bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advanced generation anti‐prostate specific membrane antigen designer T Cells for prostate cancer immunotherapy
Authors: Ma Qiangzhong , Gomes Erica M. , Lo Agnes Shuk‐Yee , Junghans Richard P. 
Published: October 2013

BACKGROUNDAdoptive immunotherapy by infusion of designer T cells (dTc) engineered with chimeric antigen receptors (CARs) for tumoricidal activity represents a potentially highly specific modality for the treatment of cancer. In this study, 2nd generation (gen) anti‐prostate specific membrane antigen (PSMA) dTc were developed for improving the efficacy of previously developed 1st gen dTc for prostate cancer immunotherapy. The 1st gen dTc are modified with chimeric immunoglobulin‐T cell receptor (IgTCR) while the 2nd gen dTc are engineered with an immunoglobulin‐CD28‐T cell receptor (IgCD28TCR), which incorporates a CD28 costimulatory signal for optimal T cell activation.METHODSA 2nd gen anti‐PSMA IgCD28TCR CAR was constructed by inserting the CD28 signal domain into the 1st gen CAR. 1st and 2nd gen anti‐PSMA dTc were created by transducing human T cells with anti‐PSMA CARs and their antitumor efficacy was compared for specific activation on PSMA‐expressing tumor contact, cytotoxicity against PSMA‐expressing tumor cells in vitro, and suppression of tumor growth in an animal model.RESULTSThe 2nd gen dTc can be optimally activated to secrete larger amounts of cytokines such as IL2 and IFNγ than 1st gen and to proliferate more vigorously on PSMA‐expressing tumor contact. More importantly, the 2nd gen dTc preserve the PSMA‐specific cytotoxicity in vitro and suppress tumor growth in animal models with significant higher potency.CONCLUSIONSOur results demonstrate that 2nd gen anti‐PSMA designer T cells exhibit superior antitumor functions versus 1st gen, providing a rationale for advancing this improved agent toward clinical application in prostate cancer immunotherapy. Prostate 74:286–296, 2014. © 2013 Wiley Periodicals, Inc.
Diamondoid diacids ('O4' species) in oil sands process‐affected water
Authors: Lengger Sabine K. , Scarlett Alan G. , West Charles E. , Rowland Steven J. 
Published: October 2013

RATIONALEAs a by‐product of oil sands extraction, large volumes of oil sands process water (OSPW) are generated, which are contaminated with a large range of water‐soluble organic compounds. The acids are thought to be derived from hydrocarbons via natural biodegradation pathways such as α‐ and β‐oxidation of alkyl substituents, which could produce mono‐ and diacids, for example. However, while several monoacids (‘O2’ species) have been identified, the presence of diacids (i.e. 'O4' species) has only been deduced from results obtained via Fourier transform infrared (FTIR) spectroscopy, Fourier transform ion cyclotron resonance high‐resolution mass spectrometry (FTICR‐HRMS) and nuclear magnetic resonance (1H‐NMR) spectroscopy and the structures have never been confirmed.METHODSAn extract of an OSPW from a Canadian tailings pond was analysed and the retention times and the electron ionization mass spectra of some analytes were compared with those of bis‐methyl esters of authentic diacids by gas chromatography × gas chromatography/time‐of‐flight mass spectrometry (GCxGC/TOFMS) in nominal and accurate mass configurations.RESULTSTwo diamondoid diacids (3‐carboxymethyladamantane‐1‐carboxylic acid and adamantane‐1,3‐dicarboxylic acid) were firmly identified as their bis‐methyl esters by retention time and mass spectral matching and several other structural isomers were more tentatively assigned. Diacids have substantially increased polarity over the hydrocarbon and monoacid species from which they probably derive: as late members of biodegradation processes they may be useful indicators of weathering and ageing, not only of OSPW, but potentially of crude oil residues more generally.CONCLUSIONSStructures of O4 species in OSPW have been identified. This confirms pathways of microbial biodegradation, which were only postulated previously, and may be a further indication that remediation of OSPW toxicity can occur by natural microbial action. The presence and abundance of these diacids might therefore be useful as a measure of biodegradation and weathering. Copyright © 2013 John Wiley & Sons, Ltd.
Characterisation of novel α‐keratin peptide markers for species identification in keratinous tissues using mass spectrometry
Authors: Solazzo Caroline , Wadsley Marc , Dyer Jolon M. , Clerens Stefan , Collins Matthew J. , Plowman Jeffrey 
Published: October 2013

RATIONALEIn ancient and/or damaged artefacts containing keratinous materials, the species of origin of the materials can be difficult to identify through visual examination; therefore, a minimally destructive methodology for species identification is required. While hair fibres from some species have seen substantial characterisation, others such as horn or baleen have received little or no attention, or lack protein sequences allowing formal identification using proteomics techniques.METHODSWe used the PMF method (Peptide Mass Fingerprinting with matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOF‐MS)) to catalogue and identify diagnostic peptide markers up to the genus level. Sequences were checked using nanoflow liquid chromatography/electrospray ionisation tandem mass spectrometry (nanoLC/ESI‐MS/MS) and unidentified peptides were searched against a theoretical database generated by substituting amino acids in keratin sequences.RESULTSSpecific peptides were identified by m/z and sequences characterised whenever possible for a range of species belonging to Bovidae and Camelidae, and for tissues such as baleen and horn. The theoretical database allowed an increase in the number of peptides of up to 10% in species with little genetic information.CONCLUSIONSA proteomics approach can successfully identify specific markers for the identification of materials to the genus level, and should be considered when identification by other means is not possible. Identification by PMF is fast, reliable and inexpensive. Copyright © 2013 John Wiley & Sons, Ltd.
Photodynamic oxidation of Escherichia coli membrane phospholipids: new insights based on lipidomics
Authors: Alves Eliana , Santos Nuno , Melo Tânia , Maciel Elisabete , Dória M. Luísa , Faustino Maria A. F. , Tomé João P. C. , Neves Maria G. P. M. S. , Cavaleiro José A. S. , Cunha Ângela , Helguero Luisa A. , Domingues Pedro , Almeida Adelaide , Domingues M. Rosário M. 
Published: October 2013

RATIONALEThe irreversible oxidation of biological molecules, such as lipids, can be achieved with a photosensitizing agent and subsequent exposure to light, in the presence of molecular oxygen. Although lipid peroxidation is an important toxicity mechanism in bacteria, the alterations caused by the photodynamic therapy on bacterial phospholipids are still unknown. In this work, we studied the photodynamic oxidation of Escherichia coli membrane phospholipids using a lipidomic approach.METHODSE. coli ATCC 25922 were irradiated for 90 min with white light (4 mW cm–2, 21.6 J cm–2) in the presence of a tricationic porphyrin [(5,10,15‐tris(1‐methylpyridinium‐4‐yl)‐20‐(pentafluorophenyl)porphyrin triiodide, Tri‐Py+‐Me‐PF]. Lipids were extracted and separated by thin‐layer chromatography. Phospholipid classes were quantified by phosphorus assay and analyzed by electrospray ionization tandem mass spectrometry. Fatty acids were analyzed by gas chromatography. Quantification of lipid hydroperoxides was performed by FOX2 assay. Analysis of the photodynamic oxidation of a phospholipid standard was also performed.RESULTSOur approach allowed us to see that the photodynamic treatment induced the formation of a high amount of lipid hydroperoxides in the E. coli lipid extract. Quantification of fatty acids revealed a decrease in the unsaturated C16:1 and C18:1 species suggesting that oxidative modifications were responsible for their variation. It was also observed that photosensitization induced the oxidation of phosphatidylethanolamines with C16:1, C18:1 and C18:2 fatty acyl chains, with formation of hydroxy and hydroperoxy derivatives.CONCLUSIONSMembrane phospholipids of E. coli are molecular targets of the photodynamic effect induced by Tri‐Py+‐Me‐PF. The overall change in the relative amount of unsaturated fatty acids and the formation of PE hydroxides and hydroperoxides evidence the damages in bacterial phospholipids caused by this lethal treatment. Copyright © 2013 John Wiley & Sons, Ltd.
Structures and Bonding Situation of the Allyl Systems and Cyclic Isomers [H2E–E(H)–EH2]–,·,+ (E = C, Si, Ge, Sn)
Authors: Gámez José A. , Hermann Markus , Frenking Gernot 
Published: October 2013

AbstractQuantum chemical calculations using DFT and ab initio methods were carried out on the structures of the title compounds. The nature of the bonding was investigated with an energy decomposition analysis. The calculations predict that the planar C2v allyl structures of the neutral and charged heavier group‐14 homologues [H2E–E(H)–EH2]–,·,+ (E = Si – Sn) are no minima on the potential energy surface. Energy minima for allyl‐type structures of the latter systems possess Cs symmetry and pyramidal EH2 groups. The energetically lowest lying form of [H2E–E(H)–EH2]–,·,+ (E = Si – Sn) has a cyclic structure for the neutral molecules and the anion and a quasi‐cyclic equilibrium arrangement for the cations. In contrast, the cyclic isomers of the carbon molecules [H2C–C(H)–CH2]–,·,+ are significantly higher in energy than the allyl structures. Energy decomposition analyses show that the lower stability of the planar C2v allyl structures of [H2E–E(H)–EH2]–,·,+ (E = Si – Sn) does not come from weak π conjugation. The relative contribution of π conjugation in the latter species is even higher than in the allyl system of carbon. The cyclic form of [H2E–E(H)–EH2]–,·,+ (E = Si – Sn) is lower in energy than the allyl form, because the σ bonding in the former structures is much stronger than in the latter. This overcompensates the higher Pauli repulsion in the cyclic form. In the carbon systems, the Pauli repulsion of the cyclic structures is very strong, because the bonds are much shorter than in the heavier homologues. Consequently, the stronger Pauli repulsion in the cyclic isomers is not compensated by the stronger attraction compared with the allyl system.
Inter‐facility Transfer of Surgical Emergencies in a Developing Country: Effects on Management and Surgical Outcomes
Authors: Khan Salma , Zafar Hasnain , Zafar Syed Nabeel , Haroon Naveed 
Published: October 2013

AbstractObjectivesOutcomes of surgical emergencies are associated with promptness of the appropriate surgical intervention. However, delayed presentation of surgical patients is common in most developing countries. Delays commonly occur due to transfer of patients between facilities. The aim of the present study was to assess the effect of delays in treatment caused by inter‐facility transfers of patients presenting with surgical emergencies as measured by objective and subjective parameters.MethodsWe prospectively collected data on all patients presenting with an acute surgical emergency at Aga Khan University Hospital (AKUH). Information regarding demographics, social class, reason and number of transfers, and distance traveled were collected. Patients were categorized into two groups, those transferred to AKUH from another facility (transferred) and direct arrivals (non‐transfers). Differences between presenting physiological parameters, vital statistics, and management were tested between the two groups by the chi square and t tests.ResultsNinety‐nine patients were included, 49 (49.5 %) patients having been transferred from another facility. The most common reason for transfer was “lack of satisfactory surgical care.” There were significant differences in presenting pulse, oxygen saturation, respiratory rate, fluid for resuscitation, glasgow coma scale, and revised trauma score (all p values <0.001) between transferred and non‐transferred patients. In 56 patients there was a further delay in admission, and the most common reason was bed availability, followed by financial constraints. Three patients were shifted out of the hospital due to lack of ventilator, and 14 patients left against medical advice due to financial limitations. One patient died.ConclusionsInter‐facility transfer of patients with surgical emergencies is common. These patients arrive with deranged physiology which requires complex and prolonged hospital care. Patients who cannot afford treatment are most vulnerable to transfers and delays.
Estimation of dieback process caused by herbivory in an endangered root‐sprouting shrub species, Paliurus ramosissimus (Lour.) Poir., using a shoot‐dynamics matrix model
Authors: Ishihama Fumiko , Fujii Shinji , Yamamoto Kazuhiko , Takada Takenori 
Published: October 2013

AbstractMortality, a critical parameter for population dynamics, is difficult to measure in long‐lived trees or clonal herbaceous species because of the extremely low frequency of deaths. A model based on shoot recruitment would be helpful to estimate the population fate of species without a sufficient number of observed deaths. Existing matrix models are applicable to the dynamics of physiologically independent shoots, but not to physiologically dependent ones. We developed a shoot‐dynamics model for plants with physiologically‐dependent shoots, and used the model to estimate the effects of herbivory and conservation measures on the dynamics of a long‐lived, shoot‐sprouting shrub species, Paliurus ramosissimus (Rhamnaceae). Two populations of the endangered shrub have been severely damaged by herbivory by sika deer. The damage was mainly to new sprouting shoots. No deaths of individual plants were observed during an 8‐year survey, and we could not estimate mortality. Thus, prediction of population dynamics based on births and deaths of individuals was impossible. Because P. ramosissimus is a shoot‐sprouting species, we instead estimated the decline of individuals using a shoot‐dynamics model. Using this model, we estimated the time to an 80 % decrease in shoot number per individual in the two populations at 37.8 and 37.2 years. These lengths suggest an immediate need for conservation measures to prevent herbivory even though no death of any individual was observed in the field survey. The estimated recovery times from the herbivory damage were 28.7 and 29.2 years if herbivory of new shoots is completely prevented by conservation measure.
Genetische Diagnostik der amyotrophen Lateralsklerose
Authors: Weydt P. , Hübers A. , Ludolph A.C. , Weishaupt J.H. 
Published: October 2013

Zusammenfassung
Die amyotrophe Lateralsklerose (ALS) ist eine schnell fortschreitende Erkrankung, die mit einer Degeneration sowohl des 1. (kortikalen) als auch des 2. (spinalen und bulbären) motorischen Neurons einhergeht. Klinisch kommt es unter anderem zu fortschreitenden, sich kontinuierlich und systematisch ausbreitenden Paresen und Atrophien der quergestreiften Muskulatur. Die Genetik der ALS hat in den vergangenen Jahren mit der Entdeckung zahlreicher neuer ALS-Gene große Fortschritte gemacht. Neben dem seit langem bekannten Gen „superoxide dismutase 1“ (SOD1) kam als mittlerweile häufigstes ALS-Gen in kaukasischen Patienten unter anderem „ chromosome 9 open reading frame 72“ (C9ORF72) hinzu sowie die weniger häufigen Mutationen in „ TAR DNA binding protein“ (TARDBP) und „ fused in sarcoma“ (FUS). Darüber hinaus wurden mehrere seltene ALS-Gene entdeckt, die von großem zellbiologischem und funktionellem Interesse sind. Die schnell angestiegene Zahl der bekannten ALS-Gene sowie die vergrößerte phänotypische Vielfalt hat die genetische Diagnostik und Beratung auf dem Gebiet der ALS deutlich komplexer werden lassen.
RENEGOTIATION OF THE WTO AGREEMENT ON AGRICULTURE: ACCOMMODATING THE NEW BIG ISSUES
Authors: Cardwell Michael , Smith Fiona 
Published: October 2013

AbstractThe WTO Agreement on Agriculture was designed to maximize trade flows at a time of surplus agricultural production. It required Members to open markets and to reduce domestic and export subsidies. Proposals for reform in the Doha Round negotiations largely adopt the same pattern. Yet, as surplus is replaced by shortage, Members are increasingly concerned about food security and the impact of agriculture on climate change. And contemporary agricultural policies crystallize around ‘sustainable intensification’, where domestic production is promoted, but not at the expense of future production. This article suggests that, although both the Agreement on Agriculture and the Doha Round proposals do provide some scope for measures to address this new policy paradigm, there are instances where they may work actively against it.
Development of microsatellite markers in Protoparmeliopsis muralis (lichenized Ascomycete) – a common lichen species
Authors: GUZOW-KRZEMIŃSKA Beata , STOCKER-WÖRGÖTTER Elfie 
Published: October 2013

AbstractLichen-forming fungi are symbiotic organisms forming a thallus with autotrophic green algae and/or cyanobacteria. Protoparmeliopsis muralis (Schreb.) Choisy is a green-algal lichen-forming fungus associating with Trebouxia photobionts. It is known as one of the most successful urban lichens in the world. In this paper, the development of microsatellite markers specific for the mycobiont of Protoparmeliopsis muralis is reported. In order to avoid algal contaminations, the pure mycobiont culture was obtained and subsequently used for DNA isolation. For DNA enrichment, the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) method was applied. Of the 380 clones sequenced, 62 contained repeats. In total, 38 primer pairs were designed and tested, and finally 7 primer pairs were polymorphic based on 21 specimens of P. muralis.
New crustose Teloschistaceae in Central Europe
Authors: VONDRÁK Jan , FROLOV Ivan , ŘÍHA Pavel , HROUZEK Pavel , PALICE Zdeněk , NADYEINA Olga , HALICI Gökhan , KHODOSOVTSEV Alexander , ROUX Claude 
Published: October 2013

AbstractCentral Europe in general is poor in Teloschistaceae lichen crusts (Caloplaca s. lat.). Diversity of these lichens is increased by the occurrence of some Arctic, Mediterranean and continental species, which are here close to the limits of their range. Examples include:
1)Caloplaca interfulgens, previously known from arid territories of northern Africa and western Asia, is recorded, surprisingly, from Austria, Czech Republic, Germany, Slovakia and southern Russia. In Central Europe, it is restricted to scattered xerothermic limestone outcrops.2)Caloplaca scabrosa, previously known only from Svalbard, is recorded from the Sudetes in the Czech Republic. It is similar to, but not conspecific with, C. furfuracea. Its diagnostic characters include a blastidiate thallus and the presence of atranorin. Our results show that atranorin is absent in the majority of taxa related to C. furfuracea with only two exceptions: the sample from Eastern Carpathians, here called C. aff. scabrosa, and in one Sudetan sample identified as C. crenularia.3)Caloplaca emilii, newly described below, is closely related to the Mediterranean C. areolata. We consider C. emilii a Mediterranean species rarely occurring in higher latitudes in Austria, the Czech Republic and Germany. It is distinguished from C. areolata mainly by the presence of vegetative diaspores (blastidia); a possible role of blastidia in the distribution pattern of C. emilii is discussed below. Status of the names Caloplaca areolata, C. isidiigera and C. spalatensisis, formerly used for the new taxon, is clarified.4)Caloplaca molariformis, newly described below, belongs to the Pyrenodesmia group (a lineage of Caloplaca without anthraquinones). It is a continental species, frequently collected on limestone or lime-rich tuffs in steppes or deserts in Turkey, Iran, western Kazakhstan and southern Russia, and is also known from eastern Ukraine and southern Slovakia. Caloplaca molariformis is characterized by its thick thallus with fungal and algal tissues arranged in high stacks.5)Caloplaca substerilis, newly described below, is distinguished from the closely related C. ulcerosa by its endophloeodal or minutely squamulose thallus with soralia formed in bark crevices or on margins of squamules. While C. ulcerosa has a maritime distribution in Europe, C. substerilis is typically a continental species. North American continental lichens called “C. ulcerosa” are phylogenetically closer and more similar to C. substerilis.The positions within Teloschistaceae of the taxa considered are demonstrated by ITS phylogenies. The distributions of C. areolata, C. emilii and C. interfulgens are mapped. The new species are fully described using more than a hundred phenotype characters, and diagnostic characters are indicated separately.
A reappraisal of Masonhalea (Parmeliaceae, Lecanorales) based on molecular and morphological data
Authors: NELSEN Matthew P. , THELL Arne , LEAVITT Steven D. , HAMPTON-MILLER Celia J. , LUMBSCH H. Thorsten 
Published: October 2013

AbstractPrevious studies have identified a close relationship between the monospecific Masonhalea richardsonii and Tuckermannopsis inermis. However, formal taxonomic changes were postponed until existing sequence data could be confirmed. Here we validate these data and discuss the transfer of T. inermis to Masonhalea (made by Lumbsch et al. in Thell & Moberg 2011), consider the morphological, anatomical and biogeographic similarities and differences between these two taxa. The two Masonhalea species both produce lateral apothecia, marginal pycnidia, a layer of cortical tissue beneath the pycnidial wall and bacillariform conidia.
Genetic diversity of the lichen-forming alga,Diplosphaera chodatii, in North America and Europe
Authors: FONTAINE Kyle M. , STOCKER-WÖRGÖTTER Elfie , BOOTH Tom , PIERCEY-NORMORE Michele D. 
Published: October 2013

AbstractDermatocarpon luridumis a subaquatic lichen which is distributed within temperate climatic zones around the world. It colonizes rock substrata along the shoreline of lakes and rivers of watersheds that regularly experience water level fluctuations. The mycobiont produces perithecia with small, simple spores that are thought to be wind dispersed. The photobiont,Diplosphaera chodatii, occurs both free-living and lichenized but little is known about its distribution and dispersal. The goal of this study was to compare the population structure of the photobiont from lakes and rivers in central North America with those of Europe. Specimens were collected in Manitoba, Canada and Austria. Population structure of the algal symbiont was assessed using the internal transcribed spacer (ITS) of ribosomal DNA (rDNA) and actin gene sequences. Results showed that genetic diversity and gene flow was high within local populations, but gene flow was low between continental populations. Low levels of gene flow between the most distant populations support the isolation-by-distance theory. The photobiont on both continents is also reported to be the photobiont for other lichen species contributing to photobiont availability forD. luridum.