bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multilevel ocean mixed layer model resolving the diurnal cycle: Development and validation
Authors: Ling Tiejun , Xu Min , Liang Xin‐Zhong , Wang Julian X. L. , Noh Yign 
Published: August 2015

AbstractThe representation of transient air‐sea interactions is critical to the prediction of the sea surface temperature diurnal cycle and daily variability. This study develops a multilevel upper ocean model to more realistically resolve these interactions. The model is based on the one‐dimensional turbulence kinetic energy closure developed by Noh et al. [2011], and incorporates new numerical techniques and improved schemes for model physics. The primary improvements include: (1) a surface momentum flux penetration scheme to better depict velocity shear in the diurnal mixed layer; (2) a solar penetration scheme to improve the penetration of visible and near‐infrared bands of solar radiation into the mixed layer ocean; (3) a scheme to resolve the cool‐skin and warm‐layer effects on sea skin temperature; (4) a vertical grid stretch scheme to achieve higher near‐surface resolution with fewer vertical levels; (5) a trapezoidal time integration scheme for flexible time steps; (6) a relaxation term of the previous daily mean difference between observed and modeled sea surface temperature. According to the numerical experiments based on the TOGA‐COARE IMET mooring buoy data and the validation by observations from the National Data Buoy Center, NOAA, the results indicate that the new upper ocean mixed layer model improves the simulation of the diurnal cycle of SST and sea skin temperature, especially in amplitude.
Desulfospira
Authors: Liesack Werner , Finster Kai 
Published: August 2015

De.sul.fo.spi' ra. L. pref.defrom; L. n.sulfursulfur; Gr. n.spiraa coil; M.L. fem. n.Desulfospiraa sulfate‐reducing coil.Desulfobacterota / Desulfobacteria / Desulfobacterales / Desulfobacteraceae / DesulfospiraCurved, often spirilloid cells 0.7–0.8 × 1–2 μm. Nonmotile. Gram negative. Endospores not formed. Anaerobic, having a respiratory type of metabolism. Fermentative growth does not occur. Catalase positive.Chemoorganotrophic or chemoautotrophic, using a wide range of organic compounds as electron donors and also as carbon sources, e.g., fatty acids, dicarboxylic acids, oxoacids, hydroxyacids, or compatible solutes;these substrates are completely oxidized to CO2. Maleate and proline are used as electron donors. Aromatic compounds and sugars are not utilized.Sulfate, sulfite, thiosulfate, and S0serve as terminal electron acceptorsand are reduced to H2S. Na+and Mg2+are required for growth. Biotin is required for growth. Cells containc‐type cytochromes and menaquinones with seven isoprenoid units. Desulfoviridin is not present. Isolated from iron‐rich, oxidized, marine surface sediment.The mol%G+C of the DNA is: 50.Type species:Desulfospira joergenseniiFinster, Liesack and Tindall 1997e, 1274 (Effective publication: Finster, Liesack and Tindall 1997c, 207.)
Pseudoalteromonas
Authors: Bowman John P. , McMeekin Thomas A. 
Published: August 2015

Pseu.do.al.te.ro.mo' nas. Gr. adj.pseudesfalse; M.L. n.Alteromonasthe genusAlteromonas; M.L. n.PseudoalteromonasfalseAlteromonas.Proteobacteria / Gammaproteobacteria / Alteromonadales / Alteromonadaceae / PseudoalteromonasStraight rods, approximately 1 × 2–3 µm, occurring singly or in pairs. Do not form spores or cysts. Do not accumulate poly‐β‐hydroxybutyrate. Nonbioluminescent.Gram negative. Motile by means of a single polar flagellum, either unsheathed or sheathed. Colonies are nonpigmented or pigmented.Chemoheterotrophic. Aerobic, possessing a strictly respiratory type of metabolismwith oxygen as the terminal electron acceptor. No growth occurs anaerobically. A constitutive arginine dihydrolase system is usually absent. One species (P. denitrificans) is able to denitrify. Utilize a range of carbon substrates, including carbohydrates, alcohols, organic acids, and amino acids. Form gelatinase and lipase. Ammonia serves as a nitrogen source. Amino acids may be required by some strains for growth.Requires Na+ions for growth. Mostly psychrotolerant, with growth occurring between 0 and 40°C. Several species produce autotoxic antibiotic compounds. Isolated from seawater, sediment, sea ice, surfaces of stones, marine algae, marine invertebrates, and salted foods. The major quinone is ubiquinone‐8 (Q‐8). Major fatty acids are C16:0, C16:1 ω7c, C17:1 ω8c, and C18:1 ω7c. Member of the orderAlteromonadales, familyAlteromonadaceae, in theGammaproteobacteria.The mol%G+C of the DNA is: 38–48 (Tm).Type species:Pseudoalteromonas haloplanktis(Zobell and Upham 1944) Gauthier, Gauthier and Christen 1995a, 759 (Alteromonas haloplanktis(Zobell and Upham 1944) Reichelt and Baumann 1973a, 438; “Vibrio haloplanktis” Zobell and Upham 1944, 261.)
Thiocapsa
Authors: Imhoff Johannes F. , Caumette Pierre 
Published: August 2015

Thi.o.cap' sa. Gr. n.thiossulfur; L. n.capsabox; M.L. fem. n.Thiocapsasulfur box.Proteobacteria / Gammaproteobacteria / Chromatiales / Chromatiaceae / ThiocapsaCells spherical, 1.0–3.0 µm in diameter, diplococci before multiplication by binary fission,nonmotile. Tetrads may be formed after consecutive division in two perpendicular planes. Individual cells surrounded by a strong slime capsule and may contain gas vesicles. Gram negative, belong to theGammaproteobacteria, and have internalphotosynthetic membranes of vesicular typecontaining the photosynthetic pigments bacteriochlorophyllaand carotenoids.The mol%G+C of the DNA is: 63.3–66.3.Type species:Thiocapsa roseopersicinaWinogradsky 1888, 84.
Calymmatobacterium
Authors: Brownell George H. 
Published: August 2015

Ca.lym.ma.to.bac.te' ri.um. Gr. n.calymmamantle, sheath; Gr. dim. neut. n.bakteriona small rod; M.L. neut. n.Calymmatobacteriumthe sheathed rodlet.Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / CalymmatobacteriumPleomorphic rods, 0.5–1.5 × 1.0–2.0 μm, with rounded ends. Occur singly or in clusters.The cells exhibit single or bipolar condensation of chromatin. Capsules are present. Gram negative. Nonmotile. The exudate from infected tissues, when stained by Wright's stain or by Giemsa stain, demonstratescharacteristic intracellular organisms in the cytoplasm of large mononuclear phagocytes(“Donovan bodies”). Can be cultivatedin vivoin the yolk sac of embryonated chicken eggs, peripheral blood mononuclear cells, and human epithelial (HEp‐2) monolayers, orin vitroon special egg yolk‐containing media; has not been reproducibly cultivated in bacteriologic media. Optimum growth temperature, 37°C. Pathogenic for humans, causingDonovanosis(granuloma inguinale).The mol%G+C of the DNA is: not known.Type species:Calymmatobacterium granulomatisAragão and Vianna 1913, 221.
Pantoea
Authors: Grimont Patrick A.D. , Grimont Francine 
Published: August 2015

Pan.toe'a. Gr. adj.pantoiosof all sorts and sources; M.L. fem. n.Pantoea[bacteria] from diverse [geographical and ecological] sources.Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / PantoeaStraight rods, 0.5–1.3 × 1.0–3.0 µm. Nonencapsulated. Nonsporeforming. Some strains form symplasmata.Most strains are motile and are peritrichously flagellated. Gram negative. Colonies on nutrient agar are smooth, translucent, and more or less convex with entire margins or heterogenous in consistency and adhering to the agar.Colonies are yellow, pale beige to pale reddish yellow, or nonpigmented. Facultatively anaerobic. Oxidase negative. Glucose dehydrogenase and gluconate dehydrogenase are producedand are active without an added cofactor. Acid is produced from the fermentation ofD‐fructose,D‐galactose, trehalose, andD‐ribose. Most strains areVoges–Proskauer positive. Lysine and ornithine are not decarboxylated. Urease negative. Pectate is not degraded. H2S is not produced from thiosulfate. Optimum temperature 30°C.N‐acetyl‐D‐glucosamine,L‐aspartate,D‐fructose,D‐galactose,D‐gluconate,D‐glucosamine,D‐glucose,L‐glutamate, glycerol,D‐mannose,D‐ribose, andD‐trehalose are utilized as sole sources of carbon and energy. 5‐Aminovalerate, benzoate, caprate, caprylate,m‐coumarate, ethanolamine, gentisate, glutarate, histamine, 3‐hydroxybenzoate, 4‐hydroxybenzoate, 3‐hydroxybutyrate, itaconate, maltitol,D‐melezitose, 1‐O‐methyl‐α‐D‐glucoside, palatinose, 3‐phenylpropionate, propionate,L‐sorbose, tricarballylate, tryptamine,D‐turanose, andL‐tyrosine are not utilized as sole sources of carbon and energy.Pantoeaspp. are isolated from plants, seeds, fruits, soils, water, and from humans (urine, blood, wounds, internal organs), and animals. Some strains are (or have been thought to be) phytopathogenic.The mol%G+C of the DNA is: 49.7–60.6.Type species:Pantoea agglomerans(Ewing and Fife 1975) Gavini Mergaert, Beji, Mielcarek, Izard, Kersters and De Ley 1989b, 343 (Enterobacter agglomerans(Beijerinck 1888) Ewing and Fife 1972, 10.)
Wigglesworthia
Authors: Aksoy Serap 
Published: August 2015

Wigg.les.worth' i.a. M.L. fem. n.Wigglesworthianamed after the parasitologist W.B. Wigglesworth.Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / WigglesworthiaObligate intracellular, bacteriome‐tissue associated, primary endosymbionts of tsetse flies. In the adult fly, the bacteria lie free in the cytoplasm of differentiated epithelial cells, bacteriocytes, which form the U‐shaped bacteriome organ (previously referred to as mycetome) in the anterior midgut (Figs. 1A, 1B). The endosymbionts are rod shaped (2–4 × 8–10 µm) with a typical Gram‐negative cell wall and inner membrane structure, lack flagella (Fig. 1C). The cells appear to divide by binary fission. The bacteria are obligate intracellular organisms, as their experimental elimination from tsetse by procaryotic‐specific antibiotic treatment, by lysozyme, or with symbiont‐specific antibodies provided in the blood meal results in retarded growth of the insect and a decrease in egg production, causing loss of the ability of these aposymbiotic hosts to reproduce (Hill et al., 1973; Nogge, 1976, 1978, 1980). In addition toWigglesworthia, tsetse harbors a secondary (S)‐symbiont in midgut tissue. The specific function(s) ofWigglesworthiaand S‐symbionts are not known; however, since the ability to reproduce can be partially restored when the aposymbiotic tsetse receive a blood meal that is supplemented with B‐complex vitamins (thiamine, pantothenic acid, pyridoxine, folic acid, and biotin), it is suggested that the gut‐tissue associated endosymbionts may play a role in metabolism that involves these compounds (Nogge, 1981). The recently sequenced genome ofWigglesworthiashows the presence of various biosynthetic pathways for vitamin metabolites (Akman et al., 2002). The 16S rDNA‐based phylogeny ofWigglesworthiacharacterized from eight different tsetse species displays concordance with their insect host species, indicating an ancient association for this bacterium with an ancestral tsetse that has subsequently radiated along with the host insect species (Chen et al., 1999b). The bacterium is not present in the ovaries, but may be transmitted to the intrauterine larvae of tsetse via its milk‐gland secretions.Type species:Wigglesworthia glossinidiaAksoy 1995b, 849.
Neurocognitive decline in HIV patients is associated with ongoing T‐cell activation in the cerebrospinal fluid
Authors: Grauer Oliver M. , Reichelt Doris , Grüneberg Ute , Lohmann Hubertus , Schneider‐Hohendorf Tilman , Schulte‐Mecklenbeck Andreas , Gross Catharina C. , Meuth Sven G. , Wiendl Heinz , Husstedt Ingo W. 
Published: August 2015

AbstractObjectiveHIV‐associated neurocognitive disorders (HAND) remain a challenge despite combination antiretroviral therapy (cART). Immune cell activation has been implicated to play a major role in the development of HAND.MethodsIn this study, we used multicolor flow cytometry on peripheral blood (PB) and cerebrospinal fluid (CSF) samples to determine the expression of HLA‐DR and programmed death‐1 (PD‐1) on CD4+ and CD8+ T cells in patients with chronic HIV infection. Expression levels were correlated with HI virus load in PB and CSF, classification of HAND and severity of magnetic resonance imaging (MRI) signal abnormalities.ResultsIn a cohort of 86 HIV patients we found that the grade of neurocognitive impairment and the severity of MRI signal abnormalities correlated with decreasing CD4/CD8‐ratios and increased frequencies of HLA‐DR expressing CD4+ and CD8+ T cells reaching the highest values in the CSF samples. Importantly, HLA‐DR upregulation was still detectable in virologically suppressed HIV patients. Further, T‐cell subpopulation analysis of 40 HIV patients showed a significant shift from naïve to effector memory (EM) T cells that was negatively correlated with the grade of neurocognitive impairment in the PB samples. Moreover, PD‐1 was significantly increased on CD4+ memory T cells with highest levels on EM T cells in HIV patients with mild or severe neurocognitive alterations.InterpretationThe CD4/CD8 ratio, the proportion of EM to naïve T cells and the immune activation profile of CD4+ and CD8+ T cells in PB and CSF might be useful parameters to monitor the efficacy of cART and to identify HIV patients at risk of further neurocognitive deterioration.
Organocatalytic Enantioselective Synthesis of Polysubstituted Spirooxindoles using a Tandem Michael–Michael Reaction
Authors: Abbaraju Santhi , Ramireddy Naresh , Rana Nirmal K. , Arman Hadi , Zhao John C.‐G. 
Published: August 2015

AbstractA highly efficient stereoselective method for the synthesis of functionalized spirooxindole derivatives with four contiguous stereogenic centers, including two adjacent quaternary stereogenic centers, was realized through an organocatalytic tandem Michael–Michael reaction. By employing a quinidine‐derived thiourea organocatalyst, the reaction between (E)‐2‐cyano‐2‐(2‐oxo‐1‐tritylindolin‐3‐ylidene)acetates and (E)‐1‐alkyl‐6‐nitro‐hex‐2‐en‐1‐ones yields the desired spirooxindole products in good yields (up to 90%) and with excellent stereoselectivities (up to 95:5 dr and 98% ee).magnified image
Ruthenium‐Catalyzed Oxidative Annulation of 6‐Anilinopurines with Alkynes via CH Activation: Synthesis of Indole‐Substituted Purines/Purine Nucleosides
Authors: Allu Srinivasarao , Kumara Swamy K. C. 
Published: August 2015

AbstractIndole‐substituted purine nucleobases have been synthesized by Ru‐catalyzed oxidative annulation of 6‐anilinopurines with internal alkynes that involves CH activation. Unsymmetrical aryl(alkyl)alkynes led to high regioselectivity. The reaction was also successful with nucleosides by delivering unprotected indole‐substituted nucleosides. In the presence of [RuCl2(p‐cymene)]2 and copper(II) acetate hydrate [Cu(OAc)2⋅H2O], in some cases, we have observed two‐fold CH activation products that exhibit fluorescence. A ruthenacycle intermediate was characterized by crystallography, which suggests that the N‐1 nitrogen atom of the purine acts as a directing group for the present transformation.magnified image
Catalytic Cross‐Coupling of Vinyl Golds with Diazonium Salts under Photoredox and Thermal Conditions
Authors: Patil Dilip V. , Yun Hokeun , Shin Senghoon 
Published: August 2015

AbstractCatalytically generated vinyl gold complexes from tert‐butyl allenoates were found to undergo an efficient cross‐coupling with arenediazonium salts. The gold(I)‐gold(III) redox cycle can be accessed under two different conditions, i.e., visible‐light photoredox as well as a thermally induced radical chain pathway. The current C(sp2)C(sp2) cross‐coupling protocol that is catalytic in gold, would make available desirable structural diversity to the traditional cross‐coupling chemistry.magnified image
Direkte Umwandlung von Estern in Arene mit 1,5‐difunktionellen Organomagnesium‐Reagentien
Authors: Link Achim , Fischer Christian , Sparr Christof 
Published: August 2015

AbstractEs wird eine direkte defunktionalisierende Umwandlung von Carbonsäureestern in Arene unter Verwendung von 1,5‐difunktionellen Organomagnesium‐Reagentien beschrieben. Ausgehend von diversen Carbonsäureestern erlaubt diese effiziente und praktikable Methode die einstufige Herstellung von Benzol‐, Anthracen‐, Tetracen‐ und Pentacenderivaten. Der zweifache nukleophile Angriff des 1,5‐Organodimagnesium‐Reagens am Ester mit nachfolgender 1,4‐Eliminierung führt zu einer unmittelbaren [5+1]‐Bildung des aromatischen Ringes.
Stereoselektive, konfigurationserhaltende Domino‐Transmetallierung sekundärer Alkyllithiumverbindungen zu funktionalisierten, sekundären Alkylkupferreagentien
Authors: Moriya Kohei , Simon Meike , Mose Rasmus , Karaghiosoff Konstantin , Knochel Paul 
Published: August 2015

AbstractMithilfe zweier aufeinanderfolgender Transmetallierungen können funktionalisierte, sekundäre Alkylkupferverbindungen unter hoher Retention der Konfiguration aus funktionalisierten, sekundären Alkyllithiumverbindungen, gebildet durch einen I/Li‐Austausch aus dem entsprechenden sekundären Alkyliodid, hergestellt werden. Diese Alkylkupferderivate reagieren mit Elektrophilen, wie Alkinylestern, Säurechloriden, Allylchloriden, Ketalen, Ethylenoxid und 3‐Iodcyclopentanon unter hoher Retention der Konfiguration. Eine verwandte Transmetallierungssequenz mit MeMgI und LaCl3⋅2 LiCl ermöglicht eine konfigurationserhaltende Addition von sekundären Alkyllithiumverbindungen an Aceton. Der Einfluss des Lösungsmittels auf die Konfigurationsstabilität sekundärer Alkylzinkreagentien wird beschrieben.
An Isolable, Photoswitchable N‐Heterocyclic Carbene: On‐Demand Reversible Ammonia Activation
Authors: Teator Aaron J. , Tian Yuan , Chen Mu , Lee Jeehiun K. , Bielawski Christopher W. 
Published: August 2015

AbstractThe first isolable, photoswitchable N‐heterocyclic carbene was synthesized and found to undergo reversible electrocyclic isomerization upon successive exposure to UV and visible radiation. The UV‐induced ring closure afforded substantial changes to the electronic structure of the dithienylethene‐based NHC, as evidenced by changes in the corresponding UV/Vis absorption and 13C NMR spectra. Likewise, molecular orbital calculations revealed diminished electron density at the carbene nucleus upon photocyclization, consistent with the enhanced electrophilicity displayed by the ring‐closed form. The photoswitchable NHC was successfully switched between its ring‐opened and ring‐closed states with high fidelity over multiple cycles. Furthermore, the ring‐closed isomer was found to undergo facile NH bond activation, allowing for the controlled capture and release of ammonia upon cycling between its isomeric states.
Self‐Guided Supramolecular Cargo‐Loaded Nanomotors with Chemotactic Behavior towards Cells
Authors: Peng Fei , Tu Yingfeng , van Hest Jan C. M. , Wilson Daniela A. 
Published: August 2015

AbstractDelivery vehicles that are able to actively seek and precisely locate targeted tissues using concentration gradients of signaling molecules have hardly been explored. The directed movement toward specific cell types of cargo‐loaded polymeric nanomotors along a hydrogen peroxide concentration gradient (chemotaxis) is reported. Through self‐assembly, bowl‐shaped poly(ethylene glycol)‐b‐polystyrene nanomotors, or stomatocytes, were formed with platinum nanoparticles entrapped in the cavity while a model drug was encapsulated in the inner compartment. Directional movement of the stomatocytes in the presence of a fuel gradient (chemotaxis) was first demonstrated in both static and dynamic systems using glass channels and a microfluidic flow. The highly efficient response of these motors was subsequently shown by their directional and autonomous movement towards hydrogen peroxide secreting neutrophil cells.
On the Mechanisms of Hydrogen‐Atom Transfer from Water to the Heteronuclear Oxide Cluster [Ga2Mg2O5].+: Remarkable Electronic Structure Effects
Authors: Li Jilai , Zhou Shaodong , Wu Xiao‐Nan , Tang Shiya , Schlangen Maria , Schwarz Helmut 
Published: August 2015

AbstractMechanistic insight into the homolytic cleavage of the OH bond of water by the heteronuclear oxide cluster [Ga2Mg2O5].+ has been derived from state‐of‐the‐art gas‐phase experiments in conjunction with quantum chemical calculations. Three pathways have been identified computationally. In addition to the conventional hydrogen‐atom transfer (HAT) to the radical center of a bridging oxygen atom, two mechanistically distinct proton‐coupled electron‐transfer (PCET) processes have been identified. The energetically most favored path involves initial coordination of the incoming water ligand to a magnesium atom followed by an intramolecular proton transfer to the lone‐pair of the bridging oxygen atom. This step, which is accomplished by an electronic reorganization, generates two structurally equivalent OH groups either of which can be liberated, in agreement with labeling experiments.
Stereoselective Retentive Domino Transmetalations of Secondary Alkyllithium Compounds to Functionalized Secondary Alkylcopper Reagents
Authors: Moriya Kohei , Simon Meike , Mose Rasmus , Karaghiosoff Konstantin , Knochel Paul 
Published: August 2015

AbstractFunctionalized secondary alkyllithium reagents obtained by I/Li exchange from the corresponding secondary alkyl iodides undergo two successive transmetalations with Me3SiCH2ZnBr⋅LiBr and CuBr⋅2 LiCl⋅Me2S to provide functionalized secondary alkylcopper compounds with high retention of configuration. These alkylcopper derivatives react further with electrophiles such as alkynyl esters, acid chlorides, allylic chlorides, ketals, ethylene oxide, and 3‐iodocyclopentanone with high retention of configuration. A related sequence of transmetalations with MeMgI and LaCl3⋅2 LiCl allows a retentive addition of secondary alkyllithium reagents to acetone. The influence of the solvent on the configurational stability of secondary alkylzinc reagents is described.
Binding of caffeine with caffeic acid and chlorogenic acid using fluorescence quenching, UV/vis and FTIR spectroscopic techniques
Authors: Belay Abebe , Kim Hyung Kook , Hwang Yoon‐Hwae 
Published: August 2015

AbstractThe interactions of caffeine (CF) with chlorogenic acid (CGA) and caffeic acid (CFA) were investigated by fluorescence quenching, UV/vis and Fourier transform infrared (FTIR) spectroscopic techniques. The results of the study indicated that the fluorescence quenching between caffeine and hydroxycinnamic acids could be rationalized in terms of static quenching or the formation of non‐fluorescent CF–CFA and CF–CGA complexes. From fluorescence quenching spectral analysis, the quenching constant (KSV), quenching rate constant (kq), number of binding sites (n), thermodynamic properties and conformational changes of the interaction were determined. The quenching constants (KSV) between CF and CGA, CFA are 1.84 × 104 and 1.04 × 104 L/mol at 298 K and their binding site n is ~ 1. Thermodynamic parameters determined using the Van't Hoff equation indicated that hydrogen bonds and van der Waal's forces have a major role in the reaction of caffeine with caffeic acid and chlorogenic acid. The 3D fluorescence, UV/vis and FTIR spectra also showed that the binding of CF with CFA and CGA induces conformational changes in CFA and CGA. Copyright © 2015 John Wiley & Sons, Ltd.