bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teaching noncovalent interactions using protein molecular evolution
Authors: Fornasari María Silvina , Parisi Gustavo , Echave Julián 
Published: July 2008

AbstractNoncovalent interactions and physicochemical properties of amino acids are important topics in biochemistry courses. Here, we present a computational laboratory where the capacity of each of the 20 amino acids to maintain different noncovalent interactions are used to investigate the stabilizing forces in a set of proteins coming from organisms adapted to different environments. Using protein sequence and structure information it is possible to evaluate the noncovalent contributions to the stabilization of a given protein fold. As a case study, we use the protein lumazine synthase from three different organisms adapted to live in extreme temperatures: one psychrophilic (optimal growth temperature, 0–20 °C), one mesophilic (optimal growth temperature, 20–50 °C), and one thermophilic (optimal growth temperature, 80–110 °C). We found that this computational laboratory for biochemistry and molecular biology courses enhances student amino acid noncovalent interaction understanding and how these interactions are involved in protein stability.
Design‐based learning for biology
Authors: Ellefson Michelle R. , Brinker Rebecca A. , Vernacchio Vincent J. , Schunn Christian D. 
Published: July 2008

AbstractGene expression is a difficult topic for students to learn and comprehend, at least partially because it involves various biochemical structures and processes occurring at the microscopic level. Designer Bacteria, a design‐based learning (DBL) unit for high‐school students, applies principles of DBL to the teaching of gene expression. Throughout the 8‐week unit, students genetically engineer bacteria to meet a need in their own lives. Through a series of investigations, discussions, and design modifications, students learn about the molecular processes and structures involved in gene expression, and how these processes and structures are dependent upon various environmental variables. This article is intended to describe the Designer Bacteria unit and report preliminary results of student progress and performance on pre‐unit and post‐unit assessments. Teacher experiences and student progress indicate that Designer Bacteria successfully taught core aspects of gene expression through DBL.
Pedagogies of engagement in science
Authors: Eberlein Thomas , Kampmeier Jack , Minderhout Vicky , Moog Richard S. , Platt Terry , Varma‐Nelson Pratibha , White Harold B. 
Published: July 2008

AbstractProblem‐based learning, process‐oriented guided inquiry learning, and peer‐led team learning are student‐centered, active‐learning pedagogies commonly used in science education. The characteristic features of each are compared and contrasted to enable new practitioners to decide which approach or combination of approaches will suit their particular situation.
Problem‐solving test: Targeted gene disruption
Authors: Szeberényi József 
Published: July 2008

AbstractTerms to be familiar with before you start to solve the test: mutation, vector, plasmid, origin of replication, promoter, introns/exons, open reading frame, transfection, circular and linear DNA, DNA integration, homologous recombination, DNA replication, gene expression, heterozygote, homozygote.
Bridging the educational research‐teaching practice gap
Authors: Anderson Trevor R. , Schönborn Konrad J. 
Published: July 2008

AbstractThe term “conceptual understanding” has been used rather loosely over the years in educational practice, with a tendency to focus on a few aspects of an extremely complex phenomenon. In this first article of a two‐part miniseries on conceptual understanding, we describe the nature of expert (versus novice) knowledge and show how the conceptual understanding of experts is multifaceted in nature requiring competence in a wide range of cognitive skills. We then discuss five such facets of conceptual understanding that require competence in the cognitive skills of memorization, integration, transfer, analogical reasoning, and system thinking. We also argue for the importance of explicitly teaching and assessing such facets of understanding as part of all molecular life science curricula so as to better prepare our students to become experts in the field. Examples of the assessment tasks that can be used to promote the development of multifaceted conceptual understanding in students are presented in Part 2 of this series.
A simple HPLC method for the quantification of mizoribine in human serum: pharmacokinetic applications
Authors: Choi Su Jin , Hur Hye Jung , Lee Sang‐Bong , Choi Mi‐Sun , Kuh Hyo‐Jeong , Shin Young‐Hee , Lee Hwa Jeong 
Published: July 2008

AbstractA simple high‐performance liquid chromatographic (HPLC) method was developed and validated for the quantification of mizoribine in human serum. After the addition of 70% perchloric acid and 3‐methylxanthine (50 µg/mL, internal standard) to human serum, the samples were mixed and centrifuged at 12,000 rpm (1432g) for 10 min. The supernatant was injected onto a C18 column eluted with a mobile phase of 20 mm Na2HPO4 and methanol (93:7, v/v, pH 3) containing 0.04% octanesulfonic acid and detected utilizing an ultraviolet detector at 275 nm. The linear calibration curve was obtained in the concentration range of 0.1–4.0 µg/mL and the lower limit of quantification was 0.1 µg/mL. This method was validated with selectivity, linearity, precision and accuracy. In addition, the method was successfully applied to estimate the pharmacokinetic parameters of mizoribine in Korean subjects following an oral administration of 100 mg mizoribine (two Bredinine® 50 mg tablets). The maximum serum concentration (Cmax) of 2.30 ± 0.83 µg/mL was reached 2.27 ± 0.66 h after an oral dose. The mean AUC0–12h and the elimination half‐life (t1/2) were 13.2 ± 4.79 µg h/mL and 3.10 ± 0.74 h, respectively. Copyright © 2008 John Wiley & Sons, Ltd.
Development and validation of a HPLC method for simultaneous quantitation of gatifloxacin, sparfloxacin and moxifloxacin using levofloxacin as internal standard in human plasma: application to a clinical pharmacokinetic study
Authors: Srinivas Nimmagadda , Narasu Lakshmi , Shankar B. Prabha , Mullangi Ramesh 
Published: July 2008

AbstractA highly selective, sensitive and accurate HPLC method has been developed and validated for the estimation of three fluoroquinolones (FQs) viz., gatifloxacin (GFC), sparfloxacin (SFC) and moxifloxacin (MFC) with 500 µL human plasma using levofloxacin (LFC) as an internal standard (IS). The sample preparation involved simple liquid–liquid extraction of GFC, SFC, MFC and IS from human plasma with ethyl acetate. The resolution of peaks was achieved with phosphate buffer (pH 2.5)–acetonitrile (80:20, v/v) at a flow rate of 1 mL/min on a Kromasil C18 column. The total chromatographic run time was 18.0 min and the simultaneous elution of GFC, SFC, MFC and IS occurred at approximately 10.8, 12.8, 17.0 and 6.0 min, respectively. The method proved to be accurate and precise at linearity range of 100–10,000 ng/mL with a correlation coefficient (r) of ≥0.999. The limit of quantitation for each of the FQs studied was 100 ng/mL. The intra‐ and inter‐day precision and accuracy values found to be within the assay variability limits as per the FDA guidelines. The developed assay method was applied to a pharmacokinetic study in human volunteers following oral administration of 400 mg GFC tablet. Copyright © 2008 John Wiley & Sons, Ltd.
Screening and analyzing the potential bioactive components from Shaofu Zhuyu decoction, using human umbilical vein endothelial cell extraction and high‐performance liquid chromatography coupled with mass spectrometry
Authors: Su Shu‐Lan , Yu Li , Hua Yong‐Qing , Duan Jin‐Ao , Deng Hai‐Shan , Tang Yu‐Ping , Lu Yin , Ding An‐Wei 
Published: July 2008

AbstractIn this paper, a useful method for screening and analyzing the potential bioactive components in bioassay‐guided fraction (SF‐11) from Shaofu Zhuyu decoction was developed using human umbilical vein endothelial cell (HUVEC) extraction and high‐performance liquid chromatography coupled with Q‐TOF/MS spectrometry. In addition, the protective effects on HUVEC damage induced by adrenaline in vitro were also investigated. The results showed that SF‐11 significantly inhibited the endothelin (ET) release and reversed the NO secretion of HUVEC (p < 0.05), and promoted the PGI2 release of HUVEC (p < 0.05). Two effective components, paeoniflorin and typhaneoside, from SF‐11 were screened and identified using live cell extract and HPLC coupled with Q‐TOF/MS spectrometry. The compounds, paeoniflorin and typhaneoside, showed significantly inhibiting effects on the ET release and reversing of NO secretion of HUVEC (p < 0.05), with similar effects to SF‐11, and promoting the PGI2 release of HUVEC at the concentration of 0.208 and 0.013 µmol/mL, respectively (p < 0.05). These data indicated that the method of live cell extraction coupled with HPLC‐MS technology is feasible, rapid and useful for screening and analyzing potential bioactive components from TCMs. Copyright © 2008 John Wiley & Sons, Ltd.
Comparison of hydrophilic interaction and reversed‐phase liquid chromatography coupled with tandem mass spectrometric detection for the determination of three pharmaceuticals in human plasma
Authors: Apostolou Constantinos , Kousoulos Constantinos , Dotsikas Yannis , Loukas Yannis L. 
Published: July 2008

AbstractIn the present study, hydrophilic interaction liquid chromatography (HILIC) and reversed‐phase liquid chromatography (RPLC) combined with tandem mass spectrometric detection (MS/MS) were evaluated and compared for the determination of donepezil, cetirizine and loratadine in human plasma, in terms of sensitivity and sample preparation procedure. A retention study for the above compounds of various polarities was performed, using both C18 and silica columns, with several aqueous–organic mobile phase ratios, in order to investigate their retention mechanism profile under HILIC and RPLC. Both chromatographic conditions were compared for chromatographic analysis of plasma samples processed with a liquid–liquid extraction (LLE) method for donepezil determination, resulting in significantly higher sensitivity under HILIC. Furthermore, HILIC and RPLC were compared for direct injection, and novel methods including LLE, solid‐phase extraction and protein precipitation protocols were developed. Direct injection technique significantly reduced sample preparation time, increasing at the same time method sensitivity. The current study contributes to broadening the range of analyzable compounds by HILIC‐MS/MS to molecules of medium polarity. Copyright © 2008 John Wiley & Sons, Ltd.
Validation and application of an HPLC‐EC method for analysis of coenzyme Q10 in blood platelets
Authors: Miles Michael V. , Tang Peter H. , Miles Lili , Steele Paul E. , Moye Mark J. , Horn Paul S. 
Published: July 2008

AbstractPrevious studies have indicated that analysis of coenzyme Q10 (CoQ10) in platelets may be clinically useful. The study objectives are to describe, validate and provide application of an HPLC‐EC method for platelet CoQ10 analysis. This method analyzes oxidized (ubiquinone‐10) and reduced (ubiquinol‐10) forms of CoQ10 using two separate injections with the electrochemical analytical cell set at neutral and oxidizing potentials. Results showed that chromatograms were free of interfering peaks. Calibration curves were constructed over a concentration range 116–2317 nmol/L (r2 = 0.99). The extraction recovery was >95%. The within‐run precision CV% was ≤4.2%, and the day‐to‐day precision was ≤9.9%. Platelets were isolated by differential centrifugation, and frozen at −70°C until analysis. The application of the method was used to compare accumulation of CoQ10 in platelets vs plasma in eight adult volunteers during a 28 day supplementation period (5 mg/kg/day of ubiquinol‐10). Mean platelet total CoQ10 was 164 pmol/109 cells, and ubiquinol‐10:total CoQ10 ratio was 0.56. During supplementation platelet CoQ10 levels were more consistent and predictable than plasma CoQ10 levels. The results indicate that this validated method for platelet ubiquinol‐10 and ubiquinone‐10 analysis is acceptable for use in the clinical laboratory, and that platelet CoQ10 may have important advantages over plasma during CoQ10 supplementation. Copyright © 2008 John Wiley & Sons, Ltd.
Liquid chromatography tandem mass spectrometry method for the quantification of amisulpride with LLOQ of 100 pg/mL using 100 µL of plasma
Authors: Nirogi Ramakrishna , Bhyrapuneni Gopinadh , Kandikere Vishwottam , Mudigonda Koteshwara , Ajjala Devender , Suraneni Ramakrishna , Mukkanti K. 
Published: July 2008

AbstractA sensitive and selective high‐performance liquid chromatography–positive ion electrospray tandem mass spectrometry method was developed and validated for the quantification of amisulpride in 100 µL of human plasma. Following liquid–liquid extraction, the analytes were separated using an isocratic mobile phase on a reverse‐phase column and analyzed by MS/MS in the multiple reaction monitoring mode using the respective (M + H)+ ions, m/z 370–242 for amisulpride and m/z 341–112 for the internal standard. The assay exhibited a linear dynamic range with a lower range of 0.1–100 ng/mL and a higher range of 1–500 ng/mL of amisulpride in human plasma. The lower limit of quantification was 0.1 ng/mL with a relative standard deviation of less than 10%. Acceptable precision and accuracy were obtained for both linearity ranges. A run time of 2.0 min for each sample made it possible to analyze more than 275 human plasma samples per day. The validated method has been successfully used to analyze plasma samples for application in pharmacokinetic studies. Copyright © 2008 John Wiley & Sons, Ltd.
High‐performance liquid chromatography assays for desmethoxyyangonin, methysticin, kavain and their microsomal metabolites
Authors: Fu Shuang , Tattam Bruce N. , Duke Colin C. , Ramzan Iqbal 
Published: July 2008

AbstractThree novel, simple and reproducible high‐performance liquid chromatography quantitative assays with UV detection were developed and validated for three major kavalactones—desmethoxyyangonin, methysticin and kavain—in rat liver microsomes using diazepam as an internal standard; liquid–liquid extraction was used for sample preparation and analysis was performed on a Shimadzu® 10A high‐performance liquid chromatography system. The analysis was carried out in reversed‐phase mode with a Luna® C18column (150 × 2.00 mm, 3 µm) at 40°C. The limit of quantitation was 0.1 µg/mL using 0.25 mL of microsomal solution. The assays were linear over the range 0.1–10 µg/mL for desmethoxyyangonin, methysticin and kavain. Quality control samples exhibited good accuracy and precision with relative standard deviations lower than 15% and recoveries between 85 and 105%. The assays exhibited satisfactory performance with high sensitivity for quantifying desmethoxyyangonin, methysticin and kavain in rat liver microsomes and were successfully used to determine the three kavalactones and their microsomal metabolites. Copyright © 2008 John Wiley & Sons, Ltd.
The anatomy of cardiac looping: A step towards the understanding of the morphogenesis of several forms of congenital cardiac malformations
Authors: Männer Jörg 
Published: July 2008

AbstractThe early embryonic heart of vertebrates is a simple tubular pump. During the early phases of its development, the initially straight embryonic heart tube becomes transformed into a helically wound loop that is normally seen with a counterclockwise winding. This process is named cardiac looping. Such looping not only establishes the basic type of topological left‐right asymmetry of the ventricular chambers but, additionally, is also said to bring the segments of the heart tube and the developing great vessels into an approximation of their definitive topographical relationships. Cardiac looping is, therefore, regarded as the key process in cardiac morphogenesis and pathologists have speculated since the beginning of the 20th century that several forms of congenital cardiac malformations (e.g., with mirror‐imaged arrangement of the ventricular chambers) might result from disturbances in looping morphogenesis. In this article a review is given on (1) differences in the usage of the term cardiac looping; (2) our current knowledge of the dynamically changing anatomy of the looping embryonic heart; and (3) our current knowledge of the role of looping anomalies in the morphogenesis of congenital cardiac malformations. Clin. Anat. 22:21–35, 2009. © 2008 Wiley‐Liss, Inc.
Omental Morgagni‐Larrey hernia: An anatomical pictorial essay
Authors: Stimec Bojan V. , Milisavljevic Milan , Malikovic Aleksandar , Fasel Jean H.D. 
Published: July 2008

AbstractThis paper reports on a case of an omental diaphragmatic hernia revealed during routine anatomical dissection of an obese 85‐year‐old male with plethoric appearance of the upper body. The hernial mass, with a size of 12 cm × 9 cm, was detected in the anterior mediastinum. It had a long peduncle originating from the transverse colon and passing through the right sternocostal diaphragmatic opening of Morgagni‐Larrey. The whole greater omentum was tightly packed and tumid within the serous hernial sac, but without signs of torquation. To our knowledge, this is the first systematic analysis of the omental hernial anatomy by a step‐by‐step iconography. Clin. Anat. 21:587–591, 2008. © 2008 Wiley‐Liss, Inc.
The interpectoral fascia flap
Authors: Beer Gertrude M. , Manestar Andrew , Manestar Mirjana 
Published: July 2008

AbstractDespite the great number of pedicled and free flaps that are available for defect and contour repair, the number of fascia flaps with an axial blood supply are sparse. Such flaps with their gliding function are mandatory, whenever coverage with very thin, well‐vascularized tissue is necessary. To the currently established fascia flaps, (the temporoparietal fascia flap, the radial forearm fascia flap, the lateral arm fascia flap, and the serratus anterior fascia flap), we want to add a new fascia flap, the interpectoral fascia flap. We dissected the interpectoral fascia flap from 20 cadavers. In each of the 40 hemichests, the trunk of the thoracoacromial vessels was selectively injected with red polyurethane and the tissue containing the pectoral branches was separated from the overlying pectoralis major muscle and converted into an independent fascia flap. The maximum flap length was 13.5 cm and the maximum breadth was 10.3 cm. The length of the vascular pedicle before entering the flap was 3.9 cm ± 1.4 cm with a range of 1.5–6.8 cm. Concerning the arc of rotation, all 40 flaps reached the posterior axillary fold, and 29 flaps (73%) reached the mandibular border. This new fascia flap has applications as pedicled and as free flap. The pedicled flap is used in the neck region, in the axillary region and as gliding tissue between the nipple‐areola complex and the pectoralis major muscle. The usage of the fascia flap as a free flap has similar characteristics as the other fascia flaps. Clin. Anat. 21:465–470, 2008. © 2008 Wiley‐Liss, Inc.
Fetal development of the human gubernaculum with special reference to the fasciae and muscles around it
Authors: Niikura Hitoshi , Okamoto Satoshi , Nagase Satoru , Takano Tadao , Murakami Gen , Tatsumi Haruyuki , Yaegashi Nobuo 
Published: July 2008

AbstractPrevious descriptions of human gubernacular embryology failed to follow some basic developmental processes, and surgically relevant structures, such as the iliopubic tract, had not been discussed relative to gubernacular development. We addressed these shortcomings in this study that examined two stage‐groups of human fetuses. At 8–12 weeks of gestation, the gubernaculum arose from the mesonephric fold at or near the gonad. Gubernacular mesenchyme communicated with the subcutaneous tissue via a narrow slit in the rectus aponeurosis. The inguinal fold, containing the inferior epigastric vessels, was separated from the gubernaculum. At 20–25 weeks of gestation, the gubernaculum connected to the testis or uterus. When the testis successfully descended to a peritoneal recess on the lateral side of the umbilical artery, the gubernaculum connected to the testis free of interference by the thick artery and its associated peritoneal fold. This may explain the known asymmetry in testicular descent. The inguinal canal was enclosed by a sheet‐like aponeurosis: its ventromedial part was composed of the rectus sheath and the external oblique aponeurosis, whereas the dorsolateral part consisted of a thick aponeurosis covering or facing the iliopsoas. The former (latter) aponeurosis seemed to develop into the inguinal ligament (the iliopubic tract) in adults. According to the topohistology of the muscles associated with the interfoveolar ligament, we identified muscle fragments around the gubernaculum as derivatives of the transversus and/or internal oblique. Consequently, the inguinal canal contained the cremaster proper developing within the gubernaculum and parts of the abdominal wall muscles mechanically incorporated into the canal. Clin. Anat. 21:547–557, 2008. © 2008 Wiley‐Liss, Inc.
Shape‐constrained flock animation
Authors: Xu Jiayi , Jin Xiaogang , Yu Yizhou , Shen Tian , Zhou Mingdong 
Published: July 2008

AbstractWe propose a novel shape‐constrained flock animation system for interactively controlling flock navigation in virtual environments. This system is capable of making the spatial distribution of a flock meet static or deforming shape constraints while performing flock simulation. Such a capability can find many applications in the entertainment industry. Given a 3D constraining shape, our system first draws a set of uniform sample points through a 3D surface mosaicing process or a stratified point sampling strategy. Once correspondences between flock members and sample points have been established, points on the target shape are used as homing destinations to guide flock migration. Under a global path control scheme, an effective fuzzy control logic, which dynamically adjusts steering forces and control forces, has been developed to create visually pleasing shape‐constrained flock animations. Copyright © 2008 John Wiley & Sons, Ltd.
Motion adaptation based on character shape
Authors: Lyard Etienne , Magnenat‐Thalmann Nadia 
Published: July 2008

AbstractWith the increasing performances of the graphics hardware, virtual reality applications are reaching a new level of realism. It is now possible to animate entire crowds of virtual avatars, or to display in real‐time highly realistic deformable characters. This new type of applications requires that characters are deformed, either to generate a large number of individuals for creating a crowd, or to match a particular shape. To make the animation fit to the animated character and to prevent self‐collisions, adapting the motion is mandatory. Unlike previous approaches which relied on skeletal models, this paper presents a method considering the actual shape of the character's body to perform the adaptation. Our approach uses spacetime optimization to remove the self‐penetration, and finally re‐establishes the balance of the motion. We also introduce an interpolation scheme based on radial basis functions that can blend pre‐calculated adaptations, and thus achieve real‐time performances. Copyright © 2008 John Wiley & Sons, Ltd.