bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of biomolecule separation by combining microscale filtration and design‐of‐experiment methods
Authors: Kazemi Amir S. , Kawka Karina , Latulippe David R. 
Published: March 2016

ABSTRACTThere is considerable interest in developing microscale (i.e., high‐throughput) methods that enable multiple filtration experiments to be run in parallel with smaller sample amounts and thus reduce the overall required time and associated cost to run the filtration tests. Previous studies to date have focused on simply evaluating the filtration capacity, not the separation performance. In this work, the stirred‐well filtration (SWF) method was used in combination with design‐of‐experiment (DOE) methods to optimize the separation performance for three binary mixtures of bio‐molecules: protein–protein, protein‐polysaccharide, and protein‐DNA. Using the parallel based format of the SWF method, eight constant‐flux ultrafiltration experiments were conducted at once to study the effects of stirring conditions, permeate flux, and/or solution conditions (pH, ionic strength). Four separate filtration tests were conducted for each combination of process variables; in total, over 100 separate tests were conducted. The sieving coefficient and selectivity results are presented to match the DOE design format and enable a greater understanding of the effects of the different process variables that were studied. The method described herein can be used to rapidly determine the optimal combination of process factors that give the best separation performance for a range of membrane‐based separations applications and thus obviate the need to run a large number of traditional lab‐scale tests. Biotechnol. Bioeng. 2016;113: 2131–2139. © 2016 Wiley Periodicals, Inc.
Why should biochemistry students be introduced to molecular dynamics simulations—and how can we introduce them?
Authors: Elmore Donald E. 
Published: March 2016

AbstractMolecular dynamics (MD) simulations play an increasingly important role in many aspects of biochemical research but are often not part of the biochemistry curricula at the undergraduate level. This article discusses the pedagogical value of exposing students to MD simulations and provides information to help instructors consider what software and hardware resources are necessary to successfully introduce these simulations into their courses. In addition, a brief review of the MD‐based activities in this issue and other sources are provided. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:118–123, 2016.
The evolution of the Krebs cycle: A promising subject for meaningful learning of biochemistry
Authors: da Costa Caetano , Galembeck Eduardo 
Published: March 2016

AbstractEvolution has been recognized as a key concept for biologists. To enhance comprehension and motivate biology undergraduates for the contents of central energetic metabolism, we addressed the Krebs cycle structure and functions in an evolutionary view. To this end, we created a study guide that contextualizes the emergence of the cyclic pathway, in light of the prokaryotic influence since the early anaerobic condition of the Earth to increase oxygen in the atmosphere. The study guide is composed of three interrelated sections: (1) a problem, designed to arouse curiosity, inform and motivate students, (2) a text about life evolution, including early microorganisms and the emergence of the Krebs cycle, and (3) questions for debate. The activity consisted on individual reading and peer discussion based on this written material, under the guidance of the instructors. The questions were designed to foster debate in an ever‐increasing level of complexity and to strengthen the main contextual aspects leading to emergence, evolving, and permanency of a complex metabolic pathway. Based on classroom observation, analysis of student's written responses, and individual interviews, we noticed they were engaged and motivated by the task, especially during group discussion. The whole experience suggests that the study guide was a stimulus to broaden the comprehension of the Krebs cycle, reinforcing the evolutionary approach as an important subject for learning purposes. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:288–296, 2016.
A decade of human genome project conclusion: Scientific diffusion about our genome knowledge
Authors: Moraes Fernanda , Góes Andréa 
Published: March 2016

AbstractThe Human Genome Project (HGP) was initiated in 1990 and completed in 2003. It aimed to sequence the whole human genome. Although it represented an advance in understanding the human genome and its complexity, many questions remained unanswered. Other projects were launched in order to unravel the mysteries of our genome, including the ENCyclopedia of DNA Elements (ENCODE). This review aims to analyze the evolution of scientific knowledge related to both the HGP and ENCODE projects. Data were retrieved from scientific articles published in 1990–2014, a period comprising the development and the 10 years following the HGP completion. The fact that only 20,000 genes are protein and RNA‐coding is one of the most striking HGP results. A new concept about the organization of genome arose. The ENCODE project was initiated in 2003 and targeted to map the functional elements of the human genome. This project revealed that the human genome is pervasively transcribed. Therefore, it was determined that a large part of the non‐protein coding regions are functional. Finally, a more sophisticated view of chromatin structure emerged. The mechanistic functioning of the genome has been redrafted, revealing a much more complex picture. Besides, a gene‐centric conception of the organism has to be reviewed. A number of criticisms have emerged against the ENCODE project approaches, raising the question of whether non‐conserved but biochemically active regions are truly functional. Thus, HGP and ENCODE projects accomplished a great map of the human genome, but the data generated still requires further in depth analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:215–223, 2016.
Room‐Temperature Practical Copper‐Catalyzed Amination of Aryl Iodides
Authors: Deldaele Christopher , Evano Gwilherm 
Published: March 2016

AbstractAn efficient and highly practical procedure is reported for the Ullmann–Goldberg‐type copper‐catalyzed amination of aryl iodides. By using a combination of copper iodide and proline in the presence of an excess of an amine, a wide range of aryl iodides can be readily aminated at room temperature. The reaction proceeds well regardless of the electronic properties of the starting aryl iodide and the amination products can be obtained without the need for purification by column chromatography in most cases. Owing to its efficiency and the mildness of the reaction conditions, this amination could also be extended to the amination of complex aryl iodides at room temperature.
Iron‐Based Fischer–Tropsch Synthesis for the Efficient Conversion of Carbon Dioxide into Isoparaffins
Authors: Geng Shunshun , Jiang Feng , Xu Yuebing , Liu Xiaohao 
Published: March 2016

AbstractIron‐based Fischer–Tropsch (FT) synthesis in combination with hydroisomerization in the presence of zeolites for the synthesis of isoparaffins from CO2/H2 was conducted in a fixed‐bed reactor. Relative to supported iron catalysts, the precipitated one efficiently converted intermediate CO into hydrocarbons by supplying a high density of FT active sites on the catalyst surface. Removing water by interstage cooling and promoting the CO conversion step in the FT synthesis were effective approaches in achieving a high CO2 conversion, because of an increase in the driving force to the reaction equilibrium. Particle mixing of 92.6 Fe7.4 K with either 0.5 Pd/β or HZSM‐5 zeolite effectively hydroisomerized the resulting FT hydrocarbons into gasoline‐range isoparaffins. Particularly, HZSM‐5 displayed a higher isoparaffin selectivity at approximately 70 %, which resulted from easier hydrocracking and hydroisomerization of the olefinic FT primary products.
Flower‐like Cu2In2ZnS5 Nanosheets: A Novel Promising Photoelectrode for Water Splitting
Authors: Hong Tiantian , Liu Zhifeng , Zhang Jing , Li Guangmin , Liu Junqi , Zhang Xueqi , Lin Shaohua 
Published: March 2016

AbstractThis paper describes a promising photoelectrochemical electrode based on a flower‐like Cu2In2ZnS5 structure composed of nanosheets and its use as a photoelectrode for photoelectrochemical (PEC) water splitting for the first time. The detailed growth of Cu2In2ZnS5 was discussed. The morphology and microstructure were characterized in detail. PEC measurements showed that on the basis of the optimal hydrothermal time, flower‐like Cu2In2ZnS5 exhibited high photoelectrochemical activity, as the photocurrent density reached up to 2.00 mA cm−2. The remarkable PEC performance stems from crucial factors, including improved light absorption, an ideal band gap value, decoupling of the directions of light absorption and charge‐carrier collection, and large surface area. Our results indicate that the flower‐like Cu2In2ZnS5 structure composed of nanosheets has enormous potential in PEC water splitting.
Cobalt‐Catalyzed Cyclization of N‐Methoxy Benzamides with Alkynes using an Internal Oxidant through C−H/N−O Bond Activation
Authors: Sivakumar Ganesan , Vijeta Arjun , Jeganmohan Masilamani 
Published: March 2016

AbstractThe cyclization of substituted N‐methoxy benzamides with alkynes in the presence of an easily affordable cobalt complex and NaOAc provides isoquinolone derivatives in good to excellent yields. The cyclization reaction is compatible with a range of functional group‐substituted benzamides, as well as ester‐ and alcohol‐substituted alkynes. The cobalt complex [CoIIICp*(OR)2] (R=Me or Ac) serves as an efficient catalyst for the cyclization reaction. Later, isoquinolone derivatives were converted into 1‐chloro and 1‐bromo substituted isoquinoline derivatives in excellent yields in the presence of POCl3 or PBr3.
Design of 2D Porous Coordination Polymers Based on Metallacrown Units
Authors: Atzeri Corrado , Marchiò Luciano , Chow Chun Y. , Kampf Jeff W. , Pecoraro Vincent L. , Tegoni Matteo 
Published: March 2016

AbstractA 12‐metallacrown‐4 (MC) complex was designed and employed as the building block in the synthesis of coordination polymers, one of which is the first permanently porous MC architecture. The connection of the four‐fold symmetric MC subunits by CuII nodes led to the formation of 2D layers of metallacrowns. Channels are present in the crystalline architecture, which exhibits permanent porosity manifested in N2 and CO2 uptake capacity.
A Cyclometalated Iridium(III) Complex Serves as a Phosphorescent Probe for Specific Mitochondrial Imaging in Living Cells
Authors: Wang Jinquan , Hou Xiaojuan , Jin Chengzhi , Chao Hui 
Published: March 2016

AbstractA new cyclometalated iridium(III) complex [Ir(2‐pq)2(HPIP)]Cl (Ir1, 2‐pq=3‐phenylisoquinoline, HPIP=2‐(2‐hydroxyphenyl)imidazo[4,5‐f]1,10‐phenanthroline) was synthesized and applied to image mitochondria in living cells. Ir1 displayed excellent ability to selectively accumulate in mitochondria of live cells with no requirement of replacement of the culture medium. Due to Ir1 exhibiting better photostability than the commercially available mitochondrial trackers, this complex could be applicable for the imaging and tracking of the mitochondrial morphological changes over long periods of time. In addition, in vitro cytotoxicity investigation revealed that Ir1 showed negligible cytotoxicity at the concentrations employed. Based on these, Ir1 is suitable for organelle‐selective imaging in living cells.
Applications of DNA Nanotechnology in Synthesis and Assembly of Inorganic Nanomaterials
Authors: Ma Yurou , Yang Xiangdong , Wei Yurong , Yuan Quan 
Published: March 2016

AbstractIn addition to its inherited genetic function, DNA is one of the smartest and most flexible self‐assembling nanomaterials with programmable and predictable features, for which, more and more scientists combine DNA with nanomaterials and put them into designing, synthesizing and assembling. In this review, four modes of action of DNA molecules are introduced in a figurative and intuitive way, based on the four different roles it plays in synthesis and assembly of nanomaterials: (a) smart linkers to guide nanoparticle assembly, (b) 2D or 3D scaffold with well‐designed binding sites, (c) nucleation sites to directly facilitate Au/Pd/Ag/Cu nanowires, nanoparticles, nano‐ arrays and (d) serving as capping agents to prevent crystal growth, and control size and morphology. To be sure, this state‐of‐the‐art combination of functional DNA molecules and inorganic nanomaterials greatly encouraged step towards the development of analytical science, life science, environmental science, and other promising field they can address. DNA‐guided nanofabrication will eventually exceed expectations far beyond our scope in the near future.
An Efficient One‐pot Three‐component Process for Synthesis of Perfluoroalkylated Quinolizines
Authors: Shen Dandan , Xu Yanjie , He Dong , Han Jing , Chen Jie , Deng Hongmei , Shao Min , Zhang Hui , Cao Weiguo 
Published: March 2016

AbstractA facile multi‐component process for the synthesis of perfluoroalkylated quinolizine derivatives was achieved using various arylidenemalononitriles, pyridine, and methyl perfluoroalk‐2‐ynoates as starting materials. Moderate yields were obtained under mild condition. The structures of perfluoroalkylated quinolizine derivatives were characterized by means of 1H NMR, 13C NMR, 19F NMR, IR, LRMS and HRMS. Furthermore, the reaction mechanism was proposed.
Specific Electrochemiluminescence of Aptamer‐Functionalized Quantum Dots with Lysozyme and Hemin as Co‐Triggers
Authors: Ji Xubo , Yao Chuanguang , Wan Ying , Song Hongxin , Xin Peng , Cui Hongda , Zheng Chenyu , Deng Shengyuan 
Published: March 2016

AbstractThis work proposed a label‐free, cost‐effective and fairly sensitive electrogenerated chemiluminescence (ECL) strategy for the specific detection of lysozyme based on the hemin/G‐quadruplex hybrid. Gold nanoparticles were spread onto the chitosan thin‐film as substrate to adsorb thiolated captures: a hairpin‐structured DNA, integrating dual head‐tail connected functional domains: one aptamer sequence for lysozyme and the other for hemin (iron(III) proto‐porphyrin IX). In the presence of the both, the hairpin conformation unfolded and transformed into the hemin/G‐quadruplex motif, which quenched the ECL emission of underlaid quantum dots significantly via the consumption of dissolved oxygen as endogenous coreactant. This construction enabled a wide linear response to lysozyme, ranging from 20 pg·mL−1 to 5 µg·mL−1, with a detection limit as low as 4.95 pg·mL−1 (e.g. 9.4 pmol·L−1), demonstrating the prospective utilization of DNA technologies in bioanalysis.
Nucleophilic Trifluoromethylthiolation of Alkyl Chlorides, Bromides and Tosylates
Authors: Xu Chunfa , Chen Qingyun , Shen Qilong 
Published: March 2016

AbstractA direct nucleophilic trifluoromethylthiolation of alkyl chlorides, bromides and tosylates with AgSCF3 was described. It was found that the presence of nBu4NI or a combination of nBu4NI/nBu4NBr significantly enhanced the reaction rates. The reaction conditions were mild, thus allowing the tolerance of a variety of functional groups.
Direct Perfluoroalkylthiolation of Few Chalcogenols
Authors: Glenadel Quentin , Billard Thierry 
Published: March 2016

AbstractTrifluoromethanesulfenamide reagent can react with alcohols, in basic conditions, or with thiols, in catalytic acid conditions, to afford the corresponding trifluoromethanesulfenates or trifluoromethyldisulfides. The use of higher homologs of this reagent leads to synthesis of the nearly unknown perfluoroalkanesulfenates and perfluoroalkyldisulfides.
Copper‐Catalyzed Aerobic Oxidation of Azinylmethanes for Access to Trifluoromethylazinylols
Authors: Zheng Gang , Liu Hao , Wang Mang 
Published: March 2016

AbstractA copper‐catalyzed oxygenation of methylazaarenes was found to occur in the absence of both ligand and additive, and has been successfully employed for the synthesis of trifluoromethylazinylketols. This synthetic strategy incorporates aerobic oxidation and a trifluoromethylation in one‐pot and provides a novel method for the trifluoromethylation of aliphatic CH bond.
Effect of N‐Terminal Acylation on the Activity of Myostatin Inhibitory Peptides
Authors: Takayama Kentaro , Nakamura Akari , Rentier Cédric , Mino Yusaku , Asari Tomo , Saga Yusuke , Taguchi Akihiro , Yakushiji Fumika , Hayashi Yoshio 
Published: March 2016

AbstractInhibition of myostatin, which negatively regulates skeletal muscle growth, is a promising strategy for the treatment of muscle atrophic disorders, such as muscular dystrophy, cachexia and sarcopenia. Recently, we identified peptide A (H‐WRQNTRYSRIEAIKIQILSKLRL‐NH2), the 23‐amino‐acid minimum myostatin inhibitory peptide derived from mouse myostatin prodomain, and highlighted the importance of its N‐terminal tryptophan residue for the effective inhibition. In this study, we synthesized a series of acylated peptide derivatives focused on the tryptophan residue to develop potent myostatin inhibitors. As a result of the investigation, a more potent derivative of peptide A was successfully identified in which the N‐terminal tryptophan residue is replaced with a 2‐naphthyloxyacetyl moiety to give an inhibitory peptide three times (1.19±0.11 μm) more potent than parent peptide A (3.53±0.25 μm). This peptide could prove useful as a new starting point for the development of improved inhibitory peptides.
Discovery of Non‐ATP‐Competitive Inhibitors of Polo‐like Kinase 1
Authors: Yun Taikangxiang , Qin Tan , Liu Ying , Lai Luhua 
Published: March 2016

AbstractPolo‐like kinase 1 (Plk1) is an evolutionarily conserved serine/threonine kinase, and its N‐terminal kinase domain (KD) controls cell signaling through phosphorylation. Inhibitors of Plk1 are potential anticancer drugs. Most known Plk1 KD inhibitors are ATP‐competitive compounds, which may suffer from low selectivity. In this study we discovered novel non‐ATP‐competitive Plk1 KD inhibitors by virtual screening and experimental studies. Potential binding sites in Plk1 KD were identified by using the protein binding site detection program Cavity. The identified site was subjected to molecular‐docking‐based virtual screening. The activities of top‐ranking compounds were evaluated by in vitro enzyme assay with full‐length Plk1 and direct binding assay with Plk1 KD. Several compounds showed inhibitory activity, and the most potent was found to be 3‐((2‐oxo‐2‐(thiophen‐2‐yl)ethyl)thio)‐6‐(pyridin‐3‐ylmethyl)‐1,2,4‐triazin‐5(4H)‐one (compound 4) with an IC50 value of 13.1±1.7 μm. Our work provides new insight into the design of kinase inhibitors that target non‐ATP binding sites.
Novel habitat use supports population maintenance in a reconfigured landscape
Authors: O'Bryan C. J. , Homyack J. A. , Baldwin R. F. , Kanno Y. , Harrison A.‐L. 
Published: March 2016

AbstractGiven the limited scope of unaltered, protected areas in most regions, understanding the contributions to imperiled species conservation by landscapes in which habitat elements have been reconfigured is critical. Commercial forestry has been a driver of altered structure and composition of forests and of distribution and character of aquatic systems. In eastern North America, extensive historical wetland drainage reconfigured hydrologic environments from low‐gradient wet flats and isolated wetlands to connected networks of linear ditches. Landscapes where both uplands and aquatic environments differ from historic conditions may affect most ecological aspects of semi‐aquatic species, including reptiles. Our objective was to determine if habitat selection and use decisions by spotted turtles (Clemmys guttata), a rare semi‐aquatic species, supported population maintenance in a reconfigured forest landscape in eastern North Carolina,USA. We captured 280 individuals and radiomarked 31 adults to examine habitat selection at multiple spatial scales with paired logistic regression, movements and home ranges with location data and utilization distributions (UDs), survival with a known‐fate model, and abundance with N‐mixture modeling. Across local and landscape scales, turtles selected features associated with ditches despite abundant, more natural aquatic depressions across the study area. Habitat metrics describing understory closure and substrate characteristics were important at local scales, and closed canopy forest and habitat heterogeneity was positively associated with activity areas at landscape‐scale spatial grains. Both movements and home ranges were centered on ditches, and turtles exploited ditches to access mates, nest sites, or uplands for estivation. In this highly reconfigured landscape, this species appeared to have sufficient behavioral plasticity to acquire key resources contributing to high survival and an abundant population. Isolation from road traffic and collection, both which negatively affect turtles elsewhere, was facilitated by limited public access. Our results suggest that conservation and management of rare species should not rely solely on habitat information gained from studies in more pristine areas because such results may not demonstrate the range in variation in behavior that might allow persistence in novel environments, absent key threats.
Non‐adherence to ivabradine and placebo and outcomes in chronic heart failure: an analysis from SHIFT
Authors: Böhm Michael , Lloyd Suzanne M. , Ford Ian , Borer Jeffrey S. , Ewen Sebastian , Laufs Ulrich , Mahfoud Felix , Lopez‐Sendon Jose , Ponikowski Piotr , Tavazzi Luigi , Swedberg Karl , Komajda Michel 
Published: March 2016

AbstractAimsIn heart failure, non‐adherence increases events; in turn, the effect of hospitalization on adherence is incompletely understood. We explored the relationship of non‐adherence to outcomes, hospitalizations with non‐adherence, and the influence of non‐adherence on treatment effects of heart rate lowering with ivabradine.Methods and resultsIn the randomized, controlled Systolic Heart failure treatment with the If‐inhibitor ivabradine Trial (SHIFT), we studied the effect of non‐adherence (n = 1287) compared with adherence (n = 5204) on cardiovascular outcomes. After adjustment, non‐adherence was associated with the primary composite endpoint of cardiovascular death and heart failure hospitalization (hazard ratio 3.47, 95% confidence interval 2.91–4.13, P < 0.0001). No interaction with the treatment groups of placebo or ivabradine (P for interaction 0.54) occurred. Similar results for cardiovascular death and heart failure hospitalization, as well as for cardiovascular hospitalization, heart failure death, and total death were observed. The effect of ivabradine was maintained in patients being adherent or becoming non‐adherent during the trial (P for interaction = 0.54). Patients with a previous hospitalization were more likely to become non‐adherent thereafter.ConclusionsNon‐adherence identifies a group at particularly high cardiovascular event risk independent of treatment allocation. Non‐adherent patients in the ivabradine group maintain a treatment benefit. Patients with previous hospitalizations are more likely to become non‐adherent and represent a group of particularly high‐risk patients in whom special attention to stimulate adherence may be valuable.Trial registrationISRCTN70429960.
Palladium‐Catalyzed Aminocarbonylation of Aryl Halides with 2,4,6‐Trichloro‐1,3,5‐triazine/Formamide Mixed Reagent
Authors: Iranpoor Nasser , Panahi Farhad , Roozbin Fatemeh , Erfan Soodabeh , Rahimi Sajjad 
Published: March 2016

AbstractIn this work, the mixture of formamide and 2,4,6‐trichloro‐1,3,5‐triazine (cyanuric chloride or TCT) is introduced as a new amidating agent in Pd‐catalyzed aminocarbonylation of aryl halides. In the presence of a catalytic amount of palladium and TCT/formamide reagent, a range of aryl halides (X = Cl, Br, I) were converted into amides efficiently in N,N‐dimethylformamide at 120 °C.