bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging external knowledge on molecular interactions in classification methods for risk prediction of patients
Authors: Porzelius Christine , Johannes Marc , Binder Harald , Beißbarth Tim 
Published: February 2011

AbstractClassification of patients based on molecular markers, for example into different risk groups, is a modern field in medical research. The aim of this classification is often a better diagnosis or individualized therapy. The search for molecular markers often utilizes extremely high‐dimensional data sets (e.g. gene‐expression microarrays). However, in situations where the number of measured markers (genes) is intrinsically higher than the number of available patients, standard methods from statistical learning fail to deal correctly with this so‐called “curse of dimensionality”. Also feature or dimension reduction techniques based on statistical models promise only limited success. Several recent methods explore ideas of how to quantify and incorporate biological prior knowledge of molecular interactions and known cellular processes into the feature selection process. This article aims to give an overview of such current methods as well as the databases, where this external knowledge can be obtained from. For illustration, two recent methods are compared in detail, a feature selection approach for support vector machines as well as a boosting approach for regression models. As a practical example, data on patients with acute lymphoblastic leukemia are considered, where the binary endpoint “relapse within first year” should be predicted.
Study of robustness of filamentous bacteriophages for industrial applications
Authors: Branston Steven , Stanley Emma , Ward John , Keshavarz‐Moore Eli 
Published: February 2011

AbstractThe development of a whole new class of industrial agents, such as biologically based nanomaterials and viral vectors, has raised many challenges for their large‐scale manufacture, principally due to the lack of essential physical data and bioprocessing knowledge. A new example is the promise of filamentous bacteriophages and their derivatives. As a result, there is now an increasing need for the establishment of strong biochemical engineering foundations to serve as a guide for future manufacture. This article investigates the effect of high‐energy fluid flow on filamentous bacteriophage M13 to determine its robustness for large‐scale processing. By the application of well‐understood ultra scale‐down predictive techniques, the viability of bacteriophage M13 was studied as a measure of its robustness and as a function of energy dissipation rate and fluid conditions. These experiments suggested that despite being perceived as a relatively fragile molecule in the literature, bacteriophage M13 should tolerate processing conditions in existing large‐scale equipment designs. No loss of viability was noted up to a maximum energy dissipation rate of 2.9 × 106 W kg−1. Furthermore, significant losses above this threshold only occurred over periods well in excess of the exposure times expected in a bioprocess environment. Filamentous bacteriophages may therefore be regarded as a viable process material for industrial applications. Biotechnol. Bioeng. 2011; 108:1468–1472. © 2011 Wiley Periodicals, Inc.
One stop shopping: feature selection, classification and prediction in a single step
Authors: Lavine Barry K. , Nuguru Kadambari , Mirjankar Nikhil 
Published: February 2011

AbstractWe report on the application of a genetic algorithm (GA) for pattern recognition that uses both supervised and transverse learning to mine spectroscopic and proteomic data. The pattern recognition GA selects features that optimize the separation of the classes in a plot of the two or three largest principal components of the data. For training sets with small amounts of labeled data (i.e. data points tagged with a class label) and large amounts of unlabeled data (i.e. data points that are not tagged with a class label), this approach is preferred, as our results show, information in the unlabeled data is used by the fitness function to guide feature selection. The advantages of incorporating transverse learning into the fitness function of the pattern recognition GA have been evaluated in two recently published studies by our group. In one study, Raman spectroscopy and the pattern recognition GA were used to develop a potential method to discriminate hardwoods, softwoods and tropical woods. In a second study, biopsy material of small round blue cell tumors analyzed by cDNA microarrays was identified as to type (Ewings sarcoma, Burkitt's lymphoma, neuroblastoma and rhabdomyosarcoma) through supervised learning implemented by the pattern recognition GA. Copyright © 2011 John Wiley & Sons, Ltd.
C5‐Functionalized DNA, LNA, and α‐L‐LNA: Positional Control of Polarity‐Sensitive Fluorophores Leads to Improved SNP‐Typing
Authors: Østergaard Michael E. , Kumar Pawan , Baral Bharat , Guenther Dale C. , Anderson Brooke A. , Ytreberg F. Marty , Deobald Lee , Paszczynski Andrzej J. , Sharma Pawan K. , Hrdlicka Patrick J. 
Published: February 2011

AbstractSingle nucleotide polymorphisms (SNPs) are important markers in disease genetics and pharmacogenomic studies. Oligodeoxyribonucleotides (ONs) modified with 5‐[3‐(1‐pyrenecarboxamido)propynyl]‐2′‐deoxyuridine monomer X enable detection of SNPs at non‐stringent conditions due to differential fluorescence emission of matched versus mismatched nucleic acid duplexes. Herein, the thermal denaturation and optical spectroscopic characteristics of monomer X are compared to the corresponding locked nucleic acid (LNA) and α‐L‐LNA monomers Y and Z. ONs modified with monomers Y or Z result in a) larger increases in fluorescence intensity upon hybridization to complementary DNA, b) formation of more brightly fluorescent duplexes due to markedly larger fluorescence emission quantum yields (ΦF=0.44–0.80) and pyrene extinction coefficients, and c) improved optical discrimination of SNPs in DNA targets. Optical spectroscopy studies suggest that the nucleobase moieties of monomers X–Z adopt anti and syn conformations upon hybridization with matched and mismatched targets, respectively. The polarity‐sensitive 1‐pyrenecarboxamido fluorophore is, thereby, either positioned in the polar major groove or in the hydrophobic duplex core close to quenching nucleobases. Calculations suggest that the bicyclic skeletons of LNA and α‐L‐LNA monomers Y and Z influence the glycosidic torsional angle profile leading to altered positional control and photophysical properties of the C5‐fluorophore.
CH Activation on Aluminum–Vanadium Bimetallic Oxide Cluster Anions
Authors: Wang Zhe‐Chen , Wu Xiao‐Nan , Zhao Yan‐Xia , Ma Jia‐Bi , Ding Xun‐Lei , He Sheng‐Gui 
Published: February 2011

AbstractAluminum–vanadium bimetallic oxide cluster anions (BMOCAs) have been prepared by laser ablation and reacted with ethane and n‐butane in a fast‐flow reactor. A time‐of‐flight mass spectrometer was used to detect the cluster distribution before and after the reactions. The observation of hydrogen‐containing products AlVO5H− and AlxV4−xO11−xH− (x=1–3) strongly suggests that AlVO5− and AlxV4−xO11−x− (x=1–3) can react with ethane and n‐butane by means of an oxidative dehydrogenation process at room temperature. Density functional theory studies have been carried out to investigate the structural, bonding, electronic, and reactive properties of these BMOCAs. Terminal‐oxygen‐centered radicals (Ot.) were found in all of the reactive clusters, and the Ot. atoms, which prefer to be bonded with Al rather than V atoms, are the active sites of these clusters. All the hydrogen‐abstraction reactions are favorable both thermodynamically and kinetically. To the best of our knowledge, this is the first example of hydrogen‐atom abstraction by BMOCAs and may shed light on understanding the mechanisms of CH activation on the surface of alumina‐supported vanadia catalysts.
Synthesis of Dodecavalent Fullerene‐Based Glycoclusters and Evaluation of Their Binding Properties towards a Bacterial Lectin
Authors: Cecioni Samy , Oerthel Vincent , Iehl Julien , Holler Michel , Goyard David , Praly Jean‐Pierre , Imberty Anne , Nierengarten Jean‐François , Vidal Sébastien 
Published: February 2011

AbstractMultivalency is playing a major role in biological processes and particularly in lectin–carbohydrate interactions. The design of high‐affinity ligands of lectins should provide molecules capable of interfering with these biological processes and potentially inhibit bacterial or viral infections. Azide–alkyne “click” chemistry was applied to the synthesis of dodecavalent fullerene‐based glycoclusters. The conjugation could be efficiently performed from alkyne or azide functions on either partners (i.e. hexakis‐fullerene adduct or glycoside). PA‐IL is a bacterial lectin from the opportunistic pathogen Pseudomonas aeruginosa and is involved in the recognition of glycoconjugates on human tissues. The glycoclusters obtained were evaluated as ligands of PA‐IL and for their potential for competing with its binding to glycosylated surfaces. The affinities measured by hemagglutination inhibition assay (HIA), enzyme‐linked lectin assay (ELLA), and surface plasmon resonance (SPR) displayed a significant “glycoside cluster effect” with up to a 12 000‐fold increase in binding when comparing a monovalent carbohydrate reference probe with a dodecavalent fullerene‐based glycocluster, albeit with some differences depending on the analytical technique.
ChemInform Abstract: Synthesis and Structure Determination of In3TeO3F7: An Indium Oxyfluorotellurate IV Derived from W Bronze Structure with Te4+ in Hexagonal Tunnels.
Authors: Jennene Boukharrata N. , Laval J. P. 
Published: February 2011

AbstractThe new title compound is prepared by solid state reaction of InF3, In2O3, and TeO2 (Pt tube, 963 K, 4 d) and its structure is determined by single crystal XRD.
ChemInform Abstract: Ab initio Structure Determination of the New Ion Conductor K2Al2O3F2 from Powder Diffraction Data.
Authors: Kubel Frank , Fleig Juergen , Pantazi Mariana , Januschewsky Judith 
Published: February 2011

AbstractThe title compound is prepared by reaction of Al(OH)3 and KF powders (Pt crucible, 800 °C, 18 h; 96 wt.% yield).
ChemInform Abstract: Syntheses and Characterization of Two New Selenides Ba5Al2Se8 and Ba5Ga2Se8.
Authors: Mei Dajiang , Yin Wenlong , Lin Zheshuai , He Ran , Yao Jiyong , Fu Peizhen , Wu Yicheng 
Published: February 2011

AbstractThe new title compounds are prepared by solid state reactions of 1:5 mixtures of M2Se3 (M: Al, Ga) and BaSe (silica tubes, Ar, 950 °C, 72 h) and their structures are determined by single crystal (M: Ga) or powder XRD (M: Al).
ChemInform Abstract: Ln4B4O11F2 (Ln: Eu, Dy): New Phases Isotypic to the Fluoride Borate Gd4B4O11F2
Authors: Pitscheider Almut , Enders Michael , Huppertz Hubert 
Published: February 2011

AbstractThe title compounds are prepared in a Walker‐type multianvil apparatus from mixtures of Ln2O3 (Ln: Eu, Dy), LnF3, and B2O3 (5 GPa, 900 °C for the Eu‐compound and 8 GPa, 1000 °C for the Dy compound, 20 min).
ChemInform Abstract: Design and Synthesis of a Novel Three‐Hindered Quadrant Bisphosphine Ligand and Its Application in Asymmetric Hydrogenation.
Authors: Huang Kexuan , Zhang Xiaowei , Emge Thomas J. , Hou Guohua , Cao Bonan , Zhang Xumu 
Published: February 2011

AbstractThe title bisphosphine appears to be a practical ligand in Rh‐catalyzed asymmetric hydrogenation reactions of functionalized olefins furnishing the products in excellent yields and enantioselectivities.
ChemInform Abstract: Silica‐Immobilized Piperazine: A Sustainable Organocatalyst for Aldol and Knoevenagel Reactions.
Authors: Shanmuganathan Saravanakumar , Greiner Lasse , Dominguez de Maria Pablo 
Published: February 2011

AbstractThe use of commercially available SIP is investigated for the cross condensation of aromatic aldehydes with acetone and for the Knoevenagel condensation of salicylaldehyde with diethyl malonate.
ChemInform Abstract: Remarkable Enhancement Effect of Potassium tert‐Butoxide/THF Solution in Base‐Induced Sommelet—Hauser Rearrangements.
Authors: Tayama Eiji , Takedachi Keisuke , Iwamoto Hajime , Hasegawa Eietsu 
Published: February 2011

AbstractThe rearrangement of (benzylammoniomethyl)esters of type (I) under the title conditions affords α‐aryl‐α‐amino acid derivatives (II) and generally only minor amounts of the [1,2] Stevens rearrangement products (III).
ChemInform Abstract: Efficient CuCl‐Catalyzed Selective and Direct Oxidation of β‐ and γ‐Substituted Aliphatic Primary Alcohols to Carboxylic Acids.
Authors: Mannam Sreedevi , Sekar Govindasamy 
Published: February 2011

AbstractThis is the first report of a ligand‐ and additive‐free copper‐catalyzed direct and selective oxidation of unactivated substituted aliphatic primary alcohols to carboxylic acids.
ChemInform Abstract: Gold‐Catalyzed Synthesis of α‐Fluoro Acetals and α‐Fluoro Ketones from Alkynes.
Authors: de Haro Teresa , Nevado Cristina 
Published: February 2011

AbstractAlkynes are selectively transformed into α‐fluoro acetals (III) and α‐fluoro ketones (IV) in the presence of alcohols and Selectfluor as a stoichiometric source of fluorine, and catalytic amounts of gold.
ChemInform Abstract: Efficient N‐Arylation Catalyzed by a Copper(I) Pyrazolyl‐Nicotinic Acid System.
Authors: Liu Hai‐Yang , Yu Zhen‐Tao , Yuan Yong‐Jun , Yu Tao , Zou Zhi‐Gang 
Published: February 2011

AbstractThe in situ generated copper complex efficiently promotes the N‐arylation of pyrazoles and imidazole with aryl/pyridyl bromides.
ChemInform Abstract: Room‐Temperature Metal‐Free Electrophilic 5‐endo‐Selective Iodocarbocyclization of 1,5‐Enynes.
Authors: Pradal Alexandre , Nasr Alexandre , Toullec Patrick Y. , Michelet Veronique 
Published: February 2011

AbstractIt is demonstrated, that functionalized 1,5‐enynes can be cyclized under mild conditions in the presence of NIS to form 1‐iodocyclopentenes structures through an unprecedented 5‐endo process.
ChemInform Abstract: Expedient Trimethylaluminum‐Promoted One‐Pot Synthesis of Functional Heteroaromatic and Carbocyclic Trifluoroethylamines.
Authors: Allendoerfer Nadine , Sudau Alexander , Braese Stefan 
Published: February 2011

AbstractThe new method includes the generation of a trifluoromethyl‐ketimine from corresponding (hetero)aryl trifluoromethyl ketones and an aniline derivative.
ChemInform Abstract: One‐Pot Asymmetric Synthesis of α‐Trifluoromethylated Amines from α‐Trifluoromethyl Ketones.
Authors: Xu Jian , Liu Zhen‐Jiang , Yang Xian‐Jin , Wang Li‐Min , Chen Guan‐Long , Liu Jin‐Tao 
Published: February 2011

AbstractReaction of α‐trifluoromethyl ketones with optically active sulfinamide (II) generates the corresponding ketimines which are subsequently reduced to give α‐trifluoromethyl amines.
ChemInform Abstract: Wet SiO2 as a Suitable Media for Fast and Efficient Reduction of Carbonyl Compounds with NaBH3CN under Solvent‐Free and Acid‐Free Conditions.
Authors: Kouhkan Mehri , Zeynizadeh Behzad 
Published: February 2011

AbstractThe system wet SiO2/NaBH3CN is shown to be an efficient catalyst for the reduction of aldehydes and ketones to the corresponding alcohols under solvent‐free conditions.
ChemInform Abstract: Highly Diastereo‐ and Enantioselective Organocatalytic Michael Addition of α‐Ketoamides to Nitroalkenes.
Authors: Basle Olivier , Raimondi Wilfried , Sanchez Duque Maria del Mar , Bonne Damien , Constantieux Thierry , Rodriguez Jean 
Published: February 2011

AbstractThe method furnishes Michael adducts with high anti selectivity (<90% d.e.) and enantioselectivity.
ChemInform Abstract: Supported Monomeric Vanadium Catalyst for Dehydration of Amides to Form Nitriles.
Authors: Sueoka Shoichiro , Mitsudome Takato , Mizugaki Tomoo , Jitsukawa Koichiro , Kaneda Kiyotomi 
Published: February 2011

AbstractA monomeric vanadium oxide species is created on the surface of hydrotalcite.
ChemInform Abstract: Palladium‐Catalyzed Reductive ortho‐Arylation: Evidence for the Decomposition of 1,2‐Dimethoxyethane and Subsequent Arylpalladium(II) Reduction.
Authors: Martins Andrew , Candito David A. , Lautens Mark 
Published: February 2011

AbstractThe title reaction is highly suitable for the synthesis of meta‐substituted biaryls.
ChemInform Abstract: Regiospecific Synthesis of Functionalized 1,3‐Diarylisobenzofurans via Palladium‐ and Rhodium‐Catalyzed Reaction of Boronic Acids with o‐Acylbenzaldehydes under Thermal or Microwave Activation.
Authors: Jacq Jerome , Bessieres Bernard , Einhorn Cathy , Einhorn Jacques 
Published: February 2011

AbstractIn most cases, the reaction under microwave‐assisted conditions provides much higher yields of the products.
ChemInform Abstract: A Remarkable Cyclization of TADDOL‐Bisthioacetate under Oxidative Conditions.
Authors: Waser Mario , Haunschmidt Manuela , Himmelsbach Markus 
Published: February 2011

AbstractAttempted oxidation of the TADDOL‐derived bisthioacetate (III) results in an unexpected cyclization and deprotection reaction giving the thiolane‐1,1‐dioxide (IV).
ChemInform Abstract: Mild and General One‐Pot Reduction and Cyclization of Aromatic and Heteroaromatic 2‐Nitroamines to Bicyclic 2H‐Imidazoles.
Authors: Hanan Emily J. , Chan Bryan K. , Estrada Anthony A. , Shore Daniel G. , Lyssikatos Joseph P. 
Published: February 2011

AbstractOptimized conditions allow the reductive cyclization of various aromatic substrates bearing a wide range of functionalities.
ChemInform Abstract: Nanocrystalline Magnesium Oxide: A Novel and Efficient Catalyst for Facile Synthesis of 2,4,5‐Trisubstituted Imidazole Derivatives (III).
Authors: Safari Javad , Khalili Shiva Dehghan , Rezaei Mehran , Banitaba Sayed Hossein , Meshkani Fereshteh 
Published: February 2011

Abstractvia three‐component, one‐pot condensation of 1,2‐diketones (I), aryl aldehydes and ammonium acetate
ChemInform Abstract: Palladium‐Catalyzed Coupling of Aldehyde‐Derived Hydrazones: Practical Synthesis of Triazolopyridines and Related Heterocycles.
Authors: Thiel Oliver R. , Achmatowicz Michal M. , Reichelt Andreas , Larsen Robert D. 
Published: February 2011

AbstractMild and selective coupling of 2‐chloropyridines with arylhydrazones, followed by oxidation of the resulting hydrazono pyridines offers an efficient entry to triazolopyridines (IV).
ChemInform Abstract: Palladium‐Catalyzed Annulations of Arynes with 2‐(2‐Iodophenoxy)‐1‐substituted Ethanones.
Authors: Li Rong‐Jiang , Pi Shao‐Feng , Liang Yun , Wang Zhi‐Qiang , Song Ren‐Jie , Chen Guo‐Xiang , Li Jin‐Heng 
Published: February 2011

AbstractThe title reaction offers a mild and efficient method for the synthesis of 6H‐benzo[c]chromenes.
ChemInform Abstract: Synthesis of New Pentacyclic Chromophores Through a Highly Regio‐ and Diastereoselective Cascade Process.
Authors: Chamas Zein el abidine , Dietz Olivier , Aubert Emmanuel , Fort Yves , Mamane Victor 
Published: February 2011

AbstractFour new bonds and two stereocenters are formed selectively in one step.
ChemInform Abstract: NHC‐Catalyzed Annulation of Enals to Tethered Dienones: Efficient Synthesis of Bicyclic Dienes.
Authors: Nair Vijay , Vellalath Sreekumar , Babu Beneesh P. , Varghese Vimal , Paul Rony Rajan , Suresh Eringathodi 
Published: February 2011

AbstractThe reaction is applied to a variety of diarylidene cyclohexanones and their piperidone analogues to afford diastereomerically pure products.
ChemInform Abstract: Preparation of 2‐Magnesiated 1,3,5‐Triazines via an Iodine—Magnesium Exchange.
Authors: Peng Zhihua , Haag Benjamin A. , Knochel Paul 
Published: February 2011

AbstractA variety of fully substituted 1,3,5‐triazines is prepared via reaction of the magnesiated or zincated derivatives, trapped with various electrophilic reagents.
ChemInform Abstract: Synthesis and Antimicrobial Activity of 2‐Phenylimino‐3‐aryl‐4‐S‐benzyl‐6‐hepta‐O‐benzoyl‐β‐D‐lactosylimino ‐2,3‐dihydro‐1,3,5‐thiadiazine Hydrochlorides.
Authors: Agrawal P. T. , Deshmukh S. P. 
Published: February 2011

AbstractAll synthesized compounds (III) are screened for antibacterial and antifungal activity.
ChemInform Abstract: Unique Phenyl Ether Type Biflavonoids, Zizyflavosides A and B with Biomimetic Synthesis for Zizyflavoside A.
Authors: Mostafa Mahmoud , Takano Fumihide , Ohta Tomihisa 
Published: February 2011

AbstractEight flavonoids are isolated from the plant zizyphus spina‐christi.
Modified correlations for the first and second critical rotor speeds, as well as break up probability in a rotary disc contactor
Authors: Molavi Hoda , Hosseinpour Sima , Bahmanyar Hossein , Niasar Mojtaba Shariaty 
Published: February 2011

AbstractA rotary disc contactor with 9.1 cm inner diameter and 28 compartments has been used to investigate the effect of continuous phase height on the first and second critical rotor speeds, as well as breakage probability by using 12 different chemical systems, in case of mass transfer and no mass transfer. Three modified correlations have been proposed to predict the first and second critical rotor speeds as well as break up probability by considering physical properties, drop size, and continuous phase height. Furthermore, estimated results of the proposed correlations were compared to the randomly selected literature data.
The association of red blood cell parameters with mortality in a population of hemodialysis patients
Authors: Michel Brian E. 
Published: February 2011

AbstractBBACKGROUND AND OBJECTIVESThe targeting of higher hemoglobin levels leads to increased cardiovascular events in patients with renal disease. This study is an attempt to discover if changes in red blood cell parameters are induced by erythropoiesis‐stimulating agents, and whether these changes are associated with mortality.METHODSA retrospective study of patients on hemodialysis at two dialysis units operated by Our Lady of Lourdes Hospital, Camden, N.J., evaluating the effect of dosage of epoetin alfa on red blood cell parameters and the relationship of these parameters with all cause mortality over the course of one year.RESULTSDosage of epoetin alfa was related to red blood cell distribution width and mean corpuscular hemoglobin concentration in a statistically significant manner. Red blood cell distribution width was significantly lower in one year survivors. Quintile analysis demonstrated a relationship between red blood cell distribution width and iron saturation with one year survival. Low MCHC is a powerful predictor of short term mortality.CONCLUSIONMean corpuscular hemoglobin concentration and red blood cell distribution width are influenced by high doses of epoetin alfa. This study should serve to stimulate further investigation of the predictive role of red blood cell parameters in mortality in patients with renal disease and anemia treated with erythropoiesis stimulating agents, in an attempt to elucidate the mechanism of increased cardiovascular events in patients targeted to higher hemoglobin levels. Dial. Transplant. © 2011 Wiley Periodicals, Inc.
Regulation of hub mRNA stability and translation by miR430 and the dead end protein promotes preferential expression in zebrafish primordial germ cells
Authors: Mickoleit Michaela , Banisch Torsten U. , Raz Erez 
Published: February 2011

AbstractThe Hu proteins are RNA‐binding proteins known to be involved in various aspects of RNA metabolism, such as nucleo‐cytoplasmic shuttling, translation, and stability. These proteins are predominantly expressed in neuronal tissues and are important for neuronal differentiation and plasticity. Here, we report on the regulation over hub mRNA stability and function in zebrafish embryos. Using reporters encoding for fluorescent proteins, we show that hub RNA is a target of global miRNA‐mediated repression, while the RNA‐binding protein Dead end (Dnd) contributes to maintenance of the expression in the primordial germ cells (PGCs). Developmental Dynamics 240:695–703, 2011. © 2011 Wiley‐Liss, Inc.