bluuebunny/crossref_metadata_2025 huggingface dataset:
Neurobiological Background for Performing Surgical Intervention in the Inferior Thalamic Peduncle for Treatment of Major Depression Disorders
Authors: Velasco Francisco , Velasco Marcos , Jiménez Fiacro , Velasco Ana Luisa , Salin-Pascual Rafael
Published: September 2005

OBJECTIVE:

To present a review of evidence for an inhibitory thalamo-orbitofrontal system related to physiopathology of major depression disorders (MDDs) and to postulate that interfering with hyperactivity of the thalamo-orbitofrontal system by means of chronic high-frequency electrical stimulation of its main fiber connection, the inferior thalamic peduncle (ITP), may result in an improvement in patients with MDD.

METHODS:

Experimentally, the thalamo-orbitofrontal system has been proposed as part of the nonspecific thalamic system. Under normal conditions, the nonspecific thalamic system induces characteristic electrocortical synchronization in the form of recruiting responses that mimic some sleep stages. It also inhibits input of irrelevant sensory stimuli, thus facilitating the process of selective attention. Permanent disruption of the system, via lesioning or temporary inactivation through cooling of the ITP with cryoprobes, results in a state of hyperkinesia, increased attention, and cortical desynchronization.

RESULTS:

Surgical lesioning of the medial part of orbitofrontal cortex and white matter overlying area 13, which includes the ITP, may result in significant improvement in MDD. Imaging studies (functional magnetic resonance imaging and positron emission tomography) consistently demonstrate hyperactivity in the orbitofrontal cortex and midline thalamic regions during episodes of MDD. This hyperactivity decreases with efficient control of MDD by medical treatment, indicating that orbitofrontal cortex and midline thalamic overactivity are related to the depressive condition. Conversely, noradrenergic and serotoninergic systems in the frontal lobes have been implicated in the pathophysiology of MDD. Although noradrenergic receptor density in the frontal lobe is consistently increased in depressed patients who commit suicide, 5-hydroxytryptamine reuptake blockers, which are potent antidepressive drugs, decrease hypermetabolism in the orbital frontal cortex in MDD. Therefore, the serotonin hypothesis for depression postulates that norepinephrine and serotonin in the frontal lobes are required to maintain antidepressive responsiveness. Dysregulation of the secretion of both neurotransmitters initiates overactivity of orbitofrontal cortex, resulting in depression. It is possible that surgical interventions in this region, including electrical stimulation of ITP, disrupt adrenergic and serotoninergic dysregulation in patients with MDD.

CONCLUSION:

Circumscribed lesions or electrical stimulation of the ITP, a discrete target easily identified by electrophysiological studies, may improve MDD. Electrical stimulation may have the advantage of being less invasive and more adjustable to patient needs.
Processing of speech signals using a microphone array for intelligent robots
Authors: Hu J , Cheng C C , Liu W H
Published: September 2005

For intelligent robots to interact with people, an efficient human-robot communication interface is very important (e.g. voice command). However, recognizing voice command or speech represents only part of speech communication. The physics of speech signals includes other information, such as speaker direction. Secondly, a basic element of processing the speech signal is recognition at the acoustic level. However, the performance of recognition depends greatly on the reception. In a noisy environment, the success rate can be very poor. As a result, prior to speech recognition, it is important to process the speech signals to extract the needed content while rejecting others (such as background noise). This paper presents a speech purification system for robots to improve the signal-to-noise ratio of reception and an algorithm with a multidirection calibration beamformer.
Iterative linear matrix inequality algorithms for fault detection with unknown inputs
Authors: Wang H , Lam J , Ding S X , Zhong M
Published: September 2005

This paper deals with the fault detection problem for linear time-invariant systems with unknown disturbances. Two separate performance indices are presented to facilitate the design of desirable fault detection observers. Iterative linear matrix inequality (LMI) algorithms are proposed in order to design a fault detection observer that aims at enhancing the fault detection and attenuating the effects due to unknown inputs. Numerical examples are employed to demonstrate the effectiveness of the proposed methods.
Robust position control of a perturbed electrical servo drive system via the adaptive fuzzy sliding-mode technique
Authors: Kung Chung-Chun , Su Kuo-Ho
Published: September 2005

A novel adaptive fuzzy sliding-mode control (AFSMC) system for high-precision position control of a perturbed electrical servo drive is developed in this paper. The proposed AFSMC system is designed via the approximation ability of a fuzzy system to mimic the good behaviour of a total sliding-mode control (TSMC) system, which is designed without the reaching phase of a conventional sliding-mode control (SMC). In the developed system, a priori knowledge of the system information is not required. Moreover, the gradually increasing estimate upper bound, which may induce the control effort into saturation and excite unstable system dynamics in some conditions, would not exist. In the proposed controller, the adaptive tuning algorithms are developed in the sense of the Lyapunov stability theorem, so that system-tracking stability can be guaranteed. Finally, the effectiveness of the proposed control scheme is verified via the experimental results of a field-oriented control permanent magnet (PM) synchronous motor.
Product Line Selection and Pricing with Modularity in Design
Authors: Hopp Wallace J. , Xu Xiaowei
Published: September 2005

This paper addresses the strategic impact of modular design on the optimal length and price of a differentiated product line. We represent consumer demand with a Bayesian logit model. We also break operations costs into product design and production components. Our analysis shows that reducing product development costs via modular design always makes it attractive to offer greater product variety. However, reducing production costs can sometimes motivate a reduction in variety for a risk-averse producer in a multiple-segment market. We also characterize the impacts of degree of modularity and production cost on price markup and market share. Finally, we show that the optimal product line length is monotonic in risk attitude and the monotonic weak majorization, partial order on product assortment.
Trade-offs Between Customer Service and Cost in Integrated Supply Chain Design
Authors: Shen Zuo-Jun Max , Daskin Mark S.
Published: September 2005

When designing supply chains, firms are often faced with the competing demands of improved customer service and reduced cost. We extend a cost-based location-inventory model (Shen et al. 2003) to include a customer service element and develop practical methods for quick and meaningful evaluation of cost/service trade-offs. Service is measured by the fraction of all demands that are located within an exogenously specified distance of the assigned distribution center. The nonlinear model simultaneously determines distribution center locations and the assignment of demand nodes to distribution centers to optimize the cost and service objectives. We use a weighting method to find all supported points on the trade-off curve. We also propose a heuristic solution approach based on genetic algorithms that can generate optimal or close-to-optimal solutions in a much shorter time compared to the weighting method. Our results suggest that significant service improvements can be achieved relative to the minimum cost solution at a relatively small incremental cost.
Organizing and the Process of Sensemaking
Authors: Weick Karl E. , Sutcliffe Kathleen M. , Obstfeld David
Published: September 2005

Sensemaking involves turning circumstances into a situation that is comprehended explicitly in words and that serves as a springboard into action. In this paper we take the position that the concept of sensemaking fills important gaps in organizational theory. The seemingly transient nature of sensemaking belies its central role in the determination of human behavior, whether people are acting in formal organizations or elsewhere. Sensemaking is central because it is the primary site where meanings materialize that inform and constrain identity and action. The purpose of this paper is to take stock of the concept of sensemaking. We do so by pinpointing central features of sensemaking, some of which have been explicated but neglected, some of which have been assumed but not made explicit, some of which have changed in significance over time, and some of which have been missing all along or have gone awry. We sense joint enthusiasm to restate sensemaking in ways that make it more future oriented, more action oriented, more macro, more closely tied to organizing, meshed more boldly with identity, more visible, more behaviorally defined, less sedentary and backward looking, more infused with emotion and with issues of sensegiving and persuasion. These key enhancements provide a foundation upon which to build future studies that can strengthen the sensemaking perspective.
Prospects for Organization Theory in the Early Twenty-First Century: Institutional Fields and Mechanisms
Authors: Davis Gerald F. , Marquis Christopher
Published: September 2005

This paper argues that research in organization theory has seen a shift in orientation from paradigm-driven work to problem-driven work since the late 1980s. A number of paradigms for the study of organizations were elaborated during the mid-1970s, including transaction cost economics, resource dependence theory, organizational ecology, new institutional theory, and agency theory in financial economics. These approaches reflected the dominant trends of the large corporations of their time: increasing concentration, diversification, and bureaucratization. However, subsequent shifts in organizational boundaries, the increased use of alliances and network forms, and the expanding role of financial markets in shaping organizational decision making all make normal science driven by the internally derived questions from these paradigms less fruitful. Instead, we argue that problem-driven work that uses mechanism-based theorizing and research that takes the field rather than the organization as the unit of analysis are the most appropriate styles of organizational research under conditions of major economic change—such as our own era. This sort of work is best exemplified by various studies under the rubric of institutional theory in the past 15 years, which are reviewed here.
Identifying Situated Cognition in Organizations
Authors: Elsbach Kimberly D. , Barr Pamela S. , Hargadon Andrew B.
Published: September 2005

Using the established definition of situated cognition in organizations as “the interaction of cognitive schemas and organizational context” (Lant 2002), we examine empirical case studies from the last 15 years to illustrate what situated cognitions in organizations might actually look like. Grounded in this research, we develop a framework that identifies how some specific forms of cognitive schemas (i.e., rule schemas, event schemas, person schemas) and specific contexts (e.g., physical contexts, institutional contexts) interact during sensemaking processes to give rise to momentary perceptions that we call situated cognitions. We present evidence that common patterns of interaction between schemas and context may occur during sensemaking in organizations. In terms of theoretical implications, our framework focuses attention on the specific interactions between context and cognition (rather than on context or cognition alone) that comprise situated cognitions, and helps to more concretely define situated cognitions as momentary or temporally bounded perceptions. We offer several practical implications of this framework for managers and suggest avenues for further elaboration on our ideas through research.
Nucleotide Diversity and Linkage Disequilibrium in Cold-Hardiness- and Wood Quality-Related Candidate Genes in Douglas Fir
Authors: Krutovsky Konstantin V , Neale David B
Published: September 2005

Nuclear sequence variation and linkage disequilibrium (LD) were studied in 15 cold-hardiness- and 3 wood quality-related candidate genes in Douglas fir [Pseudotsuga menziesii (Mirb.) Franco]. This set of genes was selected on the basis of its function in other plants and collocation with cold-hardiness-related quantitative trait loci (QTL). The single-nucleotide polymorphism (SNP) discovery panel represented 24 different trees from six regions in Washington and Oregon plus parents of a segregating population used in the QTL study. The frequency of SNPs was one SNP per 46 bp across coding and noncoding regions on average. Haplotype and nucleotide diversities were also moderately high with Hd = 0.827 ± 0.043 and π = 0.00655 ± 0.00082 on average, respectively. The nonsynonymous (replacement) nucleotide substitutions were almost five times less frequent than synonymous ones and substitutions in noncoding regions. LD decayed relatively slowly but steadily within genes. Haploblock analysis was used to define haplotype tag SNPs (htSNPs). These data will help to select SNPs for association mapping, which is already in progress.
Analysis of Repeat-Mediated Deletions in the Mitochondrial Genome of Saccharomyces cerevisiae
Authors: Phadnis Naina , Sia Rey A , Sia Elaine A
Published: September 2005

Mitochondrial DNA deletions and point mutations accumulate in an age-dependent manner in mammals. The mitochondrial genome in aging humans often displays a 4977-bp deletion flanked by short direct repeats. Additionally, direct repeats flank two-thirds of the reported mitochondrial DNA deletions. The mechanism by which these deletions arise is unknown, but direct-repeat-mediated deletions involving polymerase slippage, homologous recombination, and nonhomologous end joining have been proposed. We have developed a genetic reporter to measure the rate at which direct-repeat-mediated deletions arise in the mitochondrial genome of Saccharomyces cerevisiae. Here we analyze the effect of repeat size and heterology between repeats on the rate of deletions. We find that the dependence on homology for repeat-mediated deletions is linear down to 33 bp. Heterology between repeats does not affect the deletion rate substantially. Analysis of recombination products suggests that the deletions are produced by at least two different pathways, one that generates only deletions and one that appears to generate both deletions and reciprocal products of recombination. We discuss how this reporter may be used to identify the proteins in yeast that have an impact on the generation of direct-repeat-mediated deletions.
Identification of Quantitative Trait Loci That Regulate Arabidopsis Root System Size and Plasticity
Authors: Fitz Gerald Jonathan N , Lehti-Shiu Melissa D , Ingram Paul A , Deak Karen I , Biesiada Theresa , Malamy Jocelyn E
Published: September 2005

Root system size (RSS) is a complex trait that is greatly influenced by environmental cues. Hence, both intrinsic developmental pathways and environmental-response pathways contribute to RSS. To assess the natural variation in both types of pathways, we examined the root systems of the closely related Arabidopsis ecotypes Landsberg erecta (Ler) and Columbia (Col) grown under mild osmotic stress conditions. We found that Ler initiates more lateral root primordia, produces lateral roots from a higher percentage of these primordia, and has an overall larger root system than Col under these conditions. Furthermore, although each of these parameters is reduced by osmotic stress in both ecotypes, Ler shows a decreased sensitivity to osmotica. To understand the genetic basis for these differences, QTL for RSS under mild osmotic stress were mapped in a Ler × Col recombinant inbred population. Two robust quantitative trait loci (QTL) were identified and confirmed in near-isogenic lines (NILs). The NILs also allowed us to define distinct physiological roles for the gene(s) at each locus. This study provides insight into the genetic and physiological complexity that determines RSS and begins to dissect the molecular basis for naturally occurring differences in morphology and developmental plasticity in the root system.
The Cooperative Molecular Field Effect
Authors: Cahen D. , Naaman R. , Vager Z.
Published: September 2005

Two‐dimensional arrangements of molecules can show remarkable cooperative electronic effects. Such effects can serve to achieve direct electronic sensing of chemical and physical processes via electrostatic effects, i.e., without transfer of charge or matter between the locus of sensing and that of detection.
A CFD–PBM coupled model for gas–liquid flows
Authors: Wang Tiefeng , Wang Jinfu , Jin Yong
Published: September 2005

A computational fluid dynamics–population balance model (CFD‐PBM) coupled model was developed that combines the advantages of CFD to calculate the entire flow field and of the PBM to calculate the local bubble size distribution. Bubble coalescence and breakup were taken into account to determine the evolution of the bubble size. Different bubble breakup and coalescence models were compared. An algorithm was proposed for computing the parameters based on the bubble size distribution, including the drag force, transverse lift force, wall lubrication force, turbulent dispersion force, and bubble‐induced turbulence. With the bubble breakup and coalescence models and the interphase force formulations in this work, the CFD‐PBM coupled model can give a unified description for both the homogeneous and the heterogeneous regimes. Good agreement was obtained with the experimental results for the gas holdup, liquid velocity, and bubble size distribution. © 2005 American Institute of Chemical Engineers AIChE J, 2006
Novel experiments and a mechanistic model for macroinstabilities in stirred tanks
Authors: Paglianti A. , Montante G. , Magelli F.
Published: September 2005

In this work a new experimental technique and a simple model for the identification and the analysis of macro‐instabilities (MIs) in stirred tanks are presented. A pressure transducer is proposed for detecting the MIs that can take place inside a stirred vessel; its main advantages are the non‐intrusivity, cheapness, and simplicity of installation and operation. Moreover, it can be used for both laboratory and industrial scale stirred tanks. The experimental technique and the time series analysis method, based on Fast Fourier Transform (FFT), are shown to provide reliable information on the frequency of MIs, through the comparison of the present data with those, from literature, obtained in similar systems. Its applicability to solid‐liquid systems is also assessed. Afterwards, the data collected in several conditions differing by geometric characteristics of the stirred tanks and by the physical properties of the systems are presented. Finally, a new simplified model, based on the theory of impinging jets,1 is suggested for predicting the MI frequency. © 2005 American Institute of Chemical Engineers AIChE J, 2006
Genome‐wide SNP arrays as a diagnostic tool: Clinical description, genetic mapping, and molecular characterization of Salla disease in an Old Order Mennonite population
Authors: Strauss Kevin A. , Puffenberger Erik G. , Craig David W. , Panganiban Corrie B. , Lee Anne M. , Hu‐Lince Diane , Stephan Dietrich A. , Morton D. Holmes
Published: September 2005

An Old Order Mennonite child was evaluated for gross motor delay, truncal ataxia, and slow linear growth. The diagnostic evaluation, which included sub‐specialty consultations, neuroimaging, and metabolic testing, was long, costly, and did not yield a diagnosis. Recognition of a similarly affected second cousin prompted a genome‐wide homozygosity mapping study using high‐density single nucleotide polymorphism (SNP) arrays. SNP genotypes from two affected individuals and their parents were used to localize the disease locus to a 14.9 Mb region on chromosome 6. This region contained 55 genes, including SLC17A5, the gene encoding the lysosomal N‐acetylneuraminic acid transport protein. Direct sequencing of SLC17A5 in the proband revealed homozygosity for the 115C → T (R39C) sequence variant, the common cause of Salla disease in Finland. Three additional affected Mennonite individuals, ages 8 months to 50 years, were subsequently identified by directed molecular genetic testing. This small‐scale mapping study was rapid, inexpensive, and analytically simple. In families with shared genetic heritage, genome‐wide SNP arrays with relatively high marker density allow disease gene mapping studies to be incorporated into routine diagnostic evaluations. © 2005 Wiley‐Liss, Inc.
Facial and physical features of Aicardi syndrome: Infants to teenagers
Authors: Sutton V. Reid , Hopkins Bobbi J. , Eble Tanya N. , Gambhir Nikki , Lewis Richard A. , Van den Veyver Ignatia B.
Published: September 2005

Aicardi syndrome is a sporadic disorder that affects primarily females and is hypothesized to be caused by heterozygous mutations in an X‐linked gene. Its main features include of a triad of infantile spasms, agenesis of the corpus callosum, and distinctive chorioretinal lacunae. Additional common findings include moderate to profound mental retardation, gray matter heterotopia, gyral anomalies, and vertebral and rib defects. To date, no consistent facial dysmorphisms have been described. We examined 40 girls with Aicardi syndrome and determined that consistent facial features appeared in over half the study participants and included a prominent premaxilla, upturned nasal tip, decreased angle of the nasal bridge, and sparse lateral eyebrows. Externally apparent microphthalmia was seen in 10/40 (25%). Various skin lesions (including multiple nevi, skin tags, hemangiomas, one giant melanotic nevus, and a history of a previously removed angiosarcoma) were present in 8/40 (20%). Hand abnormalities were seen in 3/40 (7.5%) and included camptodactyly, proximal placement of the thumb and hypoplasia of the fifth finger. This study clearly delineates the existence of a distinctive facial phenotype of Aicardi syndrome not previously described. We recommend that features of a prominent premaxilla with upturned nasal tip and vascular malformations/vascular tumors be added to the modified diagnostic criteria in order to improve the ability of geneticists to diagnose Aicardi syndrome. © 2005 Wiley‐Liss, Inc.
Multiple dose pharmacokinetics of caffeine administered in chewing gum to normal healthy volunteers
Authors: Syed Shariq A. , Kamimori Gary H. , Kelly William , Eddington Natalie D.
Published: September 2005

The purpose of this study was to examine the pharmacokinetics of three doses of caffeine administered as Stay Alert® chewing gum in a multiple dose regimen.

Methods: A double‐blind, parallel randomized, four‐treatment study design was employed. The treatment groups were: 50, 100 and 200 mg caffeine and placebo. Subjects were 48 (n = 12 per group), healthy, non‐smoking, males and females who had abstained from caffeine ingestion for at least 20 h prior to dosing, who were randomly assigned to the treatment groups. Caffeine was administered at 2400, 0200 and 0400 h depending on the treatment group. Blood samples were collected pre‐dose and at 5, 15, 30, 45, 60, 75, 90 and 105 min after each caffeine dose. Samples were also collected at 7.5, 8.5 and 18 h after the last dose of caffeine. Plasma caffeine levels were analysed by a validated UV‐HPLC method.

Result: The mean Tmax after the third dosing ranged from 0.37 to 1.12 h. Cmax for 50, 100 and 200 mg was 2.69, 3.45 and 6.33 mg/l, respectively. AUCinf for 50, 100 and 200 mg group was 33.2, 46.94 and 86.94 mg/l * h, respectively. AUCinf values suggested a dose proportionate increase. Dose normalized Cmax and AUC0−τ values across doses were not significantly different, suggesting linearity was maintained after multiple doses of the Stay Alert® chewing gum. There were no group related differences in elimination.

Conclusions: The results suggest that caffeine administered in the gum formulation (Stay Alert® chewing gum) via a multiple dosing regimen provides an effective and convenient means of maintaining effective concentrations of caffeine that would in some operational scenarios be desirable for maintaining alertness and performance in sleep deprived individuals. Copyright © 2005 John Wiley & Sons, Ltd.
Transport phenomena during freezing of adipose tissue derived adult stem cells
Authors: Thirumala Sreedhar , Gimble Jeffrey M. , Devireddy Ram V.
Published: September 2005

In the present study a well‐established differential scanning calorimeter (DSC) technique is used to measure the water transport phenomena during freezing of stromal vascular fraction (SVF) and adipose tissue derived adult stem (ADAS) cells at different passages (Passages 0 and 2). Volumetric shrinkage during freezing of adipose derived cells was obtained at a cooling rate of 20°C/min in the presence of extracellular ice and two different, commonly used, cryoprotective agents, CPAs (10% DMSO and 10% Glycerol). The adipose derived cells were modeled as spheres of 50 µm diameter with an osmotically inactive volume (Vb) of 0.6Vo, where Vo is the isotonic cell volume. By fitting a model of water transport to the experimentally obtained volumetric shrinkage data, the “best‐fit” membrane permeability parameters (reference membrane permeability to water, Lpg or Lpg[cpa] and the activation energy, ELp or ELp[cpa]) were determined. The “best‐fit” membrane permeability parameters for adipose derived cells in the absence and presence of CPAs ranged from: Lpg = 23.1–111.5 × 10−15 m3/Ns (0.135–0.652 µm/min‐atm) and ELp = 43.1–168.8 kJ/mol (9.7–40.4 kcal/mol). Numerical simulations of water transport were then performed under a variety of cooling rates (5–100°C/min) using the experimentally determined membrane permeability parameters. And finally, the simulation results were analyzed to predict the optimal rates of freezing adipose derived cells in the presence and absence of CPAs. © 2005 Wiley Periodicals, Inc.
Prediction of gas‐liquid mass transfer coefficient in sparged stirred tank bioreactors
Authors: Garcia‐Ochoa Felix , Gomez Emilio
Published: September 2005

Oxygen mass transfer in sparged stirred tank bioreactors has been studied. The rate of oxygen mass transfer into a culture in a bioreactor is affected by operational conditions and geometrical parameters as well as the physicochemical properties of the medium (nutrients, substances excreted by the micro‐organism, and surface active agents that are often added to the medium) and the presence of the micro‐organism. Thus, oxygen mass transfer coefficient values in fermentation broths often differ substantially from values estimated for simple aqueous solutions. The influence of liquid phase physicochemical properties on k
La must be divided into the influence on kL and a, because they are affected in different ways. The presence of micro‐organisms (cells, bacteria, or yeasts) can affect the mass transfer rate, and thus kLa values, due to the consumption of oxygen for both cell growth and metabolite production. In this work, theoretical equations for kLa prediction, developed for sparged and stirred tanks, taking into account the possible oxygen mass transfer enhancement due to the consumption by biochemical reactions, are proposed. The estimation of k
La is carried out taking into account a strong increase of viscosity broth, changes in surface tension and different oxygen uptake rates (OURs), and the biological enhancement factor, E, is also estimated. These different operational conditions and changes in several variables are performed using different systems and cultures (xanthan aqueous solutions, xanthan production cultures by Xanthomonas campestris, sophorolipids production by Candida bombicola, etc.). Experimental and theoretical results are presented and compared, with very good results. © 2005 Wiley Periodicals, Inc.
Engineering an affinity tag for genetically encoded cyclic peptides
Authors: Naumann Todd A. , Savinov Sergey N. , Benkovic Stephen J.
Published: September 2005

Peptide expression libraries are valuable probes of cellular function. SICLOPPS technology merges the principal advantages of both genetic methods and small‐molecule approaches in yielding superior library sizes of operationally stable, structurally well‐defined entities with an established biological and medicinal record. Here, we describe development, application, and the first‐generation library implementation of an expressed affinity tag for a library of cyclic peptides. A tripeptide streptavidin‐binding motif (HPQ) proved to be compatible with presentation from a backbone cyclized template. A resulting peptide was employed as a sensitive indicator of peptide splicing, expression, and recovery as well as an affinity tag for one‐step purification. Specific recognition of the tag by streptavidin was also critical for an analysis of intein mutants. Finally, the initially identified probe was used as a template for design of a streptavidin‐responsive cyclic peptide library. © 2005 Wiley Periodicals, Inc.
Purification of different lipases from Aspergillus niger by using a highly selective adsorption on hydrophobic supports
Authors: Fernández‐Lorente Gloria , Ortiz Claudia , Segura Rosa L. , Fernández‐Lafuente Roberto , Guisán Jose M. , Palomo Jose M.
Published: September 2005

In this manuscript, we have purified three different lipases from crude preparations from Aspergillus niger in a simple fashion, secluding the esterases and other enzymes presented in the preparation. Firstly, the crude was offered at low ionic strength to octyl agarose. The support specifically adsorbed two lipases, with molecular weights of 43 and 65 kDa. Desorption with a gradient of Triton X‐100 permitted to fully purify both lipases. The addition of octadecyl‐Sepabeads support to the non‐adsorbed proteins on octyl‐agarose permitted to selectively adsorb a third lipase, having a molecular weight of 31 kDa. Desorption of the enzyme using Triton X‐100 permitted to have also a pure sample of this enzyme. A significant percentage of esterase activity remains in the supernatant, derived from esterases or lipases unable to become adsorbed on the employed supports. Furthermore, these purified lipases were immobilized via ionic adsorption on DEAE‐Sepharose and their selectivity was analyzed in the kinetic resolution of (±)‐O‐2‐butyryl‐2‐phenylacetic acid and (±)‐mandelic acid methyl ester. In the resolution of (±)‐O‐2‐butyryl‐2‐phenylacetic acid, the crude extract preparation gave a low enantioselectivity value (E = 9), whereas the three immobilized preparations of purified lipases exhibited an increase in E‐value from 11 (43 kDa lipase) to > 100 (31 kDa lipase). When (±)‐mandelic acid methyl ester was used, the crude extract preparation presented low enantioselectivity hydrolyzing the S enantiomer quicker, while the purified lipase preparations preferred the R one. In this case, the 65 kDa lipase was the most selective enzyme (E = 20). © 2005 Wiley Periodicals, Inc.
Substrate uptake tests and quantitative FISH show differences in kinetic growth of bulking and non‐bulking activated sludge
Authors: Lou Inchio , de los Reyes Francis L.
Published: September 2005

The competition between filaments and floc formers in activated sludge has been historically described using kinetic selection. However, recent studies have suggested that bacterial storage may also be an important factor in microbial selection, since the dynamic nature of substrate flows into wastewater treatment plants elicit transient responses from microorganisms. Respirometry‐based kinetic selection should thus be reevaluated by considering cell storage, and a more reliable method should be developed to include bacterial storage in the analysis of growth of filaments and floc formers in activated sludge. In this study, we applied substrate uptake tests combined with metabolic modeling to determine the growth rates, yields and maintenance coefficients of bulking and non‐bulking activated sludge developed in lab scale reactors under feast and famine conditions. The results of quantitative fluorescence in situ hybridization (FISH) showed that the filaments Eikelboom Type 1851, Type 021N, and Thiothrix nivea were dominant in bulking sludge, comprising 42.0 % of mixed liquor volatile suspended solids (MLVSS), with 61.6% of the total filament length extending from flocs into bulk solution. Only low levels of Type 1851 filament length (4.9% of MLVSS) occurred in non‐bulking sludge, 83.0% of which grew inside the flocs. The kinetic parameters determined from the substrate uptake tests were consistent with those from respirometry and showed that filamentous bulking sludge had lower growth rates and maintenance coefficients than non‐bulking sludge. These results provide support for growth kinetic differences in explaining the competitive strategy of filamentous bacteria. © 2005 Wiley Periodicals, Inc.
In silico genome‐scale reconstruction and validation of the Staphylococcus aureus metabolic network
Authors: Heinemann Matthias , Kümmel Anne , Ruinatscha Reto , Panke Sven
Published: September 2005

A genome‐scale metabolic model of the Gram‐positive, facultative anaerobic opportunistic pathogen Staphylococcus aureus N315 was constructed based on current genomic data, literature, and physiological information. The model comprises 774 metabolic processes representing approximately 23% of all protein‐coding regions. The model was extensively validated against experimental observations and it correctly predicted main physiological properties of the wild‐type strain, such as aerobic and anaerobic respiration and fermentation. Due to the frequent involvement of S. aureus in hospital‐acquired bacterial infections combined with its increasing antibiotic resistance, we also investigated the clinically relevant phenotype of small colony variants and found that the model predictions agreed with recent findings of proteome analyses. This indicates that the model is useful in assisting future experiments to elucidate the interrelationship of bacterial metabolism and resistance. To help directing future studies for novel chemotherapeutic targets, we conducted a large‐scale in silico gene deletion study that identified 158 essential intracellular reactions. A more detailed analysis showed that the biosynthesis of glycans and lipids is rather rigid with respect to circumventing gene deletions, which should make these areas particularly interesting for antibiotic development. The combination of this stoichiometric model with transcriptomic and proteomic data should allow a new quality in the analysis of clinically relevant organisms and a more rationalized system‐level search for novel drug targets. © 2005 Wiley Periodicals, Inc.
Immobilization and hybridization of DNA in a sugar polyacrylate hydrogel
Authors: Soto Carissa M. , Patterson Charles H. , Charles Paul T. , Martin Brett D. , Spector Mark S.
Published: September 2005

Using a non‐contact microarrayer, amine‐terminated probe oligonucleotides representing 20‐, 50‐, and 70‐mer fragments of the fliC gene were covalently coupled into three‐dimensional regions in a “sugar polyacrylate” hydrogel based on poly(6‐acryloyl‐β‐O‐methyl galactopyranoside‐co‐aminopropyl methacrylamide). The arrayer deposited the solution containing ssDNA probes in discrete regions on the surface of the gel (i.e. as a droplet with a ca. 450 µm diameter), allowing penetration and attachment of the ss DNA within the three dimensional region of the gel. The attachment was mediated by the homobifunctional crosslinker bis‐succinimidyl suberate. Confocal microscopy showed the density of attached probe DNA was greatest in the interior‐most regions of the gel volume. Target ssDNA (20‐ and 70‐mer) was able to diffuse through the gel and undergo successful hybridization with the probes. For target ssDNA in the concentration range 0.19 µM to 6.0 µM, there was a linear correlation between DNA concentration and the fluorescence of the gel region where hybridization occurred. © 2005 Wiley Periodicals, Inc.
Post‐translational regulation of expression and conformation of an immunoglobulin domain in yeast surface display
Authors: Parthasarathy Ranganath , Subramanian Shyamsundar , Boder Eric T. , Discher Dennis E.
Published: September 2005

Display of heterologous proteins on the surface of Saccharomyces cerevisiae is increasingly being exploited for directed evolution because of straightforward cell screens. However, yeast post‐translationally modifies proteins in ways that must be factored into library engineering and refinement. Here, we express the extracellular immunoglobulin domain of an ubiquitous mammalian membrane protein, CD47, which is implicated in cancer, immunocompatibility, and motility. CD47 has multiple sites of glycosylation and a core disulfide bond. We assess the effects of both of these post‐translational modifications on expression and antibody binding. CD47's extracellular domain is fused to the yeast mating protein Aga2p on the cell wall, and the resulting fusion protein binds several key antibodies, including a conformation‐sensitive antibody. Site‐by‐site mutagenesis of CD47's five N‐linked glycosylation sites progressively decreases expression levels on yeast, but folding appears stable. Cysteine mutations disrupt the expected core disulfide, and also decrease protein expression levels, though not to the extent seen with complete deglycosylation. However, with the core disulfide mutants, antibody binding proves to be lower than expected from expression levels and glycosylation is clearly reduced compared to wild‐type. The results indicate that glycosylation regulates heterologous display on yeast more than core disulfides do and thus suggest bounds on directed evolution by post‐translational processing. © 2005 Wiley Periodicals, Inc.
Expanded thermodynamic model for microbial true yield prediction
Authors: Xiao Jinghua , VanBriesen Jeanne M.
Published: September 2005

Thermodynamic methods to predict true yield and stoichiometry of bacterial reactions have been widely used in biotechnology and environmental engineering. However, yield predictions are often inaccurate for certain simple organic compounds. This work evaluates an existing method and identifies the cause of prediction errors for compounds with low degree of reductance of carbon. For these compounds, carbon, not energy or reducing equivalents, constrains growth. Existing thermodynamically‐based models do not account for the potential of carbon‐limited growth. The improved method described here consists of four balances: carbon balance, nitrogen balance, electron balance, and energy balance. Two efficiency terms, K1 and K2 are defined and estimated from a priori analysis. The results show that K1 and K2 are nearly the same in value so that only one coefficient, K = 0.41 is used in the modified model. Comparisons with observed yields show that use of the new model and parameters results in significantly improved yield estimation based on inclusion of the carbon balance. The average estimation error is less than 6% for the data set presented. © 2005 Wiley Periodicals, Inc.
Potassium Cerium(III) Bis(sulfate) Monohydrate, KCe(SO4)2×H2O.
Authors: Jemmali Mosbah , Walha Siwar , Ben Hassan Rached , Vaclac Petricek
Published: September 2005

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Kinetics of Thermal Dehydration and Decomposition of Hydrated Chlorides of Some 3d Transition Metals (Mn—Cu Series). Part 5. Dehydration and Decomposition of CuCl2×2H2O.
Authors: Kanungo S. B.
Published: September 2005

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Cyclopropanation of N‐Substituted 2‐Oxochromene‐ and 6‐Bromo‐2‐oxochromene‐3‐carboxamides with Zinc Enolates Derived from 1‐Aryl‐2,2‐dibromoalkanones.
Authors: Shchepin V. V. , Silaichev P. S. , Shchepin R. V. , Ezhikova M. A. , Kodess M. I.
Published: September 2005

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Microwave‐Assisted Synthesis of New Isoxazolyl Triazinethiones and Isoxazolyl Oxadiazinethiones in Dry Media.
Authors: Rajanarendar E. , Ramu K. , Karunakar D. , Ramesh P.
Published: September 2005

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Radical Addition to “Cation Pool”. Reverse Process of Radical Cation Fragmentation.
Authors: Maruyama Tomokazu , Suga Seiji , Yoshida Jun‐ichi
Published: September 2005

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Deoxygenation of N‐Oxides with Triphenylphosphine, Catalyzed by Dichlorodioxomolybdenum(VI).
Authors: Sanz Roberto , Escribano Jaime , Fernandez Yolanda , Aguado Rafael , Pedrosa Maria R. , Arnaiz Francisco J.
Published: September 2005

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Palladium‐Catalyzed Selective Amination of Haloaromatics on KF‐Alumina Surface.
Authors: Basu Basudeb , Das Pralay , Nanda Ashish K. , Das Sajal , Sarkar Sajal
Published: September 2005

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Water Is an Efficient Medium for Wittig Reactions Employing Stabilized Ylides and Aldehydes.
Authors: Dambacher Jesse , Zhao Wen , El‐Batta Amer , Anness Robert , Jiang Changchun , Bergdahl Mikael
Published: September 2005

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Iridium‐Catalyzed Oxidative Esterification Reaction of Aliphatic Aldehydes and Olefinic Alcohols with Precoordination of the Double Bond of Alcohols to Iridium.
Authors: Kiyooka Syun‐ichi , Ueno Mahuyu , Ishii Eri
Published: September 2005

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Highly Enantioselective One‐Pot, Three‐Component Imino‐Reformatsky Reaction.
Authors: Cozzi Pier Giorgio , Rivalta Eleonora
Published: September 2005

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A Convenient and Easy Synthesis of γ‐Nitro‐α‐acetamido Esters.
Authors: Ballini Roberto , Balsamini Cesarino , Diamantini Giuseppe , Savoretti Nicoletta
Published: September 2005

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Cyclic Nitriles: Diastereoselective Alkylations.
Authors: Fleming Fraser F. , Gudipati Subrahmanyam , Zhang Zhiyu , Liu Wang , Steward Omar W.
Published: September 2005

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Olefin and Enyne Cross‐Metathesis — A New Tool for the Synthesis of Alkenyl‐Substituted Azulenes.
Authors: Mikus Agnieszka , Sashuk Volodymyr , Kedziorek Mariusz , Samojlowicz Cezary , Ostrowski Stanislaw , Grela Karol
Published: September 2005

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First Transamination Reactions for the One‐Pot Synthesis of Substituted Zwitterionic Quinones.
Authors: Yang Qing‐Zheng , Siri Olivier , Braunstein Pierre
Published: September 2005

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Selective and Efficient Oxidation of Sulfides to Sulfoxides with N‐Bromosuccinimide in the Presence of β‐Cyclodextrin in Water.
Authors: Surendra K. , Krishnaveni N. Srilakshmi , Kumar V. Pavan , Sridhar R. , Rao K. Rama
Published: September 2005

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CuBr/H2O2‐Mediated Oxidative Coupling of N,N‐Dialkylarylamines in Water: A Practical Synthesis of Benzidine Derivatives.
Authors: Jiang Yanfeng , Xi Chanjuan , Yang Xianghua
Published: September 2005

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Silica Sulfuric Acid: An Efficient and Recyclable Catalyst for the Synthesis of β‐Acetamido Ketones in Single Pot.
Authors: Yakaiah T. , Reddy G. Venkat , Lingaiah B. P. V. , Narsaiah B. , Rao P. Shanthan
Published: September 2005

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Regio‐ and Stereoselective Route to Tetrasubstituted Olefins by the Palladium‐Catalyzed Three‐Component Coupling of Aryl Iodides, Internal Alkynes, and Arylboronic Acids.
Authors: Zhou Chengxiang , Larock Richard C.
Published: September 2005

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An Inexpensive and Selective Oxygenation of N‐Alkyl Imines to Oxaziridines.
Authors: Shailaja M. , Manjula A. , Rao B. Vittal
Published: September 2005

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Convenient Synthesis of ε‐Halo‐β‐ketoesters and γ,γ′‐Dibromoalkanones by Regio‐ and Chemoselective Reaction of 2‐Alkylidenetetrahydrofurans with Boron Trihalides: A “Ring‐Closure/Ring‐Cleavage” Strategy.
Authors: Bellur Esen , Langer Peter
Published: September 2005

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Titanocene‐Mediated Intramolecular Radical Vinylations.
Authors: Leca Dominique , Song Kai , Albert Matthias , Concalves Monica Grangeio , Fensterbank Louis , Lacote Emmanuel , Malacria Max
Published: September 2005

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Organic Reactions in Ionic Liquids: Ionic Liquid‐Promoted Efficient Synthesis of N‐Alkyl and N‐Arylphthalimides.
Authors: Le Zhang‐Gao , Chen Zhen‐Chu , Hu Yi , Zheng Qin‐Guo
Published: September 2005

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New Semiconducting Benzo‐TTF Salts: Synthesis and Physical Properties.
Authors: Boudiba Louiza , Kaboub Lakhemici , Gouasmia Abdelkrim , Fabre Jean M.
Published: September 2005

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1,5‐Bis(4‐dithiocarboxylate‐5‐hydroxypyrazolyl)pentane Derivatives of 5‐Pyrazolones
Authors: Avila Carolina , Flores Maria Fernanda , Molinari Aurora , Oliva Alfonso
Published: September 2005

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Synthesis of Pyrrolo‐ and Pyrido‐[1,2‐a]benzimidazolequinone Antitumor Agents Containing a Fused Cyclopropane Ring.
Authors: O'Shaughnessy John , Aldabbagh Fawaz
Published: September 2005

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Stereoselective Multicomponent Synthesis of [3‐(5‐Substituted 2‐Methoxyphenyl)‐5‐aryl‐2‐phenyltetrahydro‐4‐isoxazolyl] (2‐thienyl)methanones via 1,3‐Dipolar Cycloaddition.
Authors: Sridharan V. , Saravanakumar S. Pon , Muthusubramanian S.
Published: September 2005

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Synthesis and Antimicrobial Activity of 5‐(R1‐Benzyl)‐2‐(R‐benzylidenehydrazono)‐3‐ (2‐furylmethyl)thiazolidin‐4‐ones.
Authors: Tsyalkovskii V. M. , Kutsyk R. V. , Matiychuk V. S. , Obushak M. D. , Klyufinska T. I.
Published: September 2005

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Novel Method for the Synthesis of 1,2,4‐Oxadiazoles Using Alumina Supported Ammonium Fluoride under Solvent‐Free Condition.
Authors: Kaboudin Babak , Saadati Fariba
Published: September 2005

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Reaction of Naphthalene‐2,3‐dicarbaldehyde with Cyanide; a Unique Oxidative Condensation Product.
Authors: McGill Colin M. , Swearingen Kristian E. , Drew Kelly L. , Rasley Brian T. , Green Thomas K.
Published: September 2005

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An Efficient Procedure for the Preparation of 4‐Methyl‐2‐thiocoumarins by the Reaction of 4‐Methylcoumarins with Lawesson′s Reagent.
Authors: Levai Albert , Jekoe Jozsef
Published: September 2005

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Regioselective Addition of n‐Alkyllithiums to α,α′‐Disubstituted‐1,8‐naphthyridines: Synthesis of 6‐Amino‐3‐pyridinol Analogues of α‐Tocopherol.
Authors: Nam Tae‐gyu , Wijtmans Maikel , Pratt Derek A. , Porter Ned A.
Published: September 2005

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Polymer‐Supported Ionic Liquid Catalyzed Synthesis of 1,2,3,4‐Tetrahydro‐2‐oxopyrimidine‐5‐carboxylates via Biginelli Reaction.
Authors: Wang Zong‐Ting , Wang Shu‐Chao , Xu Li‐Wen
Published: September 2005

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A New [5 + 1]‐Annulation Route to Some Quinazoline and Fused Pyrimidine Derivatives.
Authors: Chattopadhyay Shital K. , Dey Rajat , Biswas Suman
Published: September 2005

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Regioselective Synthesis of Pyrrolo[2,3‐d]pyrimidine Derivatives by Amine Oxide Rearrangement.
Authors: Majumdar Krishna C. , Biswas Anindita , Mukhopadhyay Partha P.
Published: September 2005

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