bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simple Photogrammetry Rig for the Reliable Creation of 3D Artifact Models in the Field
Authors: Porter Samantha Thi , Roussel Morgan , Soressi Marie 
Published: February 2016

AbstractThree-dimensional (3D) artifact modeling is becoming an increasingly utilized tool in archaeology. In comparison with other methods of 3D scanning, photogrammetry has the benefits of being relatively inexpensive, mobile, and more adaptable for use in field conditions. As part of a larger project to document variability in lithic production systems across the Middle to Upper Paleolithic Transition in Western Europe, we developed a photography rig for the express purpose of systematically capturing images for the creation of 3D photogrammetric models. This low-cost rig greatly streamlines both the photo-taking and post-processing stages of model creation. Additional tips relating to the coating of difficult-to-capture objects with a mineral spray are also provided. Three-dimensional models of lithic cores from the Châtelperronian, Protoaurignacian, and Early Aurignacian levels of the site of Les Cottés (France) are presented as examples of the quality of model that can be produced using this system.
Immunologic response in treatment‐naïve HIV‐2‐infected patients: the IeDEA West Africa cohort
Authors: Balestre Eric , Ekouevi Didier Koumavi , Tchounga Boris , Eholie Serge Paul , Messou Eugène , Sawadogo Adrien , Thiébaut Rodolphe , May Margaret T , Sterne Jonathan Ac , Dabis François ,   the International Epidemiological Database to Evaluate AIDS (IeDEA) West Africa Collaboration
Published: February 2016

IntroductionResponse to antiretroviral therapy (ART) among individuals infected with HIV‐2 is poorly described. We compared the immunological response among patients treated with three nucleoside reverse‐transcriptase inhibitors (NRTIs) to boosted protease inhibitor (PI) and unboosted PI‐based regimens in West Africa.MethodsThis prospective cohort study enrolled treatment‐naïve HIV‐2‐infected patients within the International Epidemiological Databases to Evaluate AIDS collaboration in West Africa. We used mixed models to compare the CD4 count response to treatment over 12 months between regimens.ResultsOf 422 HIV‐2‐infected patients, 285 (67.5%) were treated with a boosted PI‐based regimen, 104 (24.6%) with an unboosted PI‐based regimen and 33 (7.8%) with three NRTIs. Treatment groups were comparable with regard to gender (54.5% female) and median age at ART initiation (45.3 years; interquartile range 38.3 to 51.8). Treatment groups differed by clinical stage (21.2%, 16.8% and 17.3% at CDC Stage C or World Health Organization Stage IV for the triple NRTI, boosted PI and unboosted PI groups, respectively, p=0.02), median length of follow‐up (12.9, 17.7 and 44.0 months for the triple NRTI, the boosted PI and the unboosted PI groups, respectively, p<0.001) and baseline median CD4 count (192, 173 and 129 cells/µl in the triple NRTI, the boosted PI and the unboosted PI‐based regimen groups, respectively, p=0.003). CD4 count recovery at 12 months was higher for patients treated with boosted PI‐based regimens than those treated with three NRTIs or with unboosted PI‐based regimens (191 cells/µl, 95% CI 142 to 241; 110 cells/µl, 95% CI 29 to 192; 133 cells/µl, 95% CI 80 to 186, respectively, p=0.004).ConclusionsIn this observational study using African data, boosted PI‐containing regimens had better immunological response compared to triple NRTI combinations and unboosted PI‐based regimens at 12 months. A randomized clinical trial is still required to determine the best initial regimen for treating HIV‐2 infected patients.
PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes
Authors: Gregor Ivan , Dröge Johannes , Schirmer Melanie , Quince Christopher , McHardy Alice C. 
Published: February 2016

Background.Metagenomics is an approach for characterizing environmental microbial communitiesin situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trainedPhyloPythiaSpackage, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have.Results.We have developedPhyloPythiaS+, a successor to ourPhyloPythia(S)software. The new (+) component performs the work previously done by the human expert.PhyloPythiaS+also includes a newk-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion.PhyloPythiaS+was compared toMEGAN,taxator-tk,Krakenand the genericPhyloPythiaSmodel. The results showed thatPhyloPythiaS+performs especially well for samples originating from novel environments in comparison to the other methods.Availability.PhyloPythiaS+in a virtual machine is available for installation under Windows, Unix systems or OS X on:https://github.com/algbioi/ppsp/wiki.
Remagnetization of lower Silurian black shale and insights into shale gas in the Sichuan Basin, south China
Authors: Zhang Yong , Jia Dong , Yin Hongwei , Liu Mancang , Xie Wuren , Wei Guoqi , Li Yongxiang 
Published: February 2016

AbstractThe organic‐rich lower Silurian shale of the Longmaxi Formation in the Sichuan Basin is the most important target for shale‐gas exploration in China. Most Paleozoic rocks of the Sichuan Basin have experienced extraordinarily pervasive remagnetizations. To test a hypothesized connection between hydrocarbon generation and remagnetization and contribute to shale‐gas exploration in the region, we undertook an integrated magnetic, geochemical, and petrographic study of 160 specimens from the shale. The results suggest that the shale contains a reliable remanent magnetization (Dec = 41.4°, Inc = 40.8°, and α95 = 6.8°). The magnetization predates tilting, and the paleopole plots close to the Late Triassic segment of the south China apparent polar wander path. The rock magnetic data and scanning electron microscope (SEM) observations confirm that framboidal magnetites carry the bulk of the magnetization, which suggest a Late Triassic chemical remanent magnetization in the shale. 87Sr/86Sr and magnetic analyses indicate that the amount of magnetite was unaffected by fluid alterations around the veins but is strongly covariant with the amount of total organic matter. Moreover, SEM observations reveal possible evidence of the replacement of pyrite framboids by magnetite, probably in the presence of organic acids. These analyses, therefore, suggest that the remagnetization was caused by organic maturation rather than orogenic fluids and that the maturation occurred in the Late Triassic. This timing of organic maturation has been validated by independent modeling studies and provides important constraints on the complex thermal history of the Longmaxi Shale as well as contributing to shale‐gas exploration efforts.
A two‐dimensional analytical model of petroleum vapor intrusion
Authors: Yao Yijun , Verginelli Iason , Suuberg Eric M. 
Published: February 2016

AbstractIn this study we present an analytical solution of a two‐dimensional petroleum vapor intrusion model, which incorporates a steady‐state diffusion‐dominated vapor transport in a homogeneous soil and piecewise first‐order aerobic biodegradation limited by oxygen availability. This new model can help practitioners to easily generate two‐dimensional soil gas concentration profiles for both hydrocarbons and oxygen and estimate hydrocarbon indoor air concentrations as a function of site‐specific conditions such as source strength and depth, reaction rate constant, soil characteristics and building features. The soil gas concentration profiles generated by this new model are shown in good agreement with three‐dimensional numerical simulations and two‐dimensional measured soil gas data from a field study. This implies that for cases involving diffusion dominated soil gas transport, steady state conditions and homogenous source and soil, this analytical model can be used as a fast and easy‐to‐use risk screening tool by replicating the results of 3‐D numerical simulations but with much less computational effort.
Untersuchung der Tyrosinase‐Expression in nicht‐metastatischen und metastatischen Melanomgeweben durch elektrochemische Rastersondenmikroskopie
Authors: Lin Tzu‐En , Bondarenko Alexandra , Lesch Andreas , Pick Horst , Cortés‐Salazar Fernando , Girault Hubert H. 
Published: February 2016

AbstractTrotz des enormen Fortschritts, der bei der Diagnose von Melanomen erzielt wurde, bleibt die zuverlässige Erkennung der verschiedenen Malignomstadien eine Herausforderung. Derzeitige Strategien setzen auf die optische Erfassung der Konzentration und räumlichen Verteilung spezifischer Biomarker. Neueste optische Methoden können allerdings durch Interferenzen mit Hintergrundfarben und durch Autofluoreszenz beeinflusst werden. Wir bewältigen diese Defizite hier unter Einsatz der elektrochemischen Rastersondenmikroskopie (SECM), um den prognostischen Indikator Tyrosinase (TyR) in nicht‐metastatischen und metastatischen Melanomgeweben mithilfe einer weichen Mikroelektrodensonde abzubilden. Das elektrochemische Auslesen der TyR‐Verteilung wurde durch das Adaptieren eines immunchemischen Verfahrens ermöglicht. Wir zeigen, dass die SECM die erwähnten Beschränkungen optischer Methoden übertreffen kann und bisher nicht gekannte Möglichkeiten für eine verbesserte Diagnose und das Verständnis der räumlichen Verteilung von TyR in verschiedenen Melanomstadien eröffnet.
A Unique Tryptophan C‐Prenyltransferase from the Kawaguchipeptin Biosynthetic Pathway
Authors: Parajuli Anirudra , Kwak Daniel H. , Dalponte Luca , Leikoski Niina , Galica Tomas , Umeobika Ugochukwu , Trembleau Laurent , Bent Andrew , Sivonen Kaarina , Wahlsten Matti , Wang Hao , Rizzi Ermanno , De Bellis Gianluca , Naismith James , Jaspars Marcel , Liu Xinyu , Houssen Wael , Fewer David Peter 
Published: February 2016

AbstractCyanobactins are a rapidly growing family of linear and cyclic peptides produced by cyanobacteria. Kawaguchipeptins A and B, two macrocyclic undecapeptides reported earlier from Microcystis aeruginosa NIES‐88, are shown to be products of the cyanobactin biosynthetic pathway. The 9 kb kawaguchipeptin (kgp) gene cluster was identified in a 5.26 Mb draft genome of Microcystis aeruginosa NIES‐88. We verified that this gene cluster is responsible for the production of the kawaguchipeptins through heterologous expression of the kgp gene cluster in Escherichia coli. The KgpF prenyltransferase was overexpressed and was shown to prenylate C‐3 of Trp residues in both linear and cyclic peptides in vitro. Our findings serve to further enhance the structural diversity of cyanobactins to include tryptophan‐prenylated cyclic peptides.
Quercetin‐2,4‐Dioxygenase aktiviert Sauerstoff in einem “side‐on” gebundenen O2‐Ni‐Komplex
Authors: Jeoung Jae‐Hun , Nianios Dimitrios , Fetzner Susanne , Dobbek Holger 
Published: February 2016

AbstractDie Quercetin‐2,4‐Dioxygenase (Quercetinase) von Streptomyces nutzt Nickel als Kofaktor, um die oxidative Spaltung des Flavonols Quercetin zu katalysieren. Wie dieses ungewöhnliche Metall im aktiven Zentrum die Katalyse und Sauerstoffaktivierung unterstützt, ist unklar. Wir stellen Kristallstrukturen der Ni‐Quercetinase in drei verschiedenen Zuständen vor, die direkte Einblicke geben, wie Quercetin und O2 am Ni2+‐Ion aktiviert werden. Ni2+ wird in allen drei Zuständen durch drei Histidin‐Reste und einen Glutamat‐Rest (E76) koordiniert. Wenn Quercetin bindet, ersetzt es einen Wasserliganden am Nickel und wird durch eine kurze Wasserstoffbrücke zu E76 stabilisiert, dessen Carboxylat‐Gruppe sich um 90° dreht. Diese Konformationsänderung schwächt die Wechselwirkung zwischen Nickel und dem verbleibenden Wasserliganden und bereitet eine Koordinationsstelle am Nickel zur Bindung von O2 vor. O2 bindet “side‐on” an das Ni2+‐Ion und steht senkrecht zu den C2‐C3‐ und C3‐C4‐Bindungen des Quercetins, die in den folgenden Schritten gespalten werden.
Atompräzise organometallische Zinkcluster
Authors: Banh Hung , Dilchert Katharina , Schulz Christine , Gemel Christian , Seidel Rüdiger W. , Gautier Régis , Kahlal Samia , Saillard Jean‐Yves , Fischer Roland A. 
Published: February 2016

AbstractEin Bottom‐up‐Synthesekonzept zur Herstellung metallorganischer Zinkcluster wird vorgestellt. Das Kation {[Zn10](Cp*)6Me}+ (1) wird aus der Reaktion von [Zn2Cp*2] mit [FeCp2][BAr4F] in Gegenwart von ZnMe2 erhalten. Die hohe Reaktivität von 1 erlaubt durch Zugabe geeigneter Liganden die gezielte Entfernung einzelner Zinkatome, was den Zugang zu den niedriger nuklearen Clustern {[Zn9](Cp*)6} (2) und {[Zn8](Cp*)5(tBuNC)3}+ (3) ermöglicht. Nach DFT‐Rechnungen können 1 und 2 als “closed‐shell”‐Verbindungen mit Elektronenmangel in Bezug auf die Wade‐Mingos‐Regeln beschrieben werden, da den gerüstbildenden apikalen ZnCp*‐Einheiten nicht drei, sondern nur ein Grenzorbital für Clusterbindungen zur Verfügung steht. So verhält sich Zink bei der Bildung von Metall‐Metall‐Bindungen flexibel: Es kann entweder nur ein Grenzorbital zur Verfügung stellen (wie Gruppe‐11‐Metalle), oder auch drei Grenzorbitale (wie Gruppe‐13‐Elemente).
Framework Cationization by Preemptive Coordination of Open Metal Sites for Anion‐Exchange Encapsulation of Nucleotides and Coenzymes
Authors: Zhao Xiang , Mao Chengyu , Luong Karen Tu , Lin Qipu , Zhai Quan‐Guo , Feng Pingyun , Bu Xianhui 
Published: February 2016

AbstractCationic frameworks can selectively trap anions through ion exchange, and have applications in ion chromatography and drug delivery. However, cationic frameworks are much rarer than anionic or neutral ones. Herein, we propose a concept, preemptive coordination (PC), for targeting positively charged metal–organic frameworks (P‐MOFs). PC refers to proactive blocking of metal coordination sites to preclude their occupation by neutralizing ligands such as OH−. We use 20 MOFs to show that this PC concept is an effective approach for developing P‐MOFs whose high stability, porosity, and anion‐exchange capability allow immobilization of anionic nucleotides and coenzymes, in addition to charge‐ and size‐selective capture or separation of organic dyes. The CO2 and C2H2 uptake capacity of 117.9 cm3 g−1 and 148.5 cm3 g−1, respectively, at 273 K and 1 atm, is exceptionally high among cationic framework materials.
Capturing HBCy2: Using N,O‐Chelated Complexes of Rhodium(I) and Iridium(I) for Chemoselective Hydroboration
Authors: Drover Marcus W. , Schafer Laurel L. , Love Jennifer A. 
Published: February 2016

Abstract1,3‐N,O‐chelated complexes of RhI and IrI cooperatively and reversibly stabilized the B−H bond of HBCy2 to afford six‐membered metallaheterocycles (M=Rh (7) or Ir (8)) having a δ‐[M]⋅⋅⋅H‐B agostic interaction. Treatment of these Shimoi‐type borane adducts 7 or 8 with both an aldehyde and an alkene resulted in chemoselective aldehyde hydroboration and reformation of the 1,3‐N,O‐chelated starting material. The observed chemoselectivity is inverted from that of free HBCy2, which is selective for alkene hydroboration.
A Telomerase‐Specific Doxorubicin‐Releasing Molecular Beacon for Cancer Theranostics
Authors: Ma Yi , Wang Zhaohui , Zhang Min , Han Zhihao , Chen Dan , Zhu Qiuyun , Gao Weidong , Qian Zhiyu , Gu Yueqing 
Published: February 2016

AbstractA molecular beacon‐based drug delivery system was designed for both detection of telomerase activity in living cells and telomerase‐triggered drug release for precise cancer treatment. This system is composed of a gold nanoparticle core densely packed with FITC‐labeled hairpin DNA sequences hybridized with telomerase primers. Molecules of the anticancer drug doxorubicin were intercalated into the stem region of the DNA sequence. The presence of telomerase will elongate the primers, leading to inner chain substitution followed by the release of the FITC fluorescence and the trapped doxorubicin. This molecular beacon could specifically distinguish tumor cells and normal cells based on telomerase activity, precisely release doxorubicin in response to telomerase activity in the tumor cells, and prevent toxicity to normal organs.
Charge‐Induced Unzipping of Isolated Proteins to a Defined Secondary Structure
Authors: González Flórez Ana Isabel , Mucha Eike , Ahn Doo‐Sik , Gewinner Sandy , Schöllkopf Wieland , Pagel Kevin , von Helden Gert 
Published: February 2016

AbstractHere we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N–H bend) bands can be found at positions that are typical for condensed‐phase proteins. For high charge states a new band appears, substantially red‐shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb‐driven transitions in secondary structures from mostly helical to extended C5‐type hydrogen‐bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments.
The Role of the Interface in Thin Film and Droplet Accelerated Reactions Studied by Competitive Substituent Effects
Authors: Li Yafeng , Yan Xin , Cooks R. Graham 
Published: February 2016

AbstractBased on a study of competitive substituent effects in a Claisen–Schmidt reaction, interfacial effects have been shown to play an important role in accelerated reactions that occur in thin films and droplets. A role for the interface in an accelerated C−C bond‐formation reaction between 6hydroxy‐1‐indanone and aromatic aldehydes is indicated by cooperative interactions between p‐methylbenzaldehyde and p‐nitrobenzaldehyde. Additional acceleration over that occurring in bulk reactions is seen for p‐methylbenzaldehyde, but only in the presence of p‐nitrobenzaldehyde. A decrease in the degree of acceleration is detected when the reaction is forced electrostatically to occur inside the thin film, and the interface is shown to participate in the accelerated reactions. This experimental evidence for interfacial thin film and droplet acceleration supports a recent model and builds on earlier work which locates molecules within evaporating droplets in electrosprays.
New Isolated‐Pentagon‐Rule and Skeletally Transformed Isomers of C100 Fullerene Identified by Structure Elucidation of their Chloro Derivatives
Authors: Wang Song , Yang Shangfeng , Kemnitz Erhard , Troyanov Sergey I. 
Published: February 2016

AbstractHigh‐temperature chlorination of C100 fullerene followed by X‐ray structure determination of the chloro derivatives enabled the identification of three isomers of C100 from the fullerene soot, specifically numbers 18, 425, and 417, which obey the isolated pentagon rule (IPR). Among them, isomers C1‐C100(425) and C2‐C100(18) afforded C1‐C100(425)Cl22 and C2‐C100(18)Cl28/30 compounds, respectively, which retain their IPR cage connectivities. In contrast, isomer C2v‐C100(417) gives Cs‐C100(417)Cl28 which undergoes a skeletal transformation by the loss of a C2 fragment, resulting in the formation of a nonclassical (NC) C1‐C98(NC)Cl26 with a heptagon in the carbon cage. Most probably, two nonclassical C1‐C100(NC)Cl18/22 chloro derivatives originate from the IPR isomer C1‐C100(382), although both C1‐C100(344) and even nonclassical C1‐C100(NC) can be also considered as the starting isomers.
Phase appearance during polymerization of fluorinated polyimide monomers and deposition into the microscopic‐scale trenches in supercritical carbon dioxide
Authors: Haruki Masashi , Oda Asuka , Wasada Atsuhiko , Hasegawa Yumi , Kihara Shin-ichi , Takishima Shigeki 
Published: February 2016

ABSTRACTThe phase appearance during the synthesis of fluorinated polyamic acid (PAA) from 2,2‐bis(3,4‐anhydrodicarboxyphenyl)‐hexafluoropropane (6FDA) and 2,2′‐bis(trifluoromethyl)−4,4′‐diaminobiphenyl (TFDB) in supercritical carbon dioxide (scCO2) was investigated to obtain fundamental data for the deposition of fluorinate polyimides (PI) using scCO2. All polymerizations were carried out at 30 MPa for 60 min. The experimental temperatures ranged from 50 to 70 °C, and each of the monomer concentrations ranged from 0.67 × 10−5 to 3.3 × 10−5 mol cm−3. The holding time of the transparent phases, which was the time from the beginning of the polymerization to the appearance of a turbid phase, was increased with either a decrease in the polymerization temperature or a decrease in the initial monomer concentration. The holding time of the fluorinated PAA was longer than that of the monomers of Kapton‐type PAA. The deposition of PI into the microscopic‐scale trenches that had formed on the silicon wafer was successful in scCO2. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43334.
On the inhomogeneous hydration kinetics and stiffness evolution of HNBR‐MgO reactive elastomer composites
Authors: Qu Meng , Lou Yucun , Han Dingzhi , Gewily Ahmed Amr , Robisson Agathe 
Published: February 2016

ABSTRACTSwellable elastomers are widely used in oilfield industry for sealing and zonal isolation applications. These materials need to sustain a large amount of external load after swelling. A newly developed reactive hydrogenated nitrile butadiene rubber (HNBR) based elastomer composite with magnesium oxide (MgO) as filler can swell and stiffen when exposed to water, which makes it ideal for oil field applications. However, both the filler hydration and the stiffness evolution inside this composite material are observed to be highly inhomogeneous even for samples on the length scale of millimeters. To understand this coupled diffusion‐hydration process is critical for applications of these materials with larger length scales. In this work, the hydration kinetics and stiffness evolution of the HNBR‐MgO composite are quantitatively studied on microscopic level. The extent of MgO hydration along the thickness of the sample are measured at the different stage of swelling. These results are used to determine the diffusion coefficient of water inside the composite. The diffusivity increases orders of magnitude after the filler hydration. In addition, the modulus change is non‐proportional to the degree of filler hydration as demonstrated by instrumented grid indentation on the hydrated composites. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43420.