bluuebunny/crossref_metadata_2025_split huggingface dataset:
Particle image velocimetry (PIV) study of rotating cylindrical filters for animal cell perfusion processes
Authors: Figueredo‐Cardero Alvio , Chico Ernesto , Castilho Leda , de Andrade Medronho Ricardo 
Published: August 2012

AbstractIn the present work, the main fluid flow features inside a rotating cylindrical filtration (RCF) system used as external cell retention device for animal cell perfusion processes were investigated using particle image velocimetry (PIV). The motivation behind this work was to provide experimental fluid dynamic data for such turbulent flow using a high‐permeability filter, given the lack of information about this system in the literature. The results shown herein gave evidence that, at the boundary between the filter mesh and the fluid, a slip velocity condition in the tangential direction does exist, which had not been reported in the literature so far. In the RCF system tested, this accounted for a fluid velocity 10% lower than that of the filter tip, which could be important for the cake formation kinetics during filtration. Evidence confirming the existence of Taylor vortices under conditions of turbulent flow and high permeability, typical of animal cell perfusion RCF systems, was obtained. Second‐order turbulence statistics were successfully calculated. The radial behavior of the second‐order turbulent moments revealed that turbulence in this system is highly anisotropic, which is relevant for performing numerical simulations of this system. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012
Enhanced phytase production from Achromobacter sp. PB‐01 using wheat bran as substrate: Prospective application for animal feed
Authors: Kumar Piyush , Chamoli Shivangi , Agrawal Sanjeev 
Published: August 2012

AbstractThis article deals with the optimization of the various parameters for production of phytase using Achromobacter sp. PB‐01 in submerged fermentation (SmF). A semisynthetic medium containing ingredients of phytase screening media (PSM) supplemented with 2% (w/v) sucrose, 1% (w/v) peptone, and 10% (w/v) wheat bran was found to be the best production medium among the various combinations tried. Among various surfactants added to SmF, Triton X‐100 (0.1%) exhibited a 16% increase in phytase activity. An overall 11.2 fold enhancement in enzyme activity (0.79 U/mL→8.84 U/mL) was attained when SmF was carried out using 0.5% (v/v) inoculum of a 15 h old culture of Achromobacter sp. PB‐01 at an initial pH of 5.5, temperature 30°C and allowed to grow for 48 h. Presence of accessory hydrolytic enzymes in the crude extract further added value as feed additive by mediating efficient degradation of non‐starch polysaccharides (NSP). In addition, we also investigated the efficacy of phytase on different agro‐industrial residues using in vitro experiments that simulated the conditions of the digestive tract. Results indicate that phytase from our source hydrolyze phytate efficiently with the concomitant liberation of inorganic phosphate, protein, reducing sugar, and calcium. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012
Assembly of Water‐Soluble, Dynamic, Covalent Container Molecules and Their Application in the Room‐Temperature Stabilization of Protoadamantene
Authors: Lin Zhihua , Sun Junling , Efremovska Bisera , Warmuth Ralf 
Published: August 2012

AbstractThe thermodynamically controlled reactions of water‐soluble tetraformylcavitand 2 with two equivalents of H2N(CH2)nNH2 (n=2–4) in the presence of a suitable templating guest give hemicarceplexes 1 a–c⋅guest, the yield of which depends on the match between size and shape of the guest and that of the inner phase. These hemicarceplexes are dynamic and dissociate upon addition of acid and reform upon basification. In water, they exchange guests through temporary hydrolysis of imine bonds. To test 1 b as molecular reaction flask, 3‐noradamantyldiazirine 6 was encapsulated and photolyzed at 350 nm to produce Bredt olefin protoadamantene 5 and 1‐noradamantyldiazomethane 8 in a 4:1 ratio. Encapsulated protoadamantene is stable for days at room temperature in (CD3)2SO/CD3CN (t1/2=5.5 days) and has a lifetime of several minutes in D2O.
Elucidation of the Active Conformation of Vancomycin Dimers with Antibacterial Activity against Vancomycin‐Resistant Bacteria
Authors: Nakamura Jun , Yamashiro Hidenori , Hayashi Sayaka , Yamamoto Mami , Miura Kenji , Xu Shu , Doi Takayuki , Maki Hideki , Yoshida Osamu , Arimoto Hirokazu 
Published: August 2012

AbstractCovalently linked vancomycin dimers have attracted a great deal of attention among researchers because of their enhanced antibacterial activity against vancomycin‐resistant strains. However, the lack of a clear insight into the mechanisms of action of these dimers hampers rational optimization of their antibacterial potency. Here, we describe the synthesis and antibacterial activity of novel vancomycin dimers with a constrained molecular conformation achieved by two tethers between vancomycin units. Conformational restriction is a useful strategy for studying the relationship between the molecular topology and biological activity of compounds. In this study, two vancomycin units were linked at three distinct positions of the glycopeptide (vancosamine residue (V), C terminus (C), and N terminus (N)) to form two types of novel vancomycin cyclic dimers. Active NC‐VV‐linked dimers with a stable conformation as indicated by molecular mechanics calculations selectively suppressed the peptidoglycan polymerization reaction of vancomycin‐resistant Staphylococcus aureus in vitro. In addition, double‐disk diffusion tests indicated that the antibacterial activity of these dimers against vancomycin‐resistant enterococci might arise from the inhibition of enzymes responsible for peptidoglycan polymerization. These findings provide a new insight into the biological targets of vancomycin dimers and the conformational requirements for efficient antibacterial activity against vancomycin‐resistant strains.
Competitive Assay for Theophylline Based on an Abasic Site‐Containing DNA Duplex Aptamer and a Fluorescent Ligand
Authors: Sato Yusuke , Zhang Yushuang , Nishizawa Seiichi , Seino Takehiro , Nakamura Kodai , Li Minjie , Teramae Norio 
Published: August 2012

AbstractA fluorescence assay for theophylline, one of the common drugs for acute and chronic asthmatic conditions, has been developed based on an abasic site‐containing DNA duplex aptamer (AP aptamer) in combination with an abasic site‐binding fluorescent ligand, riboflavin. The assay is based on the competitive binding of theophylline and riboflavin at the abasic (AP) site of the AP aptamer. In the absence of theophylline, riboflavin binds to the receptor nucleotide opposite the AP site, which leads to fluorescence quenching of the riboflavin. Upon addition of theophylline, competitive binding occurs between theophylline and riboflavin, which results in an effective fluorescence restoration due to release of riboflavin from the AP site. From an examination of the optimization of the AP aptamers, the complex of riboflavin with a 23‐mer AP aptamer (5′‐TCT GCG TCC AGX GCA ACG CAC AC‐3′/5′‐GTG TGC GTT GCC CTG GAC GCA GA‐3′; X: the AP site (Spacer C3, a propylene residue)) possessing cytosine as a receptor nucleotide was found to show a selective and effective fluorescence response to theophylline; the limit of detection for theophylline was 1.1 μM. Furthermore, fluorescence detection of theophylline was successfully demonstrated with high selectivity in serum samples by using the optimized AP aptamer and riboflavin.
Expanding the Scope of PNA‐Encoded Synthesis (PES): Mtt‐Protected PNA Fully Orthogonal to Fmoc Chemistry and a Broad Array of Robust Diversity‐Generating Reactions
Authors: Chouikhi Dalila , Ciobanu Mihai , Zambaldo Claudio , Duplan Vincent , Barluenga Sofia , Winssinger Nicolas 
Published: August 2012

AbstractNucleic acid‐encoded libraries are emerging as an attractive and highly miniaturized format for the rapid identification of protein ligands. An important criterion in the synthesis of nucleic acid encoded libraries is the scope of reactions that can be used to introduce molecular diversity and devise divergent pathways for diversity‐oriented synthesis (DOS). To date, the protecting group strategies that have been used in peptide nucleic acid (PNA) encoded synthesis (PES) have limited the choice of reactions used in the library synthesis to just a few prototypes. Herein, we describe the preparation of PNA monomers with a protecting group combination (Mtt/Boc) that is orthogonal to Fmoc‐based synthesis and compatible with a large palette of reactions that have been productively used in DOS (palladium cross‐couplings, metathesis, reductive amination, amidation, heterocycle formation, nucleophilic addition, conjugate additions, Pictet–Spengler cyclization). We incorporate γ‐modifications in the PNA backbone that are known to enhance hybridization and solubility. We demonstrate the robustness of this strategy with a library synthesis that is characterized by MALDI MS analysis at every step.
Additive Effects of Amines on Asymmetric Hydrogenation of Quinoxalines Catalyzed by Chiral Iridium Complexes
Authors: Nagano Takuto , Iimuro Atsuhiro , Schwenk Rino , Ohshima Takashi , Kita Yusuke , Togni Antonio , Mashima Kazushi 
Published: August 2012

AbstractThe additive effects of amines were realized in the asymmetric hydrogenation of 2‐phenylquinoxaline, and its derivatives, catalyzed by chiral cationic dinuclear triply halide‐bridged iridium complexes [{Ir(H)[diphosphine]}2(μ‐X)3]X (diphosphine=(S)‐2,2′‐bis(diphenylphosphino)‐1,1′‐binaphthyl [(S)‐BINAP], (S)‐5,5′‐bis(diphenylphosphino)‐4,4′‐bi‐1,3‐benzodioxole [(S)‐SEGPHOS], (S)‐5,5′‐bis(diphenylphosphino)‐2,2,2′,2′‐tetrafluoro‐4,4′‐bi‐1,3‐benzodioxole [(S)‐DIFLUORPHOS]; X=Cl, Br, I) to produce the corresponding 2‐aryl‐1,2,3,4‐tetrahydroquinoxalines. The additive effects of amines were investigated by solution dynamics studies of iridium complexes in the presence of N‐methyl‐p‐anisidine (MPA), which was determined to be the best amine additive for achievement of a high enantioselectivity of (S)‐2‐phenyl‐1,2,3,4‐tetrahydroquinoxaline, and by labeling experiments, which revealed a plausible mechanism comprised of two cycles. One catalytic cycle was less active and less enantioselective; it involved the substrate‐coordinated mononuclear complex [IrHCl2(2‐phenylquinoxaline){(S)‐BINAP}], which afforded half‐reduced product 3‐phenyl‐1,2‐dihydroquinoxaline. A poorly enantioselective disproportionation of this half‐reduced product afforded (S)‐2‐phenyl‐1,2,3,4‐tetrahydroquinoxaline. The other cycle involved a more active hydride–amide catalyst, derived from amine‐coordinated mononuclear complex [IrCl2H(MPA){(S)‐BINAP}], which functioned to reduce 2‐phenylquinoxaline to (S)‐2‐phenyl‐1,2,3,4‐tetrahydroquinoxaline with high enantioselectivity. Based on the proposed mechanism, an IrI–JOSIPHOS (JOSIPHOS=(R)‐1‐[(Sp)‐2‐(dicyclohexylphosphino)ferrocenylethyl]diphenylphosphine) catalyst in the presence of amine additive resulted in the highest enantioselectivity for the asymmetric hydrogenation of 2‐phenylquinoxaline. Interestingly, the reaction rate and enantioselectivity were gradually increased during the reaction by a positive‐feedback effect from the product amines.
Retro‐Diels–Alder Approach to the Synthesis of π‐Expanded Azuliporphyrins and Their Porphyrinoid Aromaticity
Authors: Okujima Tetsuo , Kikkawa Tasuku , Nakano Haruyuki , Kubota Hiroshi , Fukugami Nobumasa , Ono Noboru , Yamada Hiroko , Uno Hidemitsu 
Published: August 2012

AbstractBicyclo[2.2.2]octadiene (BCOD) fused azuliporphyrins were synthesized by 3+1 porphyrin synthesis of azulitripyrranes with diformylpyrroles. Subsequent retro‐Diels–Alder reaction of the BCOD‐fused azuliporphyrins afforded azulibenzo‐, azulidibenzo‐, and azulitribenzoporphyrins 1–5. NMR and UV/Vis spectra, as well as nucleus‐independent chemical shift (NICS) calculations revealed that 1–5 and their diprotonated dications exhibit relatively low porphyrinoid aromaticity, which was dependent on the position and number of fused benzene rings present.
Palladium‐Catalyzed Oxidative Carbocyclizations
Authors: Deng Youqian , Persson Andreas K. Å. , Bäckvall Jan‐E. 
Published: August 2012

AbstractPalladium‐catalyzed oxidative carbon–carbon bond‐forming annulations, that is, carbocyclization reactions, have recently emerged as efficient and atom‐economical routes to carbo‐ and heterocycles, whereby less functionalized substrates and fewer synthetic steps are needed to obtain a target molecule compared with traditional non‐oxidative carbon–carbon bond‐forming reactions. In this review, the synthetic efforts in palladium‐catalyzed oxidative carbocyclization reactions are summarized.
Investigations into the Formation and Stability of Cationic Rhodium Diphosphane η6‐Arene Complexes
Authors: Fischer Christian , Thede Richard , Drexler Hans‐Joachim , König Anja , Baumann Wolfgang , Heller Detlef 
Published: August 2012

AbstractRhodium–η6‐arene complexes can be generated in the presence of arenes following the hydrogenation of the diolefin in rhodium catalyst precursors of the type [Rh(PP*)(diolefin)]X (PP*=chelating diphosphane, X=noncoordinating anion). In this paper we report the characterization of such arene complexes with the ligands DuPhos, dipamp, dppe, Tangphos, dppf, and diop by means of NMR spectroscopy (31P, 103Rh) and X‐ray analysis. A procedure that follows the approach to equilibrium as a function of time monitored by using an UV/Vis diode array was used to determine 20 stability constants. Analyses were accomplished directly from the spectra by either a numeric and/or a new analytic solution of the underlying system of differential equations. Additionally thermodynamic parameters were determined in the temperature range between 278 and 318 K.
Shapes and Internal Dynamics of the 1:1 Adducts of Ammonia with trans and gauche Ethanol: A Rotational Study
Authors: Giuliano Barbara M. , Favero Laura B. , Maris Assimo , Caminati Walther 
Published: August 2012

AbstractTwo 1:1 adducts of ammonia with ethanol have been characterized by using pulsed‐jet FT microwave spectroscopy. They are formed with two different (trans and gauche), stable conformers of ethanol. Several internal‐dynamics effects are reflected in the features of the rotational spectra. The trans complex shows the tunneling effects owing to internal rotation of both ammonia and the methyl group. The rotational transitions of the gauche species exhibit a small splitting that is related to tunneling through the potential‐energy barrier between the two equivalent minima.
HOXB7 promotes invasion and predicts survival in pancreatic adenocarcinoma
Authors: Nguyen Kovochich Anne , Arensman Michael , Lay Anna R. , Rao Nagesh P. , Donahue Timothy , Li Xinmin , French Samuel W. , Dawson David W. 
Published: August 2012

AbstractBACKGROUND:The homeobox gene HOXB7 is overexpressed across a range of cancers and promotes tumorigenesis through varying effects on proliferation, survival, invasion, and angiogenesis. Although published microarray data suggest HOXB7 is overexpressed in pancreatic ductal adenocarcinoma (PDAC), its function in pancreatic cancer has not been studied.METHODS:HOXB7 message and protein levels were examined in PDAC cell lines and patient samples, as well as in normal pancreas. HOXB7 protein expression in patient tumors was determined by immunohistochemistry and correlated with clinicopathologic factors and survival. The impact of HOXB7 on cell proliferation, growth, and invasion was assessed by knockdown and overexpression in PDAC cell lines. Candidate genes whose expression levels were altered following HOXB7 knockdown were determined by microarray analysis.RESULTS:HOXB7 message and protein levels were significantly elevated in PDAC cell lines and patient tumor samples relative to normal pancreas. Evaluation of a tissue microarray of 145 resected PDACs found high HOXB7 protein expression was correlated with lymph node metastasis (P = .034) and an independent predictor of worse overall survival in multivariate analysis (hazard ratio = 1.56, 95% confidence interval = 1.02‐2.39). HOXB7 knockdown or overexpression in PDAC cell lines resulted in decreased or increased invasion, respectively, without influencing proliferation or cell viability.CONCLUSIONS:HOXB7 is frequently overexpressed in PDAC, specifically promotes invasive phenotype, and is associated with lymph node metastasis and worse survival outcome. HOXB7 and its downstream targets may represent novel clinical biomarkers or targets of therapy for inhibiting the invasive and metastatic capacity of PDAC. Cancer 2013. © 2012 American Cancer Society.
A phase 2 clinical trial of sequential neoadjuvant chemotherapy with ifosfamide, doxorubicin, and gemcitabine followed by cisplatin, gemcitabine, and ifosfamide in locally advanced urothelial cancer
Authors: Siefker‐Radtke Arlene O. , Dinney Colin P. , Shen Yu , Williams Dallas L. , Kamat Ashish M. , Grossman H. Barton , Millikan Randall E. 
Published: August 2012

AbstractBACKGROUND:Neoadjuvant chemotherapy improves the survival of patients with high‐risk urothelial cancer. However, the lack of curative alternatives to cisplatin‐based chemotherapy is limiting for patients with neuropathy or hearing loss. Sequential chemotherapy also has not been well studied in the neoadjuvant setting. The authors explored sequential neoadjuvant ifosfamide‐based chemotherapy in a patient cohort at high risk of noncurative cystectomy.METHODS:Patients with muscle‐invasive cancer and lymphovascular invasion, hydronephrosis, clinical T3b and T4a (cT3b‐4a) disease (defined as a 3‐dimensional mass on examination under anesthetic or invasion into local organs), micropapillary tumors, or upper tract disease received 3 cycles of combined ifosfamide, doxorubicin, and gemcitabine followed by 4 cycles of combined cisplatin, gemcitabine, and ifosfamide. The primary endpoint was downstaging to pT1N0M0 disease or lower.RESULTS:At a median follow‐up of 85.3 months, the 5‐year overall survival (OS) and disease‐specific survival (DSS) rates for all 65 patients were 63% and 68%, respectively (95% confidence interval: 5‐year OS rate, 0.52%‐0.76%; 5‐year DSS rate, 0.58%‐0.81%). Pathologic downstaging to pT1N0 disease or lower occurred in 50% of patients who underwent cystectomy and in 60% of patients who underwent nephroureterectomy and was correlated with the 5‐year OS rate (pT1N0 disease or lower, 87%; pT2‐pT3aN0 disease, 67%; and pT3b disease or higher or lymph node‐negative disease, 27%; P ≤ .001 for pT1 or lower vs pT2 or higher). Variant histology was associated with an inferior 5‐year DSS rate (50% vs 83% in pure transitional cell carcinoma; P = .02). The most frequent grade 3 toxicities were infection (38%), febrile neutropenia (22%), and mucositis (18%). There were 3 grade 4 toxicities (myocardial infarction, thrombocytopenia, and vomiting) and 1 grade 5 toxicity in a patient who refused antibiotics for pneumonia.CONCLUSIONS:Sequential therapy was active and maintained the historic expectation of achieving a cure. The current results strongly reinforced previous experience suggesting that pathologic downstaging to pT1N0 disease or less is a useful surrogate for eventual cure in patients with urothelial cancer. Cancer 2013. © 2012 American Cancer Society.
A randomized phase 2 study of temozolomide and bevacizumab or nab‐paclitaxel, carboplatin, and bevacizumab in patients with unresectable stage IV melanoma
Authors: Kottschade Lisa A. , Suman Vera J. , Perez Domingo G. , McWilliams Robert R. , Kaur Judith S. , Amatruda Thomas T. , Geoffroy Francois J. , Gross Howard M. , Cohen Peter A. , Jaslowski Anthony J. , Kosel Matthew L. , Markovic Svetomir N. 
Published: August 2012

AbstractBACKGROUND:Increasing evidence shows chemotherapy in combination with vascular endothelial growth factor (VEGF) inhibition is a clinically active therapy for patients with metastatic melanoma (MM).METHODS:A phase 2 trial was conducted in chemotherapy‐naive patients with unresectable stage IV MM who were randomized to temozolomide (200 mg/m2 on days 1 through 5) and bevacizumab (10 mg/kg intravenously on days 1 and 15) every 28 days (Regimen TB) or nab‐paclitaxel (100 mg/m2, or 80 mg/m2 post‐addendum 5 secondary to toxicity, on days 1, 8, and 15), bevacizumab (10 mg/kg on days 1 and 15), and carboplatin (area under the curve [AUC] 6 on day 1, or AUC 5 post‐addendum 5) every 28 days (Regimen ABC). Accrual goal was 41 patients per regimen. The primary aim of this study was to estimate progression‐free survival rate at 6 months (PFS6) in each regimen. A regimen would be considered promising if its PFS6 rate was > 60%.RESULTS:Ninety‐three eligible patients (42 TB and 51 ABC) were enrolled. The majority of patients had M1c disease (20 TB and 26 ABC). The median PFS and overall survival times with ABC were 6.7 months and 13.9 months, respectively. Median PFS time and median overall survival with TB were 3.8 months and 12.3 months, respectively. The most common severe toxicities (≥ grade 3) in both regimens were cytopenias, fatigue, and thrombosis. Among the first 41 patients enrolled onto each regimen, PFS6 rate was 32.8% (95% confidence interval: 21.1%‐51.2%) for TB and 56.1% (90% confidence interval: 44.7%‐70.4%) for ABC.CONCLUSIONS:The addition of bevacizumab to nab‐paclitaxel and carboplatin shows promising activity despite tolerability issues. Cancer 2013. © 2012 American Cancer Society.
Representation of the visual field in the primary visual area of the marmoset monkey: Magnification factors, point‐image size, and proportionality to retinal ganglion cell density
Authors: Chaplin Tristan A. , Yu Hsin‐Hao , Rosa Marcello G.P. 
Published: August 2012

AbstractThe primary visual area (V1) forms a systematic map of the visual field, in which adjacent cell clusters represent adjacent points of visual space. A precise quantification of this map is key to understanding the anatomical relationships between neurons located in different stations of the visual pathway, as well as the neural bases of visual performance in different regions of the visual field. We used computational methods to quantify the visual topography of V1 in the marmoset (Callithrix jacchus), a small diurnal monkey. The receptive fields of neurons throughout V1 were mapped in two anesthetized animals using electrophysiological recordings. Following histological reconstruction, precise 3D reconstructions of the V1 surface and recording sites were generated. We found that the areal magnification factor (MA) decreases with eccentricity following a function that has the same slope as that observed in larger diurnal primates, including macaque, squirrel, and capuchin monkeys, and humans. However, there was no systematic relationship between MA and polar angle. Despite individual variation in the shape of V1, the relationship between MA and eccentricity was preserved across cases. Comparison between V1 and the retinal ganglion cell density demonstrated preferential magnification of central space in the cortex. The size of the cortical compartment activated by a punctiform stimulus decreased from the foveal representation towards the peripheral representation. Nonetheless, the relationship between the receptive field sizes of V1 cells and the density of ganglion cells suggested that each V1 cell receives information from a similar number of retinal neurons, throughout the visual field. J. Comp. Neurol. 521:1001–1019, 2013. © 2012 Wiley Periodicals, Inc.