and microphysics may lead to major changes in cloud vertical development and precipitation. Copyright © 2010 Royal Meteorological Society
Model‐based approaches for time‐dependent dose finding with repeated binary data
Authors: Benda Norbert
Published: January 2010

The goal of a clinical Phase II dose finding study is to describe the dose response relationship and to find a target dose (TD) or dose range that ensures a certain efficacy. In many applications, however, it is useful to consider combinations of dose and time under treatment instead of the dose only. The estimation of a minimum effective dose as a function of time allows, e.g. for a decision on an optimal initial treatment duration, if this initial treatment is followed by a maintenance therapy or aftercare which is supposed to start when a certain response rate is achieved. Bretz et al. (Biometrics 2005; 61:738–748) proposed a methodology that combines formal hypothesis testing for dose response with flexible modeling of the dose response relationship and estimating a target dose. In this paper a framework is proposed that allows for an extension of this methodology to a procedure that takes into account both, dose and time under treatment based on repeated binary data. A set of nonlinear mixed effects models is considered. The primary goal of such a study is the estimation of a minimum effective dose defined by the marginal probability, either in absolute terms or relative to placebo, as a function of time.

Examples for the TD as a function of time are given under specific model assumptions using a response function which depends on a cumulated dose response over time. The proposed models are illustrated by a case study on the treatment of psoriasis. The precision of the TD estimation as given by its standard error and bias are presented under different dose–response models and scenarios. The precision conditioned on the correct underlying model shape is contrasted with the precision of a procedure that incorporates a model selection step after which the TD is estimated using the selected model, and with the precision obtained under a misspecified model. Copyright © 2010 John Wiley & Sons, Ltd.
OSMOSE: automatic structural testing of executables
Authors: Bardin Sébastien , Herrmann Philippe
Published: January 2010

Verification is usually performed on a high‐level view of the software, either specification or program source code. However, in certain circumstances verification is more relevant when performed at the machine‐code level. This paper focuses on automatic test data generation from a stand‐alone executable. Low‐level analysis is much more difficult than high‐level analysis since even the control‐flow graph is not available and bit‐level instructions have to be modelled faithfully. The paper shows how ‘path‐based’ structural test data generation can be adapted from structured language to machine code, using both state‐of‐the‐art technologies and innovative techniques. The results have been implemented in a tool named OSMOSE and encouraging experiments have been conducted. Copyright © 2010 John Wiley & Sons, Ltd.
Strategic Frame Analysis: Providing the “evidence” for evidence‐based communications
Authors: Manuel Tiffany , Davey Lynn
Published: January 2010

This article describes the five major phases of research associated with Strategic Frame Analysis, an approach to communications research and practice that advances new ways of pursuing social change of entrenched and complex social problems. This multimethod approach is characterized by multidisciplinary and iterative research techniques that give emphasis to empirical testing of potential frame effects. The logic behind this constellation of methods and the order in which they are taken up in the research cycle is discussed as an introduction to the articles that follow that review specific parts of the research trajectory.
From research to practice: Communications for social change
Authors: Davey Lynn
Published: January 2010

What happens when the research inquiry is complete and has determined which reframes will be most successful in improving public understanding of an issue and advancing policy goals? Simple dissemination of research findings is not sufficient to improve the communications capacity of the field. The author explains how cognitive science and social movements literatures form the foundation of this field‐building practice of strategic framing pedagogy.
Framing in the field: A case study
Authors: Benjamin Diane
Published: January 2010

Strategic Frame Analysis can inform the daily practice of policy advocates by bringing an evidence‐based communications approach to their work. This case study of FrameWorks' decade‐long association with the national Kids Count Network shares stories from advocates who are transforming their communications strategies, resulting in more effective advocacy for child and youth well‐being.
Predictive Factors Improving Survival After Gastrectomy in Gastric Cancer Patients with Peritoneal Carcinomatosis
Authors: Hioki Masayoshi , Gotohda Naoto , Konishi Masaru , Nakagohri Toshio , Takahashi Shinichiro , Kinoshita Taira
Published: January 2010

Background

The aim of this study was to review prognosis following gastrectomy for gastric cancer patients with synchronous peritoneal carcinomatosis and to identify predictive factors for improving survival after gastrectomy in this setting.

Methods

Records of all patients who underwent gastrectomy for gastric cancer with peritoneal dissemination in our center between 1993 and 2004 were reviewed.

Results

Data of 101 patients who underwent gastrectomy for gastric cancer with peritoneal dissemination were available. Peritoneal dissemination was classified as P1, metastasis to the adjacent peritoneum in 34 patients; P2, a few scattered metastases to the adjacent peritoneum in 13 patients; and P3, numerous metastases in 54 patients. Nineteen patients sustained 21 adverse events. Overall survival was significantly improved for those in the P1 and P2 groups compared with that for the P3 group (median of 18 months and 15 months vs. 9 months; P < 0.001). Seven factors were significant for overall survival: peritoneal carcinomatosis, peritoneal lavage cytology, macroscopic type, resection margin, extent of lymph node dissection, curative potential of gastric resection, and chemotherapy, including perioperative and postrecurrent chemotherapy. In multivariate analysis, two factors were identified as independently associated with poor survival: P3 disease (P = 0.002) and absence of chemotherapy (P = 0.009). Univariate analysis of gastric cancer patients with P1 or P2 carcinomatosis revealed only tumor differentiation to be significant.

Conclusions

Gastric cancer patients with P1/P2 carcinomatosis and well/moderately differentiated tumors are likely to have an improved survival after gastrectomy. We emphasize that patients with good performance status and P1/P2 carcinomatosis should be considered appropriate surgical candidates before embarking on palliative systemic chemotherapy alone.
Enhancing Parenting Skills Among Nonresident African American Fathers as a Strategy for Preventing Youth Risky Behaviors
Authors: Caldwell Cleopatra Howard , Rafferty Jane , Reischl Thomas M. , De Loney E. Hill , Brooks Cassandra L.
Published: January 2010

This study evaluated the effectiveness of a theoretically based, culturally specific family intervention designed to prevent youth risky behaviors by influencing the parenting attitudes and behaviors of nonresident African American fathers and the parent–child interactions, intentions to avoid violence, and aggressive behaviors of their preadolescent sons. A sample of 158 intervention and 129 comparison group families participated. ANCOVA results indicated that the intervention was promising for enhancing parental monitoring, communication about sex, intentions to communicate, race‐related socialization practices, and parenting skills satisfaction among fathers. The intervention was also beneficial for sons who reported more monitoring by their fathers, improved communication about sex, and increased intentions to avoid violence. The intervention was not effective in reducing aggressive behaviors among sons. Findings are discussed from a family support perspective, including the need to involve nonresident African American fathers in youth risky behavior prevention efforts.