bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemistry Crowdsourcing and Open Notebook Science
Authors: Bradley Jean-Claude , Owens Kevin , Williams Antony 
Published: January 2008

AbstractThis is a pre-proposal written for the NSF program CDI (Cyber-Enabled Discovery and Innovation) in Jan 2008.The current system of dissemination of scientific data and knowledge is far less efficient than it needs to be to facilitate improved collaborative science, especially considering current publication vehicles and infrastructure. There is a growing movement promoting more Open Science with the belief that a more transparent scientific process can perform far more effectively. The logical extension of this concept is full transparency - exposing a researcher's complete record of progress to the public in near real time. Not only will such a process enable ongoing data sharing it also provides an opportunity to develop collaborative communities of scientists and, at the conclusion of data acquisition, can enable communal extraction of conclusions when necessary. We have named this approach Open Notebook Science and have demonstrated its implementation and feasibility with the UsefulChem project, started in the summer of 2005, with the aim of synthesizing novel anti-malarial compounds. Our system currently uses free hosted services using general blog and wiki functions to facilitate replication across any scientific domains. These services are not chemically intelligent and are limited to text and graphic based data sharing only. For Open Notebook Chemistry the ability to intelligently manipulate, manage and search chemical structures and associated data is necessary and we have demonstrated proof of concept capabilities by integrating with the ChemSpider service, a free access online database managing chemical structures and focused on developing a structure centric community for chemists. This work will require the development of a chemically intelligent software platform to extend the capabilities of both the blog and the wiki environment for managing Open Notebook Science. The exposure of raw experimental procedures and data in a semantically rich format will enable the participation of both human and autonomous agents in the process of scientific discovery. This phenomenon of spontaneous group intelligence, referred to as "Crowdsourcing", has proven valuable in several contexts. Already, productive collaborations have been forged within the UsefulChem project with groups from Indiana University, Nanyang Technological University, the National Cancer Institute and UC San Francisco.
Elevated plasma arginase-1 does not affect plasma arginine in patients undergoing liver resection
Authors: van de Poll Marcel C. G. , Hanssen Sebastiaan J. P. , Berbée Maaike , Deutz Nicolaas E. P. , Monbaliu Diethard , Buurman Wim A. , Dejong Cornelis H. C. 
Published: January 2008

Arginine is an important substrate in health and disease. It is a commonly held view that arginase-1 release from injured erythrocytes and hepatocytes leads to arginine breakdown; however, the true relationship between plasma arginase-1 concentration and activity has remained unaddressed. In the present study, blood was sampled from patients undergoing liver resection, a known cause of hepatocyte injury and arginase-1 release, to determine arginase-1, arginine and ornithine plasma levels. Arginase activity was assessed in vitro by measuring changes in arginine and ornithine plasma levels during incubation of plasma and whole-blood samples at 37 °C. Arginase-1 plasma levels increased 8–10-fold during liver resection, whereas arginine and ornithine levels remained unchanged. In accordance with these in vivo findings, arginine and ornithine levels remained unchanged in plasma incubated at 37 °C irrespective of the arginase-1 concentration. In contrast, arginine plasma levels in whole blood decreased significantly during incubation, with ornithine increasing stoichiometrically. These changes were irrespective of arginase-1 plasma levels and were explained by arginase activity present in intact erythrocytes. Next, plasma samples with 1000-fold normal arginase-1 concentrations were obtained from patients undergoing cadaveric liver transplantation. A significant decrease in arginine plasma levels occurred in vivo and in vitro. In contrast with commonly held views, moderately increased arginase-1 plasma levels do not affect plasma arginine. Very high plasma arginase-1 levels are required to induce potential clinically relevant effects.
The Unification of Electromagnetism with the Weak Force
Authors: Langacker Paul , Mann Alfred K. 
Published: January 2008

The year 1983 marked the end of a particularly noteworthy decade in the development of elementaryparticle physics. Between 1973 and 1983 there were three accomplishments of special, perhaps historic, importance:
▹ The theoretical and experimental unification of the forces that govern all of the phenomena of both electromagnetism and the weak interactions.
▹ The recognition that the strongly interacting particles (nucleons, mesons and other hadrons) are in fact made of still smaller entities, now known as quarks, and the development of a tentative theory of the force between the quarks.
▹ The identification of three almost identical (except for mass) families of elementary “particles,” each family consisting of two quarks, one charged lepton (the electron, the muon or the tau) and a neutrino.
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony
Authors: Sakarya Onur , Kosik Kenneth S. , Oakley Todd H. 
Published: January 2008

Abstract
Motivation: Gene duplications and losses (GDLs) are important events in genome evolution. They result in expansion or contraction of gene families, with a likely role in phenotypic evolution. As more genomes become available and their annotations are improved, software programs capable of rapidly and accurately identifying the content of ancestral genomes and the timings of GDLs become necessary to understand the unique evolution of each lineage.
Results: We report EvolMAP, a new algorithm and software that utilizes a species tree-based gene clustering method to join all-to-all symmetrical similarity comparisons of multiple gene sets in order to infer the gene composition of multiple ancestral genomes. The algorithm further uses Dollo parsimony-based comparison of the inferred ancestral genes to pinpoint the timings of GDLs onto evolutionary intervals marked by speciation events. Using EvolMAP, first we analyzed the expansion of four families of G-protein coupled receptors (GPCRs) within animal lineages. Additional to demonstrating the unique expansion tree for each family, results also show that the ancestral eumetazoan genome contained many fewer GPCRs than modern animals, and these families expanded through concurrent lineage-specific duplications. Second, we analyzed the history of GDLs in mammalian genomes by comparing seven proteomes. In agreement with previous studies, we report that the mammalian gene family sizes have changed drastically through their evolution. Interestingly, although we identified a potential source of duplication for 75% of the gained genes, remaining 25% did not have clear-cut sources, revealing thousands of genes that have likely gained their distinct sequence identities within the descent of mammals.
Availability: Query server, source code and executable are available at http://kosik-web.mcdb.ucsb.edu/evolmap/index.htm
Contact: kosik@lifesci.ucsb.edu, oakley@lifesci.ucsb.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The ModFOLD server for the quality assessment of protein structural models
Authors: McGuffin Liam J. 
Published: January 2008

Abstract
Summary: The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single or multiple models. Secondly ModFOLDclust, which is a more intensive method that carries out clustering of multiple models and provides per-residue local quality assessment.
Availability: http://www.biocentre.rdg.ac.uk/bioinformatics/ModFOLD/
Contact: l.j.mcguffin@reading.ac.uk
Coimmunopurification of Phosphorylated Bacterial- and Plant-Type Phosphoenolpyruvate Carboxylases with the Plastidial Pyruvate Dehydrogenase Complex from Developing Castor Oil Seeds
Authors: Uhrig R. Glen , O'Leary Brendan , Spang H. Elizabeth , MacDonald Justin A. , She Yi-Min , Plaxton William C. 
Published: January 2008

Abstract
The phosphoenolpyruvate carboxylase (PEPC) interactome of developing castor oil seed (COS; Ricinus communis) endosperm was assessed using coimmunopurification (co-IP) followed by proteomic analysis. Earlier studies suggested that immunologically unrelated 107-kD plant-type PEPCs (p107/PTPC) and 118-kD bacterial-type PEPCs (p118/BTPC) are subunits of an unusual 910-kD hetero-octameric class 2 PEPC complex of developing COS. The current results confirm that a tight physical interaction occurs between p118 and p107 because p118 quantitatively coimmunopurified with p107 following elution of COS extracts through an anti-p107-IgG immunoaffinity column. No PEPC activity or immunoreactive PEPC polypeptides were detected in the corresponding flow-through fractions. Although BTPCs lack the N-terminal phosphorylation motif characteristic of PTPCs, Pro-Q Diamond phosphoprotein staining, immunoblotting with phospho-serine (Ser)/threonine Akt substrate IgG, and phosphate-affinity PAGE established that coimmunopurified p118 was multiphosphorylated at unique Ser and/or threonine residues. Tandem mass spectrometric analysis of an endoproteinase Lys-C p118 peptide digest demonstrated that Ser-425 is subject to in vivo proline-directed phosphorylation. The co-IP of p118 with p107 did not appear to be influenced by their phosphorylation status. Because p118 phosphorylation was unchanged 48 h following elimination of photosynthate supply due to COS depodding, the signaling mechanisms responsible for photosynthate-dependent p107 phosphorylation differ from those controlling p118's in vivo phosphorylation. A 110-kD PTPC coimmunopurified with p118 and p107 when depodded COS was used. The plastidial pyruvate dehydrogenase complex (PDCpl) was identified as a novel PEPC interactor. Thus, a putative metabolon involving PEPC and PDCpl could function to channel carbon from phosphoenolpyruvate to acetyl-coenzyme A and/or to recycle CO2 from PDCpl to PEPC.
Characterization of Pea Aphid Resistance in Medicago truncatula
Authors: Gao Ling-Ling , Klingler John P. , Anderson Jonathan P. , Edwards Owain R. , Singh Karam B. 
Published: January 2008

Abstract
To achieve a thorough understanding of plant-aphid interactions, it is necessary to investigate in detail both the plant and insect side of the interaction. The pea aphid (PA; Acyrthosiphon pisum) has been selected by an international consortium as the model species for genetics and genomics studies, and the model legume Medicago truncatula is a host of this aphid. In this study, we identified resistance to PA in a M. truncatula line, ‘Jester’, with well-characterized resistance to a closely related aphid, the bluegreen aphid (BGA; Acyrthosiphon kondoi). The biology of resistance to the two aphid species shared similarity, with resistance in both cases occurring at the level of the phloem, requiring an intact plant and involving a combination of antixenosis, antibiosis, and plant tolerance. In addition, PA resistance cosegregated in ‘Jester’ with a single dominant gene for BGA resistance. These results raised the possibility that both resistances may be mediated by the same mechanism. This was not supported by the results of gene induction studies, and resistance induced by BGA had no effect on PA feeding. Moreover, different genetic backgrounds containing a BGA resistance gene from the same resistance donor differ in resistance to PA. These results suggest that distinct mechanisms are involved in resistance to these two aphid species. Resistance to PA and BGA in the same genetic background in M. truncatula makes this plant an attractive model for the study of both plant and aphid components of resistant and susceptible plant-aphid interactions.
Modulation of the Hormone Setting byRhodococcus fasciansResults in EctopicKNOXActivation in Arabidopsis
Authors: Depuydt Stephen , Doležal Karel , Van Lijsebettens Mieke , Moritz Thomas , Holsters Marcelle , Vereecke Danny 
Published: January 2008

AbstractThe biotrophic actinomycete Rhodococcus fascians has a profound impact on plant development and a common aspect of the symptomatology is the deformation of infected leaves. In Arabidopsis (Arabidopsis thaliana), the serrated leaf margins formed upon infection resemble the leaf phenotype of transgenic plants with ectopic expression of KNOTTED-like homeobox (KNOX) genes. Through transcript profiling, we demonstrate that class-I KNOX genes are transcribed in symptomatic leaves. Functional analysis revealed that BREVIPEDICELLUS/KNOTTED-LIKE1 and mainly SHOOT MERISTEMLESS were essential for the observed leaf dissection. However, these results also positioned the KNOX genes downstream in the signaling cascade triggered by R. fascians infection. The much faster activation of ARABIDOPSIS RESPONSE REGULATOR5 and the establishment of homeostatic and feedback mechanisms to control cytokinin (CK) levels support the overrepresentation of this hormone in infected plants due to the secretion by the pathogen, thereby placing the CK response high up in the cascade. Hormone measurements show a net decrease of tested CKs, indicating either that secretion by the bacterium and degradation by the plant are in balance, or, as suggested by the strong reaction of 35S:CKX plants, that other CKs are at play. At early time points of the interaction, activation of gibberellin 2-oxidase presumably installs a local hormonal setting favorable for meristematic activity that provokes leaf serrations. The results are discussed in the context of symptom development, evasion of plant defense, and the establishment of a specific niche by R. fascians.
Tris(Bipyridine) Ruthenium(II): An Efficient Detector of Excited Species Generated by Chemiluminescent Processes*
Authors: Grijalba Mercedes Toledo , Nantes Lseli Lourenço , Cilento Giuseppe , Quina Frank H. 
Published: January 2008

ABSTRACTIn systems that are known to generate electronically excited species, the tris(bipyridine) ruthenium(II) cation, Ru(bpy)32+, ion is found to be an efficient, chemically stable, emissive energy acceptor for probing excited state formation. The chemiexcitation system employed was the thermolysis of tetramethyldioxetane. The system employed for enzymatic generation of excited species was the horseradish peroxidase‐catalyzed oxidation of appropriate substrates such as isobutyraldehyde, phenylacetal‐dehyde and indoleacetic acid. The versatility of the Ru(bpy)32+ ion is exemplified by its capacity to detect excited state formation in both chemical and enzymatic systems and in homogeneous and microheterogeneous media. The long wavelength emission and chemical stability of Ru(bpy)32+ facilitate quantitative studies of the sensi‐tization process. Possible routes leading to excitation of the Ru(bpy)32+ ion by the chemi‐ or enzyme‐generated excited species include electronic energy transfer and electron transfer‐induced luminescence.
Primary Quantum Yield and Volume Change of Phytochrome‐A Phototransformation Determined by Laser‐Induced Optoacoustic Spectroscopy*
Authors: Gensch Thomas , Churio M. Sandra , Braslavsky Silvia E. , Schaffner Kurt 
Published: January 2008

ABSTRACTThe primary quantum yield, Φ1700, for the photoconver‐sion of the red‐absorbing form of phytochrome, Pr, to the set of primary intermediates, Ii700, was redetermined by laser‐induced optoacoustic spectroscopy at very low excitation laser fluences. The Ii700 value obtained is in the range of ΦPfr reported for the complete phototransformation Pr→ Pfr (J. M. Kelly and C. Lagarias, 1985, Biochemistry24, 4003–6010). An energy level of ca 150 kJ/ mol was found for the intermediates Ii700, i.e. ca 85% of the 0–0 level of Pr. Furthermore, a molecular expansion of 7 mL/mol (equivalent to 11 Å3/molecule) was determined for the Pr→ Ii700 transformation. It reflects the protein reorganization induced by the geometrical pho‐toisomerization of the chromophore, which results in changes of bonding interactions, in particular between the chromophore and its protein surrounding.
Determining Counterion Exchange Selectivities at Micelle Surfaces from Fluorescence Decay Measurements*
Authors: Okano Laura T. , Alonso Elena O. , Waissbluth L. Oscar L. , Quina Frank H. 
Published: January 2008

ABSTRACTA method for determining counterion exchange selectivities at the surface of ionic micelles from time‐resolved fluorescence quenching measurements is developed. This method is employed to determine selectivity coefficients for thiosulfate/chloride exchange at the surface of cati‐onic hexadecyltrimethylammonium chloride micelles (KTS/CI, = 1.1 ± 0.4) and for copper (II)/sodium exchange at the surface of anionic sodium dodecyl sulfate micelles (KCu/Na= 1.3 ± 0.3). In both cases, the selectivity coefficients are found to be independent of detergent and added salt concentration.
Formation of Nitrosyl Hemoglobin and Nitrotyrosine during Murine Leishmaniasis*
Authors: Giorgio Selma , Linares Edlaine , Capurro Margareth de L. , de Bianchi Antonio G. , Augusto Ohara 
Published: January 2008

ABSTRACTPeroxynitrite, the potent oxidant formed by the fast reaction between nitric oxide and superoxide anion, has been suggested to be the reactive intermediate responsible for some of the pathologies associated with an overproduction of nitric oxide. In this report, we demonstrate that both nitric oxide and peroxynitrite are formed during infection of the susceptible mouse strain, BALBk, with Leishmania amazonensis. Nitric oxide was detected as the nitrosyl hemoglobin complex by EPR analysis of blood drawn from mice at35, 64 and 148 days of infection. The levels of nitrosyl hemoglobin complex increased with disease evolution, which in the murine model used is characterized by skin lesions, ulceration and visceral‐ization of the parasites. Peroxynitrite formation was inferred from immunoreaction of homogenates obtained from footpad lesions in the late stages of the infection with anti‐nitrotyrosine antibody; homogenates from parasites drawn from the lesions were also immunoreactive, although to a lesser extent. Analysis of protein homogenates by gel electrophoresis and western blots suggests that peroxynitrite may degrade proteins in vivo, in addition to nitrating them. The results demonstrate that peroxynitrite is formed during murine leishmaniasis and may play a role in the aggravation of the disease.
Effect of Anions from the Hofmeister Series and Urea on the Binding of the Charged and Uncharged Forms of the Local Anesthetic Tetracaine to Zwitterionic Micelles*
Authors: Ferreira Graziela S. S. , Périgo Daniel M. , Politi Mario J. , Schreier Shirley 
Published: January 2008

ABSTRACTIt is widely known that ions in the aqueous phase affect the binding of charged solutes to membranes. Here we report the effect of ions and urea on the interaction of both the charged and uncharged forms of the local anesthetic tetracaine (TTC, an aminoester derivative of ben‐zoic acid) to zwitterionic micelles. Binding was monitored by the increase in TTC fluorescence. Shifts in the emission wavelength maximum (δmax) indicated that the anesthetic was located in an environment of lower polarity. The neutral form of TTC bound to micelles to a larger extent than the protonated form, in agreement with results found for lipid bilayers (Boulanger, Leitch, Schreier and Smith, Can. J. Biochem. 58, 986–995, 1980). When ions from the Hofmeister series and urea were compared in their ability to affect the partitioning of the anesthetic, binding of both the charged and uncharged forms was found to increase upon addition of SO42– and CI− but was seen to decrease in the presence of SCN−, CIO4−‐ and urea. Solubility measurements revealed that the solubility of uncharged TTC increases in solutions containing the additives in the following order: SO42– < CI− < CIO4−‐ < dilute buffer < SCN− < urea. Spin label EPR spectra indicated that, except for CIO4−‐, the ions had little effect on micellar structure. Static light scattering measurements corroborated this result indicating a large increase in micellar molecular weight in the presence of CIO4−‐ and lesser increases for CI.‐ and SCN−. The results show that, besides affecting the binding of ionic species through an electrostatic mechanism, ions also act by altering water structure and, as a consequence, the water solubility and the tendency to partition into the less polar micellar environment of polar charged or uncharged small organic solutes such as the benzoic acid ester derivative. Moreover, evidence suggests that the ions bind directly to the zwitterionic polar groups of the micelles, leading to changes in structure and size.
Preparation and Evaluation of Arylazide‐Substituted Pyridine Adenine Dinucleotides for Photoaffinity Labeling Experiments
Authors: Liu Wenqiu , Gaines Michelle , Bao Rong , Clifford Jacquelynn , Li Yuzhou 
Published: January 2008

ABSTRACTTwo pyridine‐modified NAD’analogs, 3–(3‐azido benzo‐yl) pyridine adenine dinucleotide 1 and N‐(3‐azido‐5‐car‐boxyl) phenyl nicotinamide adenine dinucleotide 2 have been prepared and evaluated for photoaffinity labeling experiments. The syntheses were accomplished via a mammalian NADase‐catalyzed base exchange reaction. The new NAD+ analogs retained the carbonyl or carhox‐amido functional group at the 3 position of the pyridine ring. The analog 1 is the first pyridine‐modified azido derivative of NAD+ that has shown coenzyme activity in a stereospecific hydride transfer reaction catalyzed by a dehydrogenase. Both NAD+ analogs have shown potential for the study of active sites of NAD+‐utilizing enzymes.
Accelerated Degradation of the D2 Protein of Photosystem II Under Ultraviolet Radiation
Authors: Jansen Marcel A. K. , Greenberg Bruce M. , Edelman Marvin , Mattoo Autar K. , Gaba Victor 
Published: January 2008

ABSTRACTThe D2 protein of photosystem II is relatively stable in vivo under photosynthetic active radiation, but its degradation accelerates under UVB radiation. Little is known about accelerated D2 protein degradation. We characterized wavelength dependence and sensitivity toward photosystem II inhibitors. The in vivo D2 degradation spectrum resembles the pattern for the rapidly turning over D1 protein of photosystem II, with rates being maximal in the UVB region. We propose that D2 degradation, like D1 degradation, is activated by distinct photosensitizers in the UVB and visible regions of the spectrum. In both wavelength regions, photosystem II inhibitors that are known to be targeted to the D1 protein affect D2 degradation. This suggests that degradation of the two proteins is coupled, D2 degradation being influenced by events occurring at the QB niche on the D1 protein.