bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmental Stochasticity
Authors: Fujiwara Masami
Published: March 2009

Environmental stochasticity is unpredictable spatiotemporal fluctuation in environmental conditions, and it is one of the main sources of fluctuation in ecological processes. The term is often used in the ecology and evolution literature. Unpredictability is defined as a lack of ability to predict the future state precisely so that only its distribution can be known. Environment is typically defined as any set of physical, chemical and biological conditions that organisms experience, such as temperature, nutrient availability and the abundance of predators. Environmental stochasticity influences how population abundance fluctuates and affects the fate (e.g. persistence or extinction) of populations. In an evolutionary time scale, environmental stochasticity also affects life history strategy of organisms. Incorporating environmental stochasticity into analysis requires some care. Stochastic equations sometimes do not have explicit solutions so that simulations are required, and statistical analysis must separate other confounding factors such as stochastic sampling errors and demographic stochasticity.

Key Concepts

Environmental stochasticity is unpredictable spatiotemporal fluctuations in environmental conditions.

Correlation between time‐lagged environmental states is one statistical measure of its predictability.

Environmental stochasticity is reflected in the fluctuations in ecological processes and affects their fate (e.g. extinction or persistence of populations).

Observed population dynamics consist of fluctuation due to environmental stochasticity, but it is often confounded with other factors such as sampling errors and demographic stochasticity.

All of the fluctuations in ecological data are often erroneously attributed to environmental stochasticity alone.

Evolutionary dynamics are also affected by environmental stochasticity.

Autoregressive moving average (ARMA) models are an example of statistical models incorporating environmental stochasticity.

Using stochastic differential and difference equation models, mechanistic ecological models incorporating environmental stochasticity can be built.
Spinal Cord: Repair and Rehabilitation
Authors: Reier Paul J , Lane Michael A , Behrman Andrea L , Howland Dena R
Published: March 2009

Functional deficits following spinal cord injury are no longer viewed as totally irreversible. Laboratory findings indicate the ability to walk can be partially restored by individual or combined therapeutic approaches targeting specific cellular responses to trauma. In addition, certain rehabilitation strategies can enhance ambulatory capacity, as well as stimulate certain intrinsic cellular or molecular repair processes. Other findings indicate the spinal cord is not as ‘hard‐wired’ as previously believed, and that neural circuitries in the injured spinal cord undergo natural remodelling with some changes appearing to facilitate some improvements in function over time. These collective observations highlight intriguing opportunities for achieving better functional outcomes and quality of life by interfacing cellular and molecular treatments with rehabilitation techniques that can amplify natural or therapeutically directed repair mechanisms. Whereas challenges remain, interactive training/exercise is becoming recognized as a fundamental adjunct to a growing list of potential therapeutic interventions for promoting spinal cord regeneration and neuroplasticity.
The Aetiologic Spectrum of Cerebellar Ataxia: Acquired Causes of Ataxia
Authors: Todd Peter K , Taylor J Paul
Published: March 2009

Ataxia is a common finding in patients seen in neurological practice and can be the result of a wide variety of causes. Although cerebellar degeneration can be chronic and slowly progressive, acute cerebellar swelling due to infarction, oedema or haemorrhage can have rapid and catastrophic effects and is a true neurological emergency. Here we set out to briefly describe the clinical/anatomical correlates of cerebellar disease and to provide a broad differential diagnosis for patients who present with cerebellar ataxia. This article specifically focuses on acquired causes of cerebellar ataxia. A separate complementary article discusses common hereditary causes of cerebellar ataxia.

Key Concepts

Clinical syndromes associated with cerebellar dysfunction may be divided into syndromes that predominantly affect the midline cerebellar structures (gait and ocular dysfunction predominant) or the cerebellar hemisphere(s) (ipsilateral appendicular ataxia, dysarthria).

Acute onset of cerebellar ataxia is most commonly associated with vascular disorders (stroke or haemorrhage), toxins or infectious aetiologies.

Subacute onset cerebellar ataxia can result from a variety of causes, including infectious, neoplastic, autoimmune and metabolic abnormalities. Many of these causes of ataxia are treatable.

Most slowly progressive cerebellar ataxias result from neurodegenerative aetiologies, either inherited or sporadic.
Heat opens axon initial segment sodium channels: A febrile seizure mechanism?
Authors: Thomas Evan A. , Hawkins Roger J. , Richards Kay L. , Xu Ruwei , Gazina Elena V. , Petrou Steven
Published: March 2009

Objective

A number of hypotheses have been put forward as to why humans respond to fever by seizing. The current leading hypotheses are that respiratory alkalosis produces an as yet unidentified change in neural excitability or that inflammatory mediators potentiate excitatory synaptic transmission. However, it is well known that ion channel gating rates increase with increased temperature. Furthermore, skeletal and cardiac sodium channel activation can be temperature sensitive in some situations. We measured the temperature sensitivity of the brain sodium channel, NaV1.2, to determine whether febrile temperatures might produce a direct increase in neuronal excitability.

Methods

The effect of temperature on NaV1.2 electrophysiological properties was measured in a transfected mammalian cell line. The subcellular location of NaV1.2 in the mouse brain was ascertained using antibodies against NaV1.2 and ankyrin‐G. Computer simulation of a hippocampal granule cell model was used to predict the effect of temperature on action potential firing.

Results

As well as the expected increase in gating rates, the voltage dependence of activation became 7.6mV more negative when the temperature was increased from 37°C to 41°C. NaV1.2 was localized to the axon initial segment in hippocampal and cortical neurons. Computer simulation showed that increased gating rates and the more negative activation dramatically increase neuronal excitability.

Interpretation

The direct effect of heat on ion channels localized to the site of action potential initiation potentially causes a profound increase in neuronal excitability. This is likely to contribute to febrile seizure genesis. Ann Neurol 2009;66:219–226
Autism and other neuropsychiatric symptoms are prevalent in individuals with MeCP2 duplication syndrome
Authors: Ramocki Melissa B. , Peters Sarika U. , Tavyev Y. Jane , Zhang Feng , Carvalho Claudia M. B. , Schaaf Christian P. , Richman Ronald , Fang Ping , Glaze Daniel G. , Lupski James R. , Zoghbi Huda Y.
Published: March 2009

Objective

There have been no objective assessments to determine whether boys with MECP2 duplication have autism or whether female carriers manifest phenotypes. This study characterizes the clinical and neuropsychiatric phenotypes of affected boys and carrier females.

Methods

Eight families (9 males and 9 females) with MECP2 duplication participated. A detailed history, physical examination, electroencephalogram, developmental evaluation, Autism Diagnostic Observation Schedule, and Autism Diagnostic Interview–Revised were performed for each boy. Carrier females completed the Symptom Checklist‐90‐R, Wechsler Abbreviated Scale of Intelligence, Broad Autism Phenotype Questionnaire, and detailed medical and mental health histories. Size and gene content of each duplication were determined by array comparative genome hybridization. X‐chromosome inactivation patterns were analyzed using leukocyte DNA. MECP2 and IRAK1 RNA levels were quantified from lymphoblast cell lines, and western blots were performed to assess MeCP2 protein levels.

Results

All of the boys demonstrated mental retardation and autism. Poor expressive language, gaze avoidance, repetitive behaviors, anxiety, and atypical socialization were prevalent. Female carriers had psychiatric symptoms, including generalized anxiety, depression, and compulsions that preceded the birth of their children. The majority exhibited features of the broad autism phenotype and had higher nonverbal compared to verbal reasoning skills.

Interpretation

Autism is a defining feature of the MECP2 duplication syndrome in boys. Females manifest phenotypes despite 100% skewing of X‐inactivation and normal MECP2 RNA levels in peripheral blood. Analysis of the duplication size, MECP2 and IRAK1 RNA levels, and MeCP2 protein levels revealed that most of the traits in affected boys are likely due to the genomic region spanning of MECP2 and IRAK1. The phenotypes observed in carrier females may be secondary to tissue‐specific dosage alterations and require further study. Ann Neurol 2009;66:771–782
Relative Orientation of Rigid Nitroxides by PELDOR: Beyond Distance Measurements in Nucleic Acids
Authors: Schiemann Olav , Cekan Pavol , Margraf Dominik , Prisner Thomas F. , Sigurdsson Snorri Th.
Published: March 2009

Eine starre Spinmarkierung Çermöglichte es, den Abstand und die Orientierung zweier Nitroxid‐Spinmarkierungen in DNA mithilfe von PELDOR bei üblichen X‐Band‐Frequenzen zu bestimmen. Die Information über die Orientierung erhielt man, indem die Position der Detektionspulse im Nitroxidspektrum variiert wurde. Eine Simulation des Satzes von Zeitspuren ergab sehr genaue Werte für Abstände und Winkel.

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Sulfatierte und nicht sulfatierte Glycopeptid‐Erkennungsdomänen des P‐Selektin‐Glycoprotein‐Liganden 1 und ihre Bindung an P‐ und E‐Selektin
Authors: Baumann Katharina , Kowalczyk Danuta , Gutjahr Tobias , Pieczyk Markus , Jones Claire , Wild Martin K. , Vestweber Dietmar , Kunz Horst
Published: March 2009

Totalsynthese via Blockglycosylierung und selektive chemische O‐Sulfatierung von Tyrosinresten ergaben die Glycopeptid‐Erkennungsregion A (X=SO3−) des P‐Selektin‐Glycoprotein‐Liganden 1, in dem die terminale Sialinsäure der komplexen Hexasaccharid‐Seitenkette durch (S)‐Cyclohexylmilchsäure als Mimetikum ersetzt ist. In Bindungsassays zeigt die O‐sulfatierte Form A hohe Affinität zu P‐Selektin, die nicht sulfatierte Form zu E‐Selektin.

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A Different Approach to Enantioselective Organic Synthesis: Absolute Asymmetric Synthesis of Organometallic Reagents
Authors: Lennartson Anders , Olsson Susanne , Sundberg Jonas , Håkansson Mikael
Published: March 2009

Voilà, optisch aktiv: Beide Enantiomere von 1‐Chlorinden wurden ausgehend von durchweg achiralen Ausgangsmaterialien und ohne die Verwendung optisch aktiver Katalysatoren mit hoher Selektivität synthetisiert (siehe Schema). NCS=N‐Chlorsuccinimid.

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Formation of Ammonia from an Iron Nitrido Complex
Authors: Scepaniak Jeremiah J. , Young Jessica A. , Bontchev Ranko P. , Smith Jeremy M.
Published: March 2009

Radikaler Eingriff: Die Reaktion des Eisen(IV)‐Nitrid‐Komplexes [PhB(MesIm)3FeN] (siehe Bild, Mes=2,4,6‐Me3C6H2) mit 1‐Hydroxy‐2,2,6,6‐tetramethylpiperidin (TEMPO‐H) führte quantitativ zu [PhB(MesIm)3Fe(tempo)] sowie zu hohen Ausbeuten an Ammoniak. Der Mechanismus dieses Prozesses umfasst wahrscheinlich die Übertragung eines Wasserstoffatoms von TEMPO‐H auf den Nitridkomplex. Eine analoge Reaktion mit dem Triphenylmethylradikal ergab [PhB(MesIm)3FeNCPh3].

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One‐Pot Formation of Large Macrocycles with Modifiable Peripheries and Internal Cavities
Authors: Ferguson Joseph S. , Yamato Kazuhiro , Liu Rui , He Lan , Zeng Xiao Cheng , Gong Bing
Published: March 2009

Aromatische Oligohydrazid‐Makrocyclen, deren Rückgrat durch Dreizentren‐Wasserstoffbrücken in eine planare Anordnung gezwungen wird, entstehen in hohen Ausbeuten aus monomeren Disäurechloriden und Dihydraziden. Für Makrocyclen mit insgesamt sechs meta‐verknüpften Pyridin‐ und Benzolringen beträgt der Innendurchmesser ca. 10 Å. In größeren Spezies mit alternierend meta‐ und para‐verknüpften Benzolringen ragen einige Substituenten ins Ringinnere (siehe Bild).

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Stereodivergent De Novo Synthesis of Branched Amino Sugars by Lewis Acid Promoted Rearrangement of 1,2‐Oxazines
Authors: Pfrengle Fabian , Lentz Dieter , Reißig Hans‐Ulrich
Published: March 2009

Well concealed: 1,2‐oxazines such as 1 rearrange under Lewis acidic conditions to bicyclic products of type 2, which can be incorporated into oligosaccharides as protected amino sugar equivalents. Subsequent reductive steps provide unusual oligosaccharides 3 having C2‐branched 4‐amino sugar units. Most of the reactions proceed with excellent stereocontrol and allow the synthesis of a collection of stereoisomers.

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Sulfated and Non‐Sulfated Glycopeptide Recognition Domains of P‐Selectin Glycoprotein Ligand 1 and their Binding to P‐ and E‐Selectin
Authors: Baumann Katharina , Kowalczyk Danuta , Gutjahr Tobias , Pieczyk Markus , Jones Claire , Wild Martin K. , Vestweber Dietmar , Kunz Horst
Published: March 2009

Total synthesis through block glycosylation and selective chemical O‐sulfation of tyrosine residues yielded the glycopeptide recognition domain A (X=SO3−) of the P‐selectin glycoprotein ligand 1, in which the terminal sialic acid of the complex hexasaccharide side chain was replaced by (S)‐cyclohexyl lactic acid. In binding assays the O‐sulfated structure A showed high affinity towards P‐selectin, the non‐sulfated towards E‐selectin.

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A Different Approach to Enantioselective Organic Synthesis: Absolute Asymmetric Synthesis of Organometallic Reagents
Authors: Lennartson Anders , Olsson Susanne , Sundberg Jonas , Håkansson Mikael
Published: March 2009

Voilà, optical activity: Both enantiomers of 1‐chloroindene have been synthesized in high selectivity from solely achiral starting materials, and without using optically active catalysts (see scheme). These symmetry‐breaking syntheses provide a proof‐of‐concept for a new approach to asymmetric synthesis. NCS=N‐chlorosuccinimide.

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Splendid Isolation for a Nonmetallic Dication
Authors: Müller Thomas
Published: March 2009

Confined, but happy: The triflate salt of a germanium(II) dication, an atomic cation of a nonmetal, was isolated by encapsulation in [2.2.2]cryptand (see formula and molecular structure in the crystal). The cryptand satisfies the electron demand of the cation and sterically protects it (see space‐filling depiction, right).

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High Electrical Conductance of Single Molecules: A Challenge in the Series of Conjugated Oligomers
Authors: Meier Herbert
Published: March 2009

En route to molecular electronics: As extended, conjugated oligomers are desirable for molecular electronics, their electrical conductance should display a low attenuation factor. Zinc‐complexed oligo(ethynyleneporphyrindiylethynylene)s have been prepared that are distinguished by ultralow attenuation factors in single‐molecule conductance.

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Hazardous air pollutants emission from coal and oil‐fired power plants
Authors: Pudasainee Deepak , Kim Jeong‐Hun , Lee Sang‐Hyeob , Park Ju‐Myon , Jang Ha‐Na , Song Geum‐Ju , Seo Yong‐Chil
Published: March 2009

Hazardous air pollutants (HAPs) emission characteristics from coal (anthracite, bituminous) and oil‐fired power plants were studied in order to control pollutants by formulating US maximum achievable control technology (MACT)‐like regulation in Korea. Sampling and analysis were carried out according to either Korean standard test method or US EPA method. Relatively lower levels of NOx and SOx were emitted from plants burning bituminous than the anthracite coal. Less dust was emitted from oil‐fired power plants. Mercury, lead, and chromium were dominant in coal‐fired power plants, following which, nickel and chromium were emitted from oil‐fired power plants. The major volatile organic compounds (VOCs) emitted from coal‐fired plants were 1,2‐dichloroethane, benzene, carbon tetrachloride, chloroform, trichloro‐ethylene. The emission of mercury and other heavy metals in flue gas was attributed to fuel types, operating conditions, residence time in the control devices and air pollution control devices configuration. After emission tests in the field and on analysis of the continuous emission monitoring data collected from facilities under operation and consideration of other various factors, management guidelines will be suggested with special reference to US MACT‐like regulation. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd.
A novel silicate‐doped calcium‐based composite dental pulp capping agent
Authors: Chen Fangping , Mao Yuhao , Liu Changsheng , Yu Miaogen
Published: March 2009

The development of a dental pulp capping agent (DPCA) requires suitable setting time, acceptable compressive strength, favorable bioactivity, and to facilitate cementum tissue regeneration. Calcium phosphate cement (CPC) is widely used for its self‐setting, biodegradability, biocompatibility, and formability. However, a relative low strength and lack of bioactivity have limited its application. Herein, dicalcium silicate (Ca2SiO4, C2S) was introduced into CPC to prepare a novel silicate‐doped CPC/C2S composite DPCA by self‐setting in situ and its setting time, compressive strength, bioactivity, and biomineralization behaviors were investigated. The results indicated that the mechanical strength and setting time of DPCA were higher than those of pure CPC. C2S transformed into a CSH gel without disturbing the hydration of DPCA after soaking in SBF for 5 days. Moreover, much more bone‐like hydroxyapatite layers were formed, and DPCA exhibited higher bioactivity mainly in virtue of the rapid formation of CSH. DPCA with 15 wt% C2S, suggested to be the optimized composite, exhibited significantly improved bioactivity and high compressive strength, indicating that DPCA with 15 wt % C2S might have a significant pulp capping therapy advantage over the pure CPC. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd.
Patterns of query reformulation during Web searching
Authors: Jansen Bernard J. , Booth Danielle L. , Spink Amanda
Published: March 2009

Query reformulation is a key user behavior during Web search. Our research goal is to develop predictive models of query reformulation during Web searching. This article reports results from a study in which we automatically classified the query‐reformulation patterns for 964,780 Web searching sessions, composed of 1,523,072 queries, to predict the next query reformulation. We employed an n‐gram modeling approach to describe the probability of users transitioning from one query‐reformulation state to another to predict their next state. We developed first‐, second‐, third‐, and fourth‐order models and evaluated each model for accuracy of prediction, coverage of the dataset, and complexity of the possible pattern set. The results show that Reformulation and Assistance account for approximately 45% of all query reformulations; furthermore, the results demonstrate that the first‐ and second‐order models provide the best predictability, between 28 and 40% overall and higher than 70% for some patterns. Implications are that the n‐gram approach can be used for improving searching systems and searching assistance.
Restraint safety in a residential setting for persons with intellectual disabilities
Authors: Tilli David M. , Spreat Scott
Published: March 2009

The primary purpose of this study was to estimate the risks associated with the use of emergency personal restraints at a residential facility for persons with intellectual and developmental disabilities. A secondary purpose was to determine if correlates of restraint‐related injury could be determined. One in three restraints resulted in an injury, but all of the injuries were minor. In terms of prediction, frequency of aggressive behavior use was the best single predictor of restraint‐related injury. Copyright © 2009 John Wiley & Sons, Ltd.
High biological activity of a recombinant protein immobilized onto polystyrene
Authors: Kumada Yoichi , Shiritani Yuki , Hamasaki Kyoko , Ohse Takuhito , Kishimoto Michimasa
Published: March 2009

The adsorption characteristics of glutathione S‐transferases (GST) genetically fused with polystyrene (PS)‐binding peptides (PS‐tags) on PS plates with increase in hydrophilicity were studied to clarify the mechanisms of the specific interaction between the PS‐tag‐fused protein and PS plates. GST fused with the PS‐tag PS19 (RAFIASRRIKRP) preferentially interacted with hydrophilic PS plates, even in the presence of high concentrations of competitors such as Tween 20 and BSA. Both basic and aliphatic amino acids in the PS‐tags were involved in the specific interaction of PS‐tags with the surface of the hydrophilic PS plate. Genetic fusion of the PS19 variants, PS19‐4 (RAIARRIRR) and PS19‐6 (RIIIRRIRR), further improved the immobilization yield of GST in the presence of a high concentration of the competitor BSA (50 mg/mL). The PS19‐6 peptide specifically interacted with the surfaces of various hydrophilic PS plates, especially in the presence of Tween 20. Higher remaining activity was detected on all of the hydrophilic PS plates immobilized with GST‐PS19‐6 in comparison with those with wild‐type GST and GST‐PS19, and the remaining activity was further increased by the addition of Tween 20 in the adsorption state. The PS19‐6 peptide developed in this study is therefore very useful as an affinity tag that can immobilize a target protein directly onto various hydrophilic PS supports with high remaining activity.
Free heme in micromolar amounts enhances the attraction between sickle cell hemoglobin molecules
Authors: Pan Weichun , Uzunova Veselina V. , Vekilov Peter G.
Published: March 2009

We probe the role of free heme in the interactions between sickle cell hemoglobin (HbS) molecules in simulated physiological solutions: polymerization of deoxy‐HbS is the primary pathogenic event of sickle cell anemia, and HbS releases heme after autoxidation more readily than normal adult hemoglobin. We characterize these interactions in terms of osmotic virial coefficients, which we determine by static light scattering. We analyze the results in the heme‐hemoglobin system using the Kirkwood‐Goldberg model. We show that in the absence of heme, the HbS molecules weakly attract and the attraction is not due to the lowered—as a result of the sickle cell mutation—molecular charge. We show that the part of the interface between the two αβ dimers, exposed in the deoxy‐state, plays a crucial role in this attraction. We show that heme at micromolar concentrations induces strong attraction between the hemoglobin molecules. We show that the high efficacy of the heme results from the statistics of electrostatic and hydrophobic interactions between the heme and hemoglobin molecules. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1108–1116, 2009.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Gene‐expression‐based quality scores indicate optimal harvest point in Bordetella pertussis cultivation for vaccine production
Authors: van de Waterbeemd Bas , Streefland Mathieu , Pennings Jeroen , van der Pol Leo , Beuvery Coen , Tramper Johannes , Martens Dirk
Published: March 2009

The evolution of vaccine product quality during batch cultivation of Bordetella pertussis, the causative agent of whooping cough, was investigated with the goal to determine the optimal harvest point. The process was explored by measuring mRNA expression at frequent intervals during cultivation. The genes that are involved in virulence are already known for this product and changes in their expression levels are proposed to be indicative for product quality. A quantitative product quality score is calculated based on the expression levels of these virulence genes, which allows comparison of expected product quality between culture samples. Product quality scores were maximal throughout the logarithmic growth phase, but dropped significantly at the start of the stationary phase. This showed that the decreasing lactate and glutamate concentrations towards the end of the batch are critical for product quality. On‐line measurement of these nutrients allows the cultivation process to be harvested at the optimal harvest point, increasing process robustness and consistency. Biotechnol. Bioeng. 2009;103: 900–908. © 2009 Wiley Periodicals, Inc.
Tissue printing to visualize polyphenol oxidase and peroxidase in vegetables, fruits, and mushrooms
Authors: Melberg Amanda R. , Flurkey William H. , Inlow Jennifer K.
Published: March 2009

A simple tissue‐printing procedure to determine the tissue location of the endogenous enzymes polyphenol oxidase and peroxidase in a variety of vegetables, fruits, and mushrooms is described. In tissue printing, cell contents from the surface of a cut section of the tissue are transferred to an adsorptive surface, commonly a nitrocellulose membrane. Because of the considerable expense of nitrocellulose, our procedure utilizes artists' hot‐press watercolor paper as a novel and more economical alternative. Tissue prints are then exposed to an enzyme substrate from which an insoluble, colored product is produced. The appearance of color in specific areas of the print is an indication of the presence of the enzyme in those tissue locations. The experiment is designed to enable students to learn some fundamental concepts about enzymes. It has been used in an introductory‐level organic and biochemistry course for nonscience majors, but would also be appropriate for advanced high school students or could be adapted for an upper‐level undergraduate biochemistry course.
Red seaweed enzyme‐catalyzed bromination of bromophenol red: An inquiry‐based kinetics laboratory experiment for undergraduates
Authors: Jittam Piyachat , Boonsiri Patcharee , Promptmas Chamras , Sriwattanarothai Namkang , Archavarungson Nattinee , Ruenwongsa Pintip , Panijpan Bhinyo
Published: March 2009

Haloperoxidase enzymes are of interest for basic and applied bioscientists because of their increasing importance in pharmaceutical industry and environmental cleanups. In a guided inquiry‐based laboratory experiment for life‐science, agricultural science, and health science undergraduates, the bromoperoxidase from a red seaweed was used to brominate bromophenol red, a novel starting substrate. Substrate and enzyme concentration dependence of this enzyme‐catalyzed reaction as followed colorimetrically yielded initial rates of reaction that the students compared with those of their peers. The students worked as collaborative groups partially designing their own experiments and carrying them out. In performing the laboratory experiment, they were minimally guided by the instructor and teaching assistants. To engage the students before the laboratory, a short activity involving the enzyme‐induced color change was carried out. At the end of the laboratory session, student groups discussed their results in front of the class and reached their own conclusions. Most students had better understanding of important concepts in enzyme kinetics and showed good attitude toward the overall student‐centered laboratory exercise.
Problem‐solving test: The mechanism of action of a human papilloma virus oncoprotein
Authors: Szeberényi József
Published: March 2009

Terms to be familiar with before you start to solve the test: human papilloma virus; cervical cancer; oncoproteins; malignant transformation; retinoblastoma protein; cell cycle; quiescent and cycling cells; cyclin/cyclin‐dependent kinase (Cdk) complexes; E2F; S‐phase genes; enhancer element; proto‐oncogenes; tumor suppressor genes; radioactive labeling; immunoprecipitation; SDS‐polyacrylamide gel electrophoresis; autoradiography; protein phosphorylation and dephosphorylation; gene induction; agarose beads; centrifugation; Western blot analysis; phases of cell cycle; generation time.
Using clickers to improve student engagement and performance in an introductory biochemistry class
Authors: Addison Stephen , Wright Adrienne , Milner Rachel
Published: March 2009

As part of ongoing efforts to enhance teaching practices in a large‐class introductory biochemistry course, we have recently tested the effects of using a student response system (clickers) on student exam performances and engagement with the course material. We found no measurable difference in class mean composite examination score for students taught with clickers than for those taught in traditional lectures. However, there were significantly more students in the highest achievement category (91–100%) in the section that incorporated clickers than in any other section over five academic terms. Overall, students gave high approval ratings for the use of the clickers, particularly in increasing their participation and engagement in lectures. However, students who reported their performance to be in the lowest performance categories gave a lower level of approval for the use of the clickers than those who reported their performance to be in the higher performance categories. The implications for using clickers to improve teaching in biochemistry are discussed.
Enzymatic digestibility and pretreatment degradation products of AFEX‐treated hardwoods (Populus nigra)
Authors: Balan Venkatesh , Sousa Leonardo da Costa , Chundawat Shishir P. S. , Marshall Derek , Sharma Lekh N. , Chambliss C. Kevin , Dale Bruce E.
Published: March 2009

There is a growing need to find alternatives to crude oil as the primary feed stock for the chemicals and fuel industry and ethanol has been demonstrated to be a viable alternative. Among the various feed stocks for producing ethanol, poplar (Populus nigra × Populus maximowiczii) is considered to have great potential as a biorefinery feedstock in the United States, due to their widespread availability and good productivity in several parts of the country. We have optimized AFEX pretreatment conditions (180°C, 2:1 ammonia to biomass loading, 233% moisture, 30 minutes residence time) and by using various combinations of enzymes (commercical celluloses and xylanases) to achieve high glucan and xylan conversion (93 and 65%, respectively). We have also identified and quantified several important degradation products formed during AFEX using liquid chromatography followed by mass spectrometry (LC‐MS/MS). As a part of degradation product analysis, we have also quantified oligosaccharides in the AFEX water wash extracts by acid hydrolysis. It is interesting to note that corn stover (C4 grass) can be pretreated effectively using mild AFEX pretreatment conditions, while on the other hand hardwood poplar requires much harsher AFEX conditions to obtain equivalent sugar yields upon enzymatic hydrolysis. Comparing corn stover and poplar, we conclude that pretreatment severity and enzymatic hydrolysis efficiency are dictated to a large extent by lignin carbohydrate complexes and arabinoxylan cross‐linkages for AFEX. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009
Plant Cytochrome CYP74 Family: Biochemical Features, Endocellular Localisation, Activation Mechanism in Plant Defence and Improvements for Industrial Applications
Authors: Hughes Richard K. , De Domenico Stefania , Santino Angelo
Published: March 2009

Not just another P450: Shown here is a model of the overall structure of CYP74C3 with the putative membrane‐binding region that is required for enzyme activation. Members of the CYP74 family of cytochrome P450 enzymes are specialised in the metabolism of hydroperoxides and play an important role in oxylipin metabolism, which is one of the main defence mechanisms employed by plants.

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In order to respond to their rapidly changing environments, plants have evolved complex signalling pathways, which enable tight control over stress responses. Recent work has shed new light on one of these pathways that involves the different classes of plant oxylipins that are produced through the CYP74 pathway. These phytochemicals play an important role in plant defence, and can act as direct antimicrobials or as signalling molecules that inducing the expression of defence genes. The fine‐tuning regulation of defence responses, which depends on the precise cross‐talk among different signalling pathways, has important consequences for plant fitness and is a new, challenging area of research. In this review we focus on new data relating to the physiological significance of different phyto‐oxylipins and related enzymes. Moreover, recent advances in the biotechnological production of oxylipins are also discussed.
A co‐training algorithm for multi‐view data with applications in data fusion
Authors: Culp Mark , Michailidis George
Published: March 2009

In several scientific applications, data are generated from two or more diverse sources (views) with the goal of predicting an outcome of interest. Often it is the case that the outcome is not associated with any single view. However, the synergy of all measurements from each view may yield a more predictive classifier. For example, consider a drug discovery application in which individual molecules are described partially by several assay screens based on diverse profiles and partially by their chemical structural fingerprints. A common classification problem is to determine whether the molecule is associated with a particular disease. In this paper, a co‐training algorithm is developed to utilize data from diverse sources to predict the common class variable. Novel enhancements for variable importance, robustness to a mislabeled class variable, and a technique to handle unbalanced classes are applied to the motivating data set, highlighting that the approach attains strong performance and provides useful diagnostics for data analytic purposes. In addition, comparisons to a framework with data fusion using partial least squares (PLS) are also assessed on real data. An R package for performing the proposed approach is provided as Supporting information. Copyright © 2003 John Wiley & Sons, Ltd.
Oxidation of Tertiary Amines by Cytochrome P450—Kinetic Isotope Effect as a Spin‐State Reactivity Probe
Authors: Li Chunsen , Wu Wei , Cho Kyung‐Bin , Shaik Sason
Published: March 2009

Two types of tertiary amine oxidation processes, namely, N‐dealkylation and N‐oxygenation, by compound I (Cpd I) of cytochrome P450 are studied theoretically using hybrid DFT calculations. All the calculations show that both N‐dealkylation and N‐oxygenation of trimethylamine (TMA) proceed preferentially from the low‐spin (LS) state of Cpd I. Indeed, the computed kinetic isotope effects (KIEs) for the rate‐controlling hydrogen abstraction step of dealkylation show that only the KIELS fits the experimental datum, whereas the corresponding value for the high‐spin (HS) process is much higher. These results second those published before for N,N‐dimethylaniline (DMA), and as such, they further confirm the conclusion drawn then that KIEs can be a sensitive probe of spin state reactivity. The ferric‐carbinolamine of TMA decomposes most likely in a non‐enzymatic reaction since the FeO bond dissociation energy (BDE) is negative. The computational results reveal that in the reverse reaction of N‐oxygenation, the N‐oxide of aromatic amine can serve as a better oxygen donor than that of aliphatic amine to generate Cpd I. This capability of the N‐oxo derivatives of aromatic amines to transfer oxygen to the heme, and thereby generate Cpd I, is in good accord with experimental data previously reported.
Base‐Catalyzed Highly Stereoselective Conversion of γ‐Hydroxy‐α,β‐acetylenic Esters to γ‐Acetoxy Dienoates
Authors: Yue Yang , Yu Xiao‐Qi , Pu Lin
Published: March 2009

A convenient route with high stereo control to γ‐acetoxy dienoates is provided by the reaction of methyl propiolate with aldehydes in the presence of ZnEt2 and N‐methylimidazole at room temperature, followed by the catalytic conversion of the resulting γ‐hydroxy‐α,β‐acetylenic esters with p‐N,N‐dimethylaminopyridine (DMAP) in acetic anhydride (see scheme).

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γ‐Hydroxy‐α,β‐acetylenic esters can be conveniently prepared from the reaction of methyl propiolate with aldehydes in the presence of ZnEt2 and N‐methylimidazole at room temperature. It is discovered that the γ‐hydroxy‐α,β‐acetylenic esters can be catalyzed by p‐N,N‐dimethylaminopyridine (DMAP) in acetic anhydride to generate the γ‐acetoxy dienoates with high stereo control. The mechanism of this conversion is investigated by NMR ananlyses and isotope labeling experiments. An intramolecular Diels–Alder reaction of a γ‐acetoxy dienoate is conducted to show the synthetic potential of these compounds.
A New Quantum Chemical Approach to the Magnetic Properties of Oligonuclear Transition‐Metal Complexes: Application to a Model for the Tetranuclear Manganese Cluster of Photosystem II
Authors: Pantazis Dimitrios A. , Orio Maylis , Petrenko Taras , Zein Samir , Bill Eckhard , Lubitz Wolfgang , Messinger Johannes , Neese Frank
Published: March 2009

Broken‐symmetry DFT calculations on transition‐metal clusters with more than two centers allow the hyperfine coupling constants to be extracted. Application of the proposed theoretical scheme to a tetranuclear manganese complex that models the S2 state of the oxygen‐evolving complex of photosystem II yields hyperfine parameters that can be directly compared with experimental data. The picture shows the metal–oxo core of the model and the following parameters; exchange coupling constant Jij, the expectation value of the site‐spin operator ${{\left\langle {{\rm S}_{\rm z}^{({\rm{{\rm K}}})} } \right\rangle }}$, and the isotropic hyperfine coupling ${{{\rm A}_{{\rm{{\rm iso}}}}^{{\rm{({\rm K})}}} }}$ parameters.

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The reliable correlation of structural features and magnetic or spectroscopic properties of oligonuclear transition‐metal complexes is a critical requirement both for research into innovative magnetic materials and for elucidating the structure and function of many metalloenzymes. We have developed a novel method that for the first time enables the extraction of hyperfine coupling constants (HFCs) from broken‐symmetry density functional theory (BS‐DFT) calculations on clusters. Using the geometry‐optimized tetranuclear manganese complex [Mn4O6(bpy)6]4+/3+ as a model, we first examine in detail the calculation of exchange coupling constants J through the BS‐DFT approach. Complications arising from the indeterminacy of experimentally fitted J constants are identified and analyzed. It is found that only the energy levels derived from Hamiltonian diagonalization are a physically meaningful basis for comparing theory and experiment. Subsequently, the proposed theoretical scheme is applied to the calculation of 55Mn HFCs of the MnIII,IV,IV,IV state of the complex, which is similar to the S2 state of the oxygen‐evolving complex (OEC) in photosystem II of oxygenic photosynthesis. The new approach performs reliably and accurately, and yields calculated HFCs that can be directly compared with experimental data. Finally, we carefully examine the dependence of HFC on the J value and draw attention to the sensitivity of the calculated values to the exchange coupling parameters. The proposed strategy extends naturally to hetero‐oligonuclear clusters of arbitrary shape and nuclearity, and hence is of general validity and usefulness in the study of magnetic metal clusters. The successful application of the new approach presented here is a first step in the effort to establish correlations between the available spectroscopic information and the structural features of complex metalloenzymes like OEC.
A General Palladium‐Catalyzed Amination of Aryl Halides with Ammonia
Authors: Schulz Thomas , Torborg Christian , Enthaler Stephan , Schäffner Benjamin , Dumrath Andreas , Spannenberg Anke , Neumann Helfried , Börner Armin , Beller Matthias
Published: March 2009

A new robust palladium/phosphine catalyst system for the selective monoarylation of ammonia with different aryl bromides and chlorides has been developed. The active catalyst is formed in situ from [Pd(OAc)2] and air‐ and moisture‐stable phosphines as easy‐to‐handle pre‐catalysts. The productivity of the catalyst system is comparable to that of competitive Pd/phosphine systems; full conversion is achieved with most substrates with 1–2 mol % of Pd source and a fourfold excess of ligand (L).

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ChemInform Abstract: Supported Metal Nanoparticles on Porous Materials. Methods and Applications
Authors: White Robin J. , Luque Rafael , Budarin Vitality L. , Clarke James H. , Macquarrie Duncan J.
Published: March 2009

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Convective diffusion in a parallel plate duct with one catalytic wall — Laminar Flow — First order reaction part I — Analytical
Authors: Gidaspow Dimitri
Published: March 2009

CHARLES W. SOLBRIG

The problem of convective diffusion with a first order reaction on one wall of a catalytic reactor is solved to implement the determination of rate constants from overall conversion measurements. The analysis applies to an isothermal gas mixture with constant physical properties and a parabolic velocity profile. A complete separation of variables, an entrance region, and a fully developed solution as well as asymptotic expressions for large eigenvalues are presented.

A formula is given which expresses the Nusselt number as a function of the rate constants. These quantities combine as additive resistances to form an effective rate constant. By analogy, one could apply these results to a plate heat exchanger with a finite wall resistance.
Convective diffusion in a parallel plate duct with one catalytic wall—laminar flow—first order reaction: Part II: Experimental
Authors: Kvlacki Francis A. , Gidaspow Dmitri
Published: March 2009

The catalytic reaction rate of combustion of hydrogen in air on platinized alumina was measured in a flat rectangular flow reactor with one catalytic wall in laminar flow. Since the rate of reaction is very high, this measurement normally must be made in turbulent flow. However, with the aid of the measured concentration profiles and the analysis presented in Part I, it was possible to ascertain the reaction rate in the laminar flow regime. The rate constants compare well with literature values which were measured in the turbulent flow regime. Average Nusselt numbers for mass transfer calculated for the diffusionally limited cases were in good agreement with those obtained from Part I.

A narrow rectangular channel (aspect ratio = 8:1) with 16‐in. of one wall comprising the reactive section was constructed for this investigation. The channel has a long preheat section, an adiabatic section with multiple heaters, and thermocouples for maintaining isothermal conditions. Two micrometer mounted probes are inserted through the wall opposite the replaceable catalytic section. Concentrations are measured at the inlet, inside the reactive section, and at the outlet in a mixing chamber.
Interphase mass transfer in binary liquid systems — Laminar liquid jets
Authors: Fosberg T. M. , Heideger W. J.
Published: March 2009

Interphase mass transfer was investigated in binary liquid systems using the laminar jet technique. A mathematical model of the mass transfer process was developed and appropriate experimental measurements were made in the cyclohexanol‐water, isobutanol‐water and ethyl acetate‐water systems. Good correspondence was obtained between predicted and measured mass transfer rates, which was taken to validate the use of the model. In particular the results indicated that, within the limits of experimental accuracy, interfacial equilibrium prevails in these systems for contact times on the order of one‐half second.
Gas mixing in fluidized beds containing screen packings
Authors: Chen B. H. , Osberg G. L.
Published: March 2009

Gas mixing was studied in a fluidized bed containing hollow, open‐wall packings using a continuous injection of oxygen as a tracer.

During bed expansion, the reciprocal of mixing length, u/E1, for a gas‐fiuidized bed containing packings of dimension less than 3‐in. was found to decrease and then increase with the expansion ratio, Δ, passing through a minimum, in contrast to an unpacked fluidized bed for which no minimum u/E1, was reported.

The minimum u/E1, occurred always at Δ = 0.30, independent of column diameter, of the shape or of the size of the packing, and of the size of the fluidizing particle. Values of the minimum u/E1's for a fluidized bed packed with various screen cylinders depended upon the size of the packing, dn, and of the fluidized particle, d1,. An empirical correlation of (u/E1)mn, with d1, and dn is presented.
Selective extraction of potassium chloride from saskatchewan sylvinite ore
Authors: Taylor J. B. , Hunt M. R. , Despault G. J. , Agyako A. H.
Published: March 2009

The distribution of potassium chloride in Saskatchewan sylvinite ore samples has been investigated using autoradiography. Saturated or nearly saturated aqueous solutions of sodium chloride have been used in an attempt to selectively leach out the potassium chloride from the ore. Selective leaching can only be achieved in ores having a contiguous association of potassium chloride crystals. Ores richer than 30% potassium chloride can be expected to fulfil this condition. Accompanying the dissolution of potassium chloride is a simultaneous recrystallization of sodium chloride which accumulates on the dissolving face of the potassium chloride and prevents further extraction. Trace amounts ofPb2+orMn2+ions prevent the accumulation of recrystallized sodium chloride and ensure that the dissolution of potassium chloride proceeds to completion. ThePb2+ion severely retards the dissolution of both sodium and potassium chlorides.Mn2+ion has little or no effect on the kinetics of the dissolution process and is accordingly the preferred additive.
Wall to fluid heat transfer in liquid fluidised beds: Part 2
Authors: Asmund B. W , Smith J. W.
Published: March 2009

Wall to fluid heat transfer coefficients and radial temperature profiles have been obtained for beds of hydrodynamically similar spheres fluidized with water in a 2.058 inch pipe at a constant heat flux. From packed bed to open pipe conditions, heat transport occurs mainly by turbulent mixing, although conduction through the particles and possibly particle convection have some effect at low porosities. This result contradicts a previously published prediction based on model calculations using erroneous temperature profiles(24). The model predicts a minor role for particle convection when appropriate temperature profiles are used.

A series model based on the observed shift of thermal resistance from the wall region to the bulk of the bed with decreasing porosity is used to correlate heat transfer coefficients. The shift in resistance largely accounts for the maximum in heat transfer coefficient plots.