bluuebunny/crossref_metadata_2025_split huggingface dataset:
A workflow to increase the detection rate of proteins from unsequenced organisms in high‐throughput proteomics experiments
Authors: Grossmann Jonas , Fischer Bernd , Baerenfaller Katja , Owiti Judith , Buhmann Joachim M. , Gruissem Wilhelm , Baginsky Sacha 
Published: November 2007

AbstractWe present and evaluate a strategy for the mass spectrometric identification of proteins from organisms for which no genome sequence information is available that incorporates cross‐species information from sequenced organisms. The presented method combines spectrum quality scoring, de novo sequencing and error tolerant BLAST searches and is designed to decrease input data complexity. Spectral quality scoring reduces the number of investigated mass spectra without a loss of information. Stringent quality‐based selection and the combination of different de novo sequencing methods substantially increase the catalog of significant peptide alignments. The de novo sequences passing a reliability filter are subsequently submitted to error tolerant BLAST searches and MS‐BLAST hits are validated by a sampling technique. With the described workflow, we identified up to 20% more groups of homologous proteins in proteome analyses with organisms whose genome is not sequenced than by state‐of‐the‐art database searches in an Arabidopsis thaliana database. We consider the novel data analysis workflow an excellent screening method to identify those proteins that evade detection in proteomics experiments as a result of database constraints.
A phase 2 study of aztreonam lysine for inhalation to treat patients with cystic fibrosis and Pseudomonas aeruginosa infection
Authors: Retsch‐Bogart George Z. , Burns Jane L. , Otto Kelly L. , Liou Theodore G. , McCoy Karen , Oermann Christopher , Gibson Ronald L. ,   AZLI Phase II Study Group
Published: November 2007

AbstractBackgroundAztreonam lysine for inhalation (AZLI) is being developed for treatment of CF patients with Pseudomonas aeruginosa airway infection.MethodsThis double‐blind, randomized, placebo‐controlled Phase 2 study evaluated the safety, tolerability and efficacy of 75 and 225 mg AZLI administered BID for 14 days using the eFlow® Electronic Nebulizer (Pari Innovative Manufacturers, Inc., Midlothian, VA). Patients were 13 years and older with FEV1 ≥ 40% predicted, chronic P. aeruginosa infection, and had used no anti‐pseudomonal antibiotics for 56 days.ResultsOf 131 patients screened, 105 received AZLI or placebo. Mean age was 26 years and mean FEV1 percent predicted was 77% at baseline. There was a statistically significant reduction, compared to placebo, in P. aeruginosa CFU density in each AZLI group at Days 7 and 14 (P < 0.001). The planned primary analysis, percent change in FEV1 at Day 14, demonstrated no statistically significant difference. Post hoc analysis demonstrated significant increase in FEV1 at Day 7 for the subset of patients with baseline FEV1 < 75% predicted in the 225 mg AZLI group. Bronchodilator use was associated with greater improvement in FEV1, as well as greater reduction in P. aeruginosa bacterial density and higher plasma aztreonam concentrations in the 225 mg AZLI group. Adverse events were similar between placebo and AZLI although there was a trend toward increased respiratory symptoms in the 225 mg AZLI group.ConclusionThese data support the further development of AZLI and provide information for the design of subsequent studies. Pediatr Pulmonol. 2008; 43:47–58. © 2007 Wiley‐Liss, Inc.
Elimination and exchange of trifluoroacetate counter‐ion from cationic peptides: a critical evaluation of different approaches
Authors: Roux Stéphane , Zékri Elisabeth , Rousseau Bernard , Paternostre Maïté , Cintrat Jean‐Christophe , Fay Nicolas 
Published: November 2007

AbstractMost synthesized peptides are nowadays produced using solid‐phase procedures. Due to cleavage and purification conditions, they are mainly obtained in the presence of trifluoroacetic acid (TFA) and, for cationic peptides, as trifluoroacetate (TF‐acetate) salts. However, TF‐acetate interferes with physicochemical characterizations using infrared spectroscopy and might significantly affect the in vivo studies. Thus, TF‐acetate exchange by another counter‐ion is often required. Up to now, the classical procedure has consisted of freeze‐drying the peptide several times in the presence of an excess of a stronger acid than TFA (pKa ∼0): generally HCl (pKa = − 7). This approach means that working at pH < 1 can induce peptide degradation. We therefore tested three different approaches to exchange the tightly bound TF‐acetate counter‐ion from the dicationic octapeptide lanreotide: (i) reverse‐phase HPLC, (ii) ion‐exchange resin, and (iii) deprotonation/reprotonation cycle of the amino groups. The first two approaches allow the partial to almost complete exchange of the TF‐acetate counter‐ion by another ion from an acid weaker than TFA, such as acetic acid (pKa = 4.5), and the third requires a basic solution that permits the complete removal of TF‐acetate counter‐ion. The efficiency of these three procedures was tested and compared by using different analytical techniques such as 19F‐NMR, 1H‐NMR and attenuated total reflectance Fourier transformed infrared spectroscopy (ATR FT‐IR). We also show that ATR‐IR can be used to monitor the TFA removal. The counter‐ion exchange procedures described in this study are easy to carry out, fast, harmless and reproducible. Moreover, two of them offer the very interesting possibility of exchanging the initial TF‐acetate by any other counter‐ion. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Distance dependence of long‐range electron transfer through helical peptides
Authors: Kai Minako , Takeda Kazuki , Morita Tomoyuki , Kimura Shunsaku 
Published: November 2007

AbstractHelical peptides of 8mer, 16mer, and 24mer carrying a disulfide group at the N‐terminal and a ferrocene moiety at the C‐terminal were synthesized, and they were self‐assembled on gold by a sulfur–gold linkage. Infrared reflection–absorption spectroscopy and ellipsometry confirmed that they formed a monolayer with upright orientation. Cyclic voltammetry showed that the electron transfer from the ferrocene moiety to gold occurred even with the longest 24mer peptide. Chronoamperometry and electrochemical impedance spectroscopy were carried out to determine the standard electron transfer rate constants. It was found that the dependence of the electron‐transfer rates on the distance was significantly weak with the extension of the chain from 16mer to 24mer (decay constant β = 0.02–0.04). This dependence on distance cannot be explained by an electron tunneling mechanism even if increased hydrogen‐bonding cooperativity or molecular dynamics is considered. It is thus concluded that this long‐range electron transfer is operated by an electron hopping mechanism. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Surface characterization of plasma‐modified polyethylene by contact angle experiments and ATR‐FTIR spectroscopy
Authors: De Geyter N. , Morent R. , Leys C. 
Published: November 2007

AbstractPolymers such as polyethylene (PE) have a low surface free energy and therefore often require a modification of their surface properties before any use. Nonthermal plasma treatment is a convenient and environmentally friendly way to obtain these modifications by introducing new chemical groups at the surface without affecting the bulk properties. Therefore, in this article, a PE film is treated with a dielectric barrier discharge (DBD) operating in air at medium pressure (5.0 kPa). The surface properties of the plasma‐treated PE films are characterized using contact angle measurements, surface free energy calculations and ATR‐FTIR spectroscopy. The polymer films show a remarkable increase in surface free energy after plasma treatment. ATR‐FTIR spectroscopy of the plasma‐treated PE films reveals that plasma treatment introduces oxygen‐containing functionalities, such as ketones, aldehydes, alcohols and carboxylic acids on the PE surface leading to the increased surface free energy. Copyright © 2008 John Wiley & Sons, Ltd.
Joint modelling of repeated measurements and time‐to‐event outcomes: The fourth Armitage lecture
Authors: Diggle Peter J. , Sousa Inês , Chetwynd Amanda G. 
Published: November 2007

AbstractIn many longitudinal studies, the outcomes recorded on each subject include both a sequence of repeated measurements at pre‐specified times and the time at which an event of particular interest occurs: for example, death, recurrence of symptoms or drop out from the study. The event time for each subject may be recorded exactly, interval censored or right censored. The term joint modelling refers to the statistical analysis of the resulting data while taking account of any association between the repeated measurement and time‐to‐event outcomes. In this paper, we first discuss different approaches to joint modelling and argue that the analysis strategy should depend on the scientific focus of the study. We then describe in detail a particularly simple, fully parametric approach. Finally, we use this approach to re‐analyse data from a clinical trial of drug therapies for schizophrenic patients, in which the event time is an interval‐censored or right‐censored time to withdrawal from the study due to adverse side effects. Copyright © 2007 John Wiley & Sons, Ltd.
Two‐dimensional benchmark solution for buckling and vibration of simply supported hybrid piezoelectric angle‐ply flat panels
Authors: Dumir P.C. , Kapuria S. , Kumari P. , Nath J.K. 
Published: November 2007

AbstractA benchmark 2D piezothermoelasticity exact solution is presented, based on state space approach for buckling and free vibration response of simply supported laminated hybrid angle‐ply panels in cylindrical bending under initial in‐plane thermo‐electromechanical loads. A mixed formulation of governing equations for the incremental problem of buckling/vibration is presented in terms of eight primary variables: three displacements, electric potential, three transverse stresses, and transverse electric displacement. The entities are expanded in Fourier series that satisfy the end conditions. The governing equations reduce to a z‐invariant state equation with the state vector of eight variables. The state vector at the bottom of the laminate is related to that at its top through a global transfer matrix using continuity/jump conditions at the layer interfaces. The eight homogenous boundary conditions at the top and the bottom of the angle‐ply panel are used to set up four homogeneous equations for u, v, w, and ϕ/Dz at the bottom. The determinant of their coefficient matrix is set to zero to obtain the buckling parameter or natural frequency. Benchmark results are presented for hybrid highly inhomogeneous test panel, composite panel, and sandwich panel. The effect of exclusion of the pre‐buckling strains in the formulation on the buckling temperature is investigated. The effects of thickness parameter, and the electric boundary conditions on the buckling loads are illustrated. The enhancement of buckling temperature by the application of actuation potential is discussed. The present benchmark solution would help assess 1D theories for buckling of hybrid angle‐ply panel.
Adolescent aggression: Effects of gender and family and school environments
Authors: Estévez López Estefanía , Pérez Sergio Murgui , Ochoa Gonzalo Musitu , Ruiz David Moreno 
Published: November 2007

ABSTRACTThe present study examined the influence of family and classroom environments on the development of particular individual characteristics, including level of empathy, attitude to institutional authority and perceived social reputation, and the role these characteristics may in turn play in school aggression. Participants were 1319 adolescents aged 11–16 (47% male) drawn from state secondary schools in Valencia (Spain). Since previous studies suggest that these variables may contribute differentially to aggressive behaviour depending on adolescent gender, two different mediational structural models were calculated, respectively, for boys and girls. Results obtained confirmed the associations expected among the variables considered in the structural equations tested and pointed out different paths for boys and girls. Overall, our findings suggested that a positive family environment seems to be a stronger protective factor for girls in the development of problems of behaviour at school, whereas for boys this is the case for a positive classroom environment. This model accounted for 40% of the variance in aggression at school for boys and 35% for girls.
Breaking of resonance and regularizing effect of a first order quasi-linear term in some elliptic equations
Authors: Abdellaoui Boumediene , Peral Ireneo , Primo Ana 
Published: November 2007

In this article we study the problem

\text{(P)}\:
\begin{cases}
−\mathrm{\Delta }u + |\mathrm{∇}u|^{q} = \lambda g(x)u + f(x) & \text{in }\Omega , \\ u > 0 & \text{in }\Omega , \\ u = 0 & \text{on }\partial \Omega ,
\end{cases}

with

1⩽q⩽2

and

f,g

are positive measurable functions. We give assumptions on

g

with respect to

q

for which for all

\lambda > 0

and all

f \in L^{1}

,

f⩾0

, problem (P) has a positive solution. In particular we focus our attention on

g(x) = {}^{1}/_{|x|^{2}}

to prove that the assumptions on

g

are optimal.

Résumé
Dans cet article nous étudions le problème

\text{(P)}\:
\begin{cases}
−\mathrm{\Delta }u + |\mathrm{∇}u|^{q} = \lambda g(x)u + f(x) & \text{in }\Omega , \\ u > 0 & \text{in }\Omega , \\ u = 0 & \text{on }\partial \Omega ,
\end{cases}

où

1⩽q⩽2

et

f,g

sont des fonctions mesurables positives. Nous donnons des hypothèses sur

g

dépendant de

q

telles que pour tout

\lambda > 0

et pour tout

f \in L^{1}

,

f⩾0

, le problème (P) a une solution positive. Nous portons une attention particulière au cas

g(x) = {}^{1}/_{|x|^{2}}

pour montrer que les hypothèses sur

g

sont optimales.
Identification of a novel small Arabidopsis protein interacting with gamma‐tubulin complex protein 3
Authors: Janski Natacha , Herzog Etienne , Schmit Anne‐Catherine 
Published: November 2007

AbstractIn higher plants, microtubules (MTs) show dynamic structural changes during cell cycle and development progression. A precise control of MT nucleation at dispersed sites is one way used to regulate the cytoskeletal organization. Some gamma‐tubulin complex proteins (GCPs) were previously identified in Arabidopsis thaliana (At). They are directly involved in the nucleation process. Nevertheless, no additional player which may anchor the nucleating complex or regulate the nucleation activity has been found in plant cells so far. Therefore, our aim was the identification of Arabidopsis proteins interacting with MT nucleating complexes and particularly with AtGCP3. Performing a yeast two‐hybrid screen, we discovered a new protein which we called AtGCP3 Interacting Protein 1 (AtGIP1). The possible role of this protein during the nucleation process is discussed.
Is the gap between guidelines and clinical practice in heart failure treatment being filled? Insights from the IMPACT RECO survey
Authors: de Groote P. , Isnard R. , Assyag P. , Clerson P. , Ducardonnet A. , Galinier M. , Jondeau G. , Leurs I. , Thébaut J.‐F. , Komajda M. 
Published: November 2007

AbstractBackgroundRecent registries have shown that recommended drugs for the treatment of chronic heart failure (CHF) are under‐prescribed in daily practice.AimsTo determine prescription rates of CHF drugs, and to assess predictive factors for drug prescription using data from a large panel of French cardiologists.Methods and resultsWe included 1919 outpatients, with NYHA class II–IV heart failure and a left ventricular ejection fraction <40%. The most frequently prescribed drugs were diuretics (83%), angiotensin converting enzyme inhibitors (ACE‐I) (71%), beta‐blockers (65%), spironolactone (35%) and angiotensin receptor blockers (ARB) (21%); 61% of patients received a combination of a beta‐blocker and an ACE‐I or ARB. Target doses were reached in 49% of the patients for ACE‐I, but in only 18% for beta‐blockers and in 9% for ARBs. Multivariate analyses showed that age >75 years was an independent factor associated with under‐prescription of ACE‐I‐ARBs, beta‐blockers or spironolactone. Renal failure was associated with a lower prescription of ACE‐I‐ARB and spironolactone, and asthma was a predictor of under‐prescription of beta‐blockers.ConclusionsIn this contemporary survey, prescription rates of CHF drugs were higher than previously reported. However, dosages were lower than those recommended in guidelines. Age remained an independent predictor of under‐prescription of CHF drugs.
Improvement but no cure of left ventricular systolic dysfunction in treated heart failure patients
Authors: Murphy Niamh F. , O'Loughlin Christina , Ledwidge Mark , McCaffrey Dermot , McDonald Kenneth 
Published: November 2007

AbstractBackgroundRecent advances in pharmacological and pacemaker‐based treatments for heart failure (HF) have brought about significant improvements in left ventricular function.AimsTo identify the proportion of treated systolic HF patients in whom left ventricular systolic function improves and/or returns to normal.MethodsThis was a retrospective analysis of 221 HF patients. Improvement in left ventricular function was defined as an improvement in ejection fraction (LVEF) of ≥10% on echocardiography. Return to normal was defined as an improvement of LVEF to ≥50% and a reduction in left ventricular end diastolic diameter to ≤55 mm. Changes in BNP were also recorded.ResultsImprovement in LVEF was observed in 44.3% of patients and return to normal systolic function in 10.9%, only 2.3% had both a return to normal echocardiographic parameters and a BNP<100 pg/ml. A higher percentage of the improved group were on target doses of β‐blockers (p=0.004). Baseline BNP was not a predictor of improvement. There was a trend towards a reduction in HF readmissions in the improved group (p=0.07) but no difference in the risk of death or all‐cause readmission.ConclusionWhile a substantial proportion of treated HF patients have an improvement in left ventricular function over time, only a small proportion return to normal dimensions and LVEF, underlining the permanent nature of ventricular damage in the vast majority of patients.
NFAT signaling in neural development and axon growth
Authors: Nguyen Tuan , Di Giovanni Simone 
Published: November 2007

AbstractThe NFAT (nuclear factor of activated T‐cells) family of transcription factors functions as integrators of multiple signaling pathways by binding to chromatin in combination with other transcription factors and coactivators to regulate genes central for many developmental systems. Recent experimental evidence has shown that the calcineurin/NFAT signaling pathway is important in axonal growth and guidance during vertebrate development. In fact, studies with triple NFATc2/c3/c4 mutant mice demonstrate that the extension and organization of sensory axon projection and commissural axon growth are both dependent upon NFAT activity. Neurotrophin and L‐type calcium channel signaling modulate intracellular calcium levels to regulate the nuclear import and transcriptional activity of NFAT by activating the phosphatase calcineurin. The rephosphorylation and subsequent export of NFAT from the nucleus is mediated by several kinases, including GSK‐3β, which contribute to the fine tuning of NFAT transcriptional activity in neurons.However, currently, no direct transcriptional targets for NFAT have been identified in a chromatin environment in the nervous system. Undiscovered are also the binding partners of NFAT that might combinatorially regulate specific genes important for neuronal development.This review will discuss the current knowledge related to NFAT signaling in the nervous system development and the potential for future research directions.
Comparison between anopheline mosquitoes (Diptera: Culicidae) caught using different methods in a malaria endemic area of Papua New Guinea
Authors: Hii J.L.K. , Smith T. , Mai A. , Ibam E. , Alpers M.P. 
Published: November 2007

AbstractThe mosquito sampling efficiency of CDC (Centers for Disease Control) miniature light traps hung adjacent to mosquito nets, was compared with that of both indoor and outdoor human-bait collections in ten villages in the Wosera area of Papua New Guinea. The most frequently collected anopheline in the matched indoor and light trap samples was Anopheles koliensis Owen, followed by A. punctulatusDönitz, A. karwari (James), A. farauti Laveran (sensu lato), A. longirostris Brug and A. bancroftii Giles. All species were much less frequent in the light traps than in landing catches. The hypothesis that the numbers of mosquitoes in light traps are proportional to human landing catches was examined using regression models that allowed for sampling error in both entomological measurements. Light traps under-sampled A. punctulatus and A. farautis.l. at high densities. The models indicated that the ratio of light trap to landing catch females of A. koliensis and A. karwari increased with increasing mosquito density. Light trap catches of A. longirostris were proportional to indoor landing rates but when outdoor landing rates were high this species was under-sampled by light traps. Numbers of A. bancroftii in light traps were found to be proportional to those in outdoor landing catches, but were negatively related to those attempting to bite indoors. Circumsporozoite positivity rates for both Plasmodium falciparum Welch and P. vivax (Grassi & Feletti) in A. punctulatus and A. farauti s.l. were significantly higher in light trap collections than in either indoor or outdoor landing catches, suggesting that light traps may selectively sample older mosquitoes of these species.
The use of vertical-looking radar to continuously monitor the insect fauna flying at altitude over southern England
Authors: Smith A.D. , Reynolds D.R. , Riley J.R. 
Published: November 2007

AbstractThe continuous automatic monitoring of the aerial density, biomass and relative diversity of high-flying insect faunas has been made practicable by a new, vertical-looking radar. This inexpensive radar system, with its novel signal analysis capability, represents a major advance over earlier vertical-beam radars because it provides estimates of the body mass of individual overflying insects, as well as measurements of their direction and speed of movement. This paper summarizes data collected over a three-month period by the new radar in the height range from 150 m to c.1 km, over agricultural land in Worcestershire, England. The day-to-day variation in the numbers of insects and their altitudinal and diurnal patterns of flight activity are presented. Examples are also given of distributions of mass, displacement speed and direction, and orientation direction. The potential of the new radar for various research and operational monitoring tasks is briefly discussed.