bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histidine affinity tags affect MSP142 structural stability and immunodominance in mice
Authors: Khan Farhat , Legler Patricia M. , Mease Ryan M. , Duncan Elizabeth H. , Bergmann‐Leitner Elke S. , Angov Evelina 
Published: November 2011

AbstractInclusion of affinity tags has greatly facilitated process development for protein antigens, primarily for their recovery from complex mixtures. Although generally viewed as supportive of product development, affinity tags may have unintended consequences on protein solubility, susceptibility to aggregation, and immunogenicity. Merozoite surface protein 1 (MSP1), an erythrocytic stage protein of Plasmodium falciparum and a candidate malaria vaccine, was used to evaluate the impact of a metal ion affinity‐tag on both protein structure and the induction of immunity. To this end, codon harmonized gene sequences from the P. falciparum MSP142 of FVO and 3D7 parasites were cloned and purified with and without a histidine (His) tag. We report on the influence of His‐affinity tags on protein expression levels, solubility, secondary structure, thermal denaturation, aggregation and the impact on humoral and cellular immune responses in mice. While the overall immunogenicity induced by His‐tagged MSP142 proteins is greater, the fine specificity of the humoral and cellular immune responses is altered relative to anti‐parasitic antibody activity and the breadth of T‐cell responses. Thus, the usefulness of protein tags may be outweighed by their potential impact on structure and function, stressing the need for caution in their use.See accompanying commentary by Randolph DOI: 10.1002/biot.201100459
An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics
Authors: Albright Catherine J. , Hall David J. 
Published: November 2011

AbstractHuman rhinovirus (HRV) is one of the most common human respiratory pathogens and is responsible for the majority of upper respiratory illnesses. Recently, a phylogeny was constructed from all known American Type Culture Collection (ATCC) HRV sequences. From this study, three HRV classifications (HRVA, HRVB, and HRVC) were determined and techniques for classifying new isolates of HRV were reported. The genetic change of this virus in specific populations over time is of great interest to understand the evolution and epidemiology of viruses. To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. Students will learn a variety of techniques including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis as well as bioinformatic skills though examination of sequences from the HRV‐field isolates. Furthermore, students can look at symptom data from subjects to investigate correlations between symptom severity and factors such as stress and sleep patterns. Such information can be used to examine hypotheses regarding HRV mutation, symptom severity and epidemiology. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Vol. 39, No. 6, pp. 457–458, 2011
Synthesis of Platinum–Ruthenium Nanoparticles under Supercritical CO2 and their Confinement in Carbon Nanotubes: Hydrogenation Applications
Authors: Castillejos Eva , Jahjah Mohamad , Favier Isabelle , Orejón Arantxa , Pradel Christian , Teuma Emmanuelle , Masdeu‐Bultó Anna M. , Serp Philippe , Gómez Montserrat 
Published: November 2011

AbstractBimetallic platinum–ruthenium nanoparticles stabilised by pyridine‐ and monophosphine‐based ligands were prepared either in supercritical CO2 or in THF. TEM analyses evidenced a tendency of the nanoparticles prepared in supercritical CO2 to agglomerate. Both types of bimetallic nanoparticles were further confined into functionalised multiwalled carbon nanotubes. Upon confinement, PtRu nanoparticles stabilised by phosphine ligands appeared more agglomerated than those stabilised by the pyridine ligand. These materials were applied to cinnamaldehyde hydrogenation. Confined PtRu nanoparticles showed higher catalytic activity and selectivity than unsupported nanoparticles.
Biophysical and Cellular‐Uptake Properties of Mixed‐Sequence Pyrrolidine–Amide Oligonucleotide Mimics
Authors: Worthington Roberta J. , Micklefield Jason 
Published: November 2011

AbstractPreviously we introduced the positively charged pyrrolidine–amide oligonucleotide mimics (POM), which possess a pyrrolidine ring and amide linkage in place of the sugar–phosphodiester backbone of natural nucleic acids. Short POM homo‐oligomers have shown promising DNA and RNA recognition properties. However, to better understand the properties of POM and to assess their potential for use as modulators of gene expression and bioanalytical or diagnostic tools, more biologically relevant, longer, mixed‐sequence oligomers need to be studied. In light of this, several mixed‐sequence POM oligomers were synthesised, along with fluorescently labelled POM oligomers and a POM–peptide conjugate. UV thermal denaturation showed that mixed‐sequence POMs hybridise to DNA and RNA with high affinity but slow rates of association and dissociation. The sequence specificity, influence of terminal amino acids, and the effect of pH and ionic strength on the DNA and RNA hybridisation properties of POM were extensively investigated. In addition, isothermal titration calorimetry (ITC) was used to investigate the thermodynamic parameters of the binding of a POM–peptide conjugate to DNA. Cellular uptake experiments have also shown that a fluorescently labelled POM oligomer is taken up into HeLa cells. These findings demonstrate that POM has the potential for use in a variety of applications, alongside other modified nucleic acids developed to date, such as peptide nucleic acids (PNA) and phosphoramidate morpholino oligomers (PMO).
ChemInform Abstract: Anomalous Reduction of Araliphatic Ketones with Complex Boron Hydrides.
Authors: DEM'YANOVICH V. M. , KHLEBNIKOV V. A. 
Published: November 2011

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Bioactive Marine Metabolites Series. Part 63. Ritterazine A, a Highly Cytotoxic Dimeric Steroidal Alkaloid, from the Tunicate Ritterella tokioka
Authors: FUKUZAWA S. , MATSUNAGA S. , FUSETANI N. 
Published: November 2011

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Operational Cost Comparison of Several Pre‐Treatment Techniques for OMW Treatment
Authors: Coşkun Tamer , Debik Eyüp , Demır Neslihan Manav 
Published: November 2011

AbstractOlive mill wastewaters (OMWs), which are known to have deep impacts on the receiving water bodies due to their high‐strength contents of organic materials and color, must be treated before discharge. For this reason; a number of research studies have been available in current literature related to the treatment of OMWs. However, no widely accepted treatment alternatives have been proposed yet. The common results of these studies suggest that OMWs must be pretreated prior to final purification processes. This study focuses on the comparison of alternative pre‐treatment processes in the aspect of chemical oxygen demand (COD) removal and costs of operation. Centrifuging, lime precipitation, acid cracking, and electrocoagulation processes were performed to compare removal efficiencies and operational costs. The COD removal efficiencies for centrifuging, lime precipitation, acid cracking, and electrocoagulation processes were determined to be 30.1, 24.1, 20.0, 53.7%, respectively, with operational costs being $0.30, $0.37, $1.42, and $11.60 per cubic meter of wastewater treated, respectively. The centrifuging process was concluded to be the most appropriate one according to the COD removal efficiency and cost of operation.
Removal of Pyridine from Aqueous Solution by Adsorption on an Activated Carbon Cloth
Authors: Alonso‐Davila Pedro , Torres‐Rivera Oliva L. , Leyva‐Ramos Roberto , Ocampo‐Perez Raul 
Published: November 2011

AbstractPyridine is a very toxic pollutant that has to be removed from wastewater. In this work, adsorption of pyridine on activated carbon cloth (ACC) is studied as a possible alternative for eliminating pyridine from aqueous solution. The ACC was produced from polyacrylonitrile. The adsorption equilibrium data of pyridine on ACC was obtained in a batch adsorber. The experimental data was interpreted with the isotherms of Langmuir, Freundlich, and Prausnitz‐Radke (PR), and the PR isotherm better represented the experimental data. The capacity of ACC for adsorbing pyridine was favored increasing the solution pH from 3 to 6, and this effect was due to the π–π dispersive and electrostatic interactions between the pyridine species in solution and the surface complexes of ACC. The modified Langmuir model fitted reasonably well the influence of pH on the adsorption capacity. In this model was assumed that both neutral pyridine and pyridinium were simultaneously adsorbed on ACC accordingly to the experimental results. The adsorption capacity was almost independent of temperature. The reversibility study revealed that 75% of the pyridine can be desorbed from ACC indicating that part of the pyridine was irreversibly adsorbed, and possibly chemisorbed.
High‐Affinity, Selective σ Ligands of the 1,2,3,4‐Tetrahydro‐1,4′‐silaspiro[naphthalene‐1,4′‐piperidine] Type: Syntheses, Structures, and Pharmacological Properties
Authors: Tacke Reinhold , Bertermann Rüdiger , Burschka Christian , Dörrich Steffen , Fischer Markus , Müller Barbara , Meyerhans Géraldine , Schepmann Dirk , Wünsch Bernhard , Arnason Ingvar , Bjornsson Ragnar 
Published: November 2011

AbstractThe 1′‐organyl‐1,2,3,4‐tetrahydrospiro[naphthalene‐1,4′‐piperidine] derivatives 1 a–4 a [for which organyl=benzyl (1 a), 4‐methoxybenzyl (2 a), 2‐phenylethyl (3 a), or 3‐methylbut‐2‐enyl (4 a)] are high‐affinity, selective σ1 ligands. The corresponding sila‐analogues 1 b–4 b (replacement of the carbon spirocenter with a silicon atom) were synthesized in multistep syntheses, starting from dichlorodivinylsilane, and were isolated as the hydrochlorides 1 b⋅HCl–4 b⋅HCl. Compounds 1 a⋅HCl–4 a⋅HCl and 1 b⋅HCl–4 b⋅HCl were structurally characterized by NMR spectroscopy (1H, 13C, 29Si) in solution, and the C/Si analogues 3 a⋅HCl and 3 b⋅HCl were studied by single‐crystal X‐ray diffraction. These structural investigations were complemented by computational studies. The σ1 and σ2 receptor affinities of the C/Si pairs 1 a/1 b–4 a/4 b were studied with radioligand binding assays. The σ1 receptor affinity of the silicon compounds 1 b–4 b is slightly higher than that of the corresponding carbon analogues 1 a–4 a. Because affinity for the σ2 receptor is decreased by the C/Si exchange, the σ1/σ2 selectivity of the silicon compounds is considerably improved, indicating that the C→Si switch strategy is a powerful tool for modulating both pharmacological potency and selectivity.
Triazole, Benzotriazole, and Naphthotriazole as Copper Corrosion Inhibitors: I. Molecular Electronic and Adsorption Properties
Authors: Kokalj Anton , Kovačević Nataša , Peljhan Sebastijan , Finšgar Matjaž , Lesar Antonija , Milošev Ingrid 
Published: November 2011

AbstractThe gas‐phase adsorption of 1,2,3‐triazole, benzotriazole, and naphthotriazole—considered as corrosion inhibitors—on copper surfaces was studied and characterized using density functional theory (DFT) calculations. We find that the molecule–surface bond strength increases with increasing molecular size, thus following the sequence: triazole<benzotriazole<naphthotriazole. This trend is explained in terms of molecular electronegativity and chemical hardness, which decrease monotonously as the molecular size increases. While the electronegativity of triazole is almost degenerate with the work function of Cu(111) surface, the electronegativity of larger acenotriazoles is smaller. The difference in electronegativity between the Cu(111) and the acenotriazoles thus increases with increasing the molecular size, which, together with decreasing the molecular hardness, results in larger molecule‐to‐metal electron charge transfer and stronger molecule–surface bonds.
Free tissue transfer for head and neck reconstruction in solid organ transplant patients
Authors: Miller Matthew W. , Dean Nichole R. , Cannady Steven B. , Rosenthal Eben L. , Wax Mark K. 
Published: November 2011

AbstractBackgroundPatients with head and neck malignancies who have had solid organ transplant and require free tissue transfer are a unique population. This study was performed to evaluate the effect of immunosuppression on the rate of perioperative complications and the success of free tissue transfer in the head and neck.MethodsComplications in solid organ transplant patients undergoing free tissue transfer for reconstruction of head and neck malignancies from 1998 to 2010 were evaluated.ResultsA total of 22 flaps in 17 patients were performed. Eight patients (11 of 22 flaps) had complications. The median hospital stay was 6 days (range, 4–26 days). The median length of follow‐up was 13.5 months (range, 3.5–49.9 months).ConclusionsSolid organ transplant patients are at an increased risk of de novo malignancies due to chronic immunosuppression. This study demonstrates that free tissue transfer is a viable option in transplant patients with morbidity similar to nontransplant patients. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
Zinc and its role in age‐related inflammation and immune dysfunction
Authors: Wong Carmen P. , Ho Emily 
Published: November 2011

AbstractZinc is an essential micronutrient required for many cellular processes, especially for the normal development and function of the immune system. Zinc homeostasis and signaling are critical in immune activation, and an imbalance in zinc homeostasis is associated with the development of chronic diseases. Zinc deficiency causes significant impairment in both adaptive and innate immune responses, and promotes systemic inflammation. The elderly are a population particularly susceptible to zinc deficiency. National surveys indicate that a significant portion of the aged population has inadequate zinc intake, and a decline in zinc status is observed with age. There are remarkable similarities between the hallmarks of zinc deficiency and immunological dysfunction in aged individuals. Both zinc deficiency and the aging process are characterized by impaired immune responses and systemic low grade chronic inflammation. It has been hypothesized that age‐related zinc deficiency may be an important factor contributing to immune dysfunction and chronic inflammation during the aging process. In this review, we discuss the effects of zinc status on aging, potential molecular and epigenetic mechanisms contributing to age‐related decline in zinc status, and the role of zinc in age‐related immune dysfunction and chronic inflammation.
Revitalization and analysis of operation of the autonomous photovoltaic system of the Uacari Floating Lodging House, Amazon‐Brazil
Authors: Macêdo Wilson , Galhardo Marcos , Almeida Marcelo , Pinto Aimé Carvalho , Pinho João , Modesto Josivaldo , Penha José , Brito Otacilio 
Published: November 2011

ABSTRACTThis paper presents the main problems found in photovoltaic systems in the Amazon Region and the actions to be performed for restructuring and correcting the operation of such systems. These problems and solutions are exemplified on the basis of the diagnosis and revitalization of the 2.5‐kWp photovoltaic installation that belongs to the central module of the Uacari Floating Lodging House. The paper was accomplished as part of the agreement between the Group of Studies and Development of Energy Alternatives (GEDAE) and the Mamirauá Institute of Sustainable Development to assess several photovoltaic facilities in the area covered by the institute. Concluding the paper, some operational results of the revitalized system are presented. Copyright © 2011 John Wiley & Sons, Ltd.
A universal combinatorial design of antibody framework to graft distinct CDR sequences: A bioinformatics approach
Authors: Haidar Jaafar N. , Yuan Qing‐An , Zeng Lin , Snavely Mark , Luna Xenia , Zhang Haifan , Zhu Wei , Ludwig Dale L. , Zhu Zhenping 
Published: November 2011

AbstractAntibody (Ab) humanization is crucial to generate clinically relevant biologics from hybridoma‐derived monoclonal antibodies (mAbs). In this study, we integrated antibody structural information from the Protein Data Bank with known back‐to‐mouse mutational data to build a universal consensus of framework positions (10 heavy and 7 light) critical for the preservation of the functional conformation of the Complimentarity Determining Region of antibodies. On the basis of FR consensus, we describe here a universal combinatorial library suitable for humanizing exogenous antibodies by CDR‐grafting. The six CDRs of the murine anti‐human EGFR Fab M225 were grafted onto a distinct (low FR sequence similarity to M225) human FR sequence that incorporates at the 17 FR consensus positions the permutations of the naturally observed amino acid diversities. Ten clones were selected from the combinatorial library expressing phage‐displayed humanized M225 Fabs. Surprisingly, 2 of the 10 clones were found to bind EGFR with stronger affinity than M225. Cell‐based assays demonstrated that the 10 selected clones retained epitope specificity by blocking EGFR phosphorylation and thus hindering cellular proliferation. Our results suggest that there is a universal and structurally rigid near‐CDR set of FR positions that cooperatively support the binding conformation of CDRs. Proteins 2011. © 2012 Wiley Periodicals, Inc.
Frameless stereotactic targeting devices: technical features, targeting errors and clinical results
Authors: Widmann Gerlig , Schullian Peter , Ortler Martin , Bale Reto 
Published: November 2011

AbstractBackgroundBrain biopsies (BB) and depth electrode placements (DEP) are increasingly performed using frameless stereotactic targeting devices. This paper is intended to provide a comprehensive review of the technical features, targeting errors and clinical results.MethodsA PubMed literature search from 1995–2010 was performed.Results(A) Modified stereotactic arcs, (B) arm‐based devices with and without aiming facilities, and (C) skull affixed devices were found. Guidance technologies were navigation systems (all groups), prospective stereotaxy and custom designed platforms (group C). Mean total errors ranged between 4.4 and 5.4 mm for BB and 2.0 and 3.2 mm for DEP. Diagnostic yield of BB was 89–100%. The clinical success rate for DEP was 96–100%.ConclusionsFrameless stereotactic targeting devices may reach targeting errors and clinical results comparable with standard frame‐based stereotaxy. Advantages and disadvantages of different devices should be acknowledged to ensure optimal technical performance. Copyright © 2011 John Wiley & Sons, Ltd.
In quest of the science in statistical fault localization
Authors: Chan W. K. , Cai Yan 
Published: November 2011

SUMMARYMany researchers employ various statistical methods to locate faults in faulty programs. Like other researchers, we sometimes have made mistakes in the quest of making statistical fault localization both practical and scientific. In this experience report, we reflect on our work conducted on this topic, organize our isolated experiences in the format of models and errors, and cast them in the context of statistics. Copyright © 2011 John Wiley & Sons, Ltd.
Intra‐ and interoperator reliability of manual and semi‐automated measurements of intracranial translucency
Authors: Karl K. , Kagan K. O. , Chaoui R. 
Published: November 2011

AbstractObjectivesTo assess the reproducibility of fetal intracranial translucency (IT) measurements performed manually or with SonoNT®, a semi‐automated caliper placement technique recently introduced for nuchal translucency thickness (NT) measurement.MethodsThis was a retrospective study using 116 stored images of the head (mid‐sagittal plane) from normal fetuses in dorsoposterior position at 11–13 weeks. Two experienced operators each measured the IT separately, twice manually and twice using the semi‐automated software. Intraoperator and interoperator repeatability were assessed. The mean of the two manual measurements of the more experienced Operator 2 was considered as the ‘gold standard’.ResultsSeven cases were excluded as the IT could not be recognized by the semi‐automated software. In the remaining 109 cases, the interquartile range of the mean IT measurement was 1.9–2.4 mm for Operator 1 and 1.8–2.3 mm for Operator 2 for both the manual and the semi‐automated IT measurements. The intraoperator SD for manual measurements was 0.091 mm for Operator 1 and 0.088 mm for Operator 2, and for semi‐automated measurements it was 0.054 mm for Operator 1 and 0.067 mm for Operator 2. Concerning interoperator bias of the manual measurements, the mean difference between Operator 1 and Operator 2 was − 0.09 (95% CI, − 0.11 to − 0.07) mm. With respect to the gold standard, the mean bias of the semi‐automated measurements was 0.01 (95% CI − 0.01 to 0.03) mm for Operator 1 and − 0.09 (95% CI − 0.11 to − 0.07) mm for Operator 2, indicating good agreement.ConclusionsManual IT measurements are reproducible. In addition, IT can be assessed reliably using the semi‐automated NT algorithm, leading to standardization of the IT assessment process. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Optimal designs for IEEE 802.15.4 wireless sensor networks
Authors: Monsalve Alvaro , Vu Hai L. , Vo Quoc Bao 
Published: November 2011

ABSTRACTThis paper investigates the maximum achievable channel throughput in a single‐channel and single‐hop wireless sensor network using IEEE 802.15.4 Medium Access Control (MAC) protocol. We introduce a simple mean‐field approach to model the Carrier Sense Multiple Access with Collision Avoidance mechanism of the 802.15.4 MAC protocol under unsaturated conditions. We derive a set of expressions such as optimal sensing rate of a sensor node, its corresponding failure probability, and the channel throughput for both saturated and unsaturated networks. With those expressions, we propose several network designs to achieve the optimal throughput by choosing the appropriate MAC parameters. We validate the proposed optimal designs using ns‐2 simulations. Furthermore, we evaluate the network lifetime expectancy of the optimal designs and compare it with the lifetime of network settings under saturated conditions that use the default MAC parameters of IEEE 802.15.4. Copyright © 2011 John Wiley & Sons, Ltd.