bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonspecific electrostatic binding characteristics of the heparin‐antithrombin interaction
Authors: Seyrek Emek , Dubin Paul L. , Henriksen Jens 
Published: March 2007

AbstractWe evaluated the role of nonspecific electrostatic binding in the interaction of antithrombin (AT) with heparin (Hp), a paradigmatic protein‐glycosaminoglycan (GAG) system. To do so, we obtained the ionic‐strength dependence of the binding constant, since a common feature in protein‐polyelectrolyte systems is a maximum in affinity in the ionic strength range 10 mM <I<30 mM (Seyrek et al, Biomacromolecules 2003, 4, 273‐282). Because this feature is seen for both synthetic and biological polyelectrolytes, and because the value of Imax correlates with protein size and charge asymmetry through the Debye length (Seyrek et al, Biomacromolecules 2003, 4, 273‐282), this behavior appears to be a signature of non‐specific electrostatic protein‐polyelectrolyte binding. Binding of AT to both standard (14 kDa) Hp and partially degraded (5 kDa) low molecular weight heparin (LMWH) exhibited this same behavior. Capillary electrophoresis (CZE) of Hp and LMWH yielded electropherograms whose remarkable breadth revealed the enormous heterogeneity of average charge density among the innumerable molecular species of Hp and LMWH. These distributions were somewhat reduced after affinity chromatography (AC) fractionation, indicating that the high‐affinity fraction was generally depleted of the lower‐charge species. Size‐exclusion chromatography coupled with Electrospray Mass Spectrometry confirmed lower levels of sulfation for the lower affinity fractions. Comparisons of LMWH with Dermatan sulfate (DS) by CZE and AC suggested a correlation between the relative absence of very highly charged components in DS and its weaker binding to AT. These findings point to a significant role of the charge density of GAG chains in their affinity for AT. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 249–259, 2007.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
A scaleable manufacturing process for pro‐EP‐B2, a cysteine protease from barley indicated for celiac sprue
Authors: Vora Harmit , McIntire James , Kumar Pawan , Deshpande Milind , Khosla Chaitan 
Published: March 2007

AbstractCeliac Sprue is an inflammatory disease of the small intestine triggered by ingestion of dietary gluten, a family of glutamine and proline rich proteins found in common foodgrains such as wheat, rye, and barley. One potential therapy for this lifelong disease anticipates using an oral protease to detoxify gluten in vivo. Recent studies have shown that EP‐B2 (endoprotease B, isoform 2) from barley is a promising example of such a glutenase, thus warranting its large‐scale production for animal safety and human clinical studies. Here we describe a scaleable fermentation, refolding and purification process for the production of gram to kilogram quantities of pro‐EP‐B2 (zymogen form of EP‐B2) in a lyophilized form. A fed‐batch E. coli fermentation system was developed that yields 0.3–0.5 g purified recombinant protein per liter culture volume. Intracellular degradation of pro‐EP‐B2 during the fermentation was overcome by manipulating the fermentation temperature and duration of protein expression. A simple refolding protocol was developed using a fast dilution method to refold the enzyme at concentrations greater than 0.5 mg/mL. Kinetic analysis showed that pro‐EP‐B2 refolding is a first‐order reaction with an estimated rate constant of 0.15 h−1. A lyophilization procedure was developed that yielded protein with 85% recoverable activity after 7 weeks of storage at room temperature. The process was successfully scaled up to 100 L with comparable purity and recovery. Biotechnol. Bioeng. 2007; 98: 177–185. © 2007 Wiley Periodicals, Inc.
Analysis of lipid hydrolytic activity by esterase on blotting membrane followed by separation using non‐denaturing two‐dimensional gel electrophoresis
Authors: Shimazaki Youji , Miyamoto Masayuki 
Published: March 2007

AbstractAfter separation by microscale non‐denaturing two‐dimensional gel electrophoresis (2DE) and transferring to a blotting membrane, major proteins are detected by a staining of direct blue 71 in a neutral solution. The carboxylesterase on the membrane hydrolyzes phosphatidylcholine after the spot of carboxylesterase is excised from the membrane, and incubated with phosphatidylcholine. Lipids of human serum proteins and the purified human high density lipoprotein (HDL) are removed by enzymatic hydrolysis when human serum proteins and the purified HDL are respectively incubated with the spot of carboxylesterase on the membrane. These results indicate that carboxylesterase on the membrane hydrolyzes not only lipids such as phosphatidylcholine but also lipids of lipoproteins such as HDL after separation by the 2DE, transferring to the membrane and staining without impairing the activity. These results also indicate that a micro‐immobilized enzyme reactor on the membrane can be produced when biological enzymes are separated by microscale 2DE, transferred to the membrane and stained without impairing their activities. Biotechnol. Bioeng. 2007;98: 732–736. © 2007 Wiley Periodicals, Inc.
Determination of the Conformation of the Human VDAC1 N‐Terminal Peptide, a Protein Moiety Essential for the Functional Properties of the Pore
Authors: De Pinto Vito , Tomasello Flora , Messina Angela , Guarino Francesca , Benz Roland , La Mendola Diego , Magrì Antonio , Milardi Danilo , Pappalardo Giuseppe 
Published: March 2007

AbstractMitochondrial porin or VDAC (voltage‐dependent anion‐selective channel) is the most abundant protein in the mitochondrial outer membrane. The structure of VDAC has been predicted to be a transmembrane β‐barrel with an α‐helix at the N terminus. It is a matter of debate as to whether this putative α‐helix plays a structural role as a component of the pore walls or a function in the pore activity. We have synthesised the human VDAC1 (HVDAC1) N‐terminal peptide Ac‐AVPPTYADLGKSARDVFTK‐NH2 (Prn2–20) and determined its structure by CD and NMR spectroscopy. CD studies show that the Prn2–20 peptide exists in aqueous solvent as an unstructured peptide with no stable secondary structure. In membrane‐mimetic SDS micelles or water/trifluoroethanol, however, it assumes an amphipathic α‐helix conformation between Tyr5 and Val16, as deduced from NMR. No ordered structure was observed in dodecyl β‐maltoside. Differential scanning calorimetric measurements were carried out in order to examine the membrane affinity of the peptide. Upon interaction with the negatively charged 1,2 dipalmitoyl‐sn‐glycero‐3‐phosphoserine membrane, Prn2–20 exhibited distinctive behaviour, suggesting that electrostatics play an important role. Interaction between the peptide and artificial bilayers indicates that the peptide lies on the membrane surface. Recombinant HVDAC1 deletion mutants, devoid of seven or 19 N‐terminal amino acids, were used for transfection of eukaryotic cells. Over‐expression of HVDAC1 increases the number of Cos cells with depolarised mitochondria, and this effect is progressively reduced in cells transfected with HVDAC1 lacking those seven or 19 amino acids. The mitochondrial targeting of the deletion mutants is unaffected. The overall picture emerging from our experiments is that the VDAC N‐terminal peptide plays a role in the proper function of this protein during apoptotic events.
The impact of olive oil consumption pattern on the risk of acute coronary syndromes: the cardio2000 case–control study
Authors: Kontogianni Meropi D. , Panagiotakos Demosthenes B. , Chrysohoou Christina , Pitsavos Christos , Zampelas Antonis , Stefanadis Christodoulos 
Published: March 2007

AbstractBackgroundAccording to epidemiological and metabolic studies monounsaturated fatty acids (MUFAs) seem to exert a protection against coronary heart disease (CHD) risk. The aim of the present study was to evaluate the association between the pattern of edible oils and fats consumption and the prevalence of a first, nonfatal event of an acute coronary syndrome (ACS) in a Greek sample.MethodsSeven hundred males and 148 females patients with first event of an ACS and 1078 population‐based controls, age and sex matched, were randomly selected. Detailed information regarding their medical records, alcohol intake, physical activity and smoking habits was recorded. Nutritional habits were evaluated with a semi‐quantitative food‐frequency questionnaire and use of oils in daily cooking or preparation of food was also recorded. Multiple logistic regression analysis estimated the odds ratio (OR) of having ACS by types of oil used, after taking into account the effect of several confounders.ResultsExclusive use of olive oil was associated with 47% (95% confidence interval (CI) 0.4–0.71) lower likelihood of having ACS, compared to nonuse, after adjusting for BMI, smoking, physical activity level, educational status, the presence of family history of CHD, as well as hypertension, hypercholesterolemia and diabetes. Consumption of olive oil in combination with other oils or fats was not significantly associated with lower odds of ACS compared to no olive oil consumption (p = 0.14).ConclusionsExclusive use of olive oil during food preparation seems to offer significant protection against CHD, irrespective of various clinical, lifestyle and other characteristics of the participants. Copyright © 2007 Wiley Periodicals, Inc.
Predictors of tumor response and downstaging in patients who receive preoperative chemoradiation for rectal cancer
Authors: Das Prajnan , Skibber John M. , Rodriguez‐Bigas Miguel A. , Feig Barry W. , Chang George J. , Wolff Robert A. , Eng Cathy , Krishnan Sunil , Janjan Nora A. , Crane Christopher H. 
Published: March 2007

AbstractBACKGROUNDThe objective of this study was to identify predictive factors for pathologic complete response and tumor downstaging after preoperative chemoradiation for rectal cancer.METHODSBetween 1989 and 2004, 562 patients with nonmetastatic rectal adenocarcinoma received preoperative chemoradiation and underwent mesorectal excision. The median radiation dose was 45 Gray (Gy) (range, 19.8–58.6 Gy), 77% of patients received concurrent infusional 5‐fluorouracil, 20% of patients received concurrent capecitabine, and 3% of patients received other regimens.RESULTSNineteen percent of patients achieved a pathologic complete response (CR), whereas 20% of patients had only microscopic residual disease at surgery, and 61% of patients had macroscopic residual disease at surgery. Downstaging of the tumor stage occurred in 57% of patients. The results from a univariate analysis indicated that tumor circumferential extent >60% (P = .033) and pretreatment carcinoembryonic antigen (CEA) level >2.5 ng/mL (P = .015) were associated significantly with lower pathologic CR rates. The univariate analysis also indicated that tumor circumferential extent >60% (P = .001), pretreatment CEA level >2.5 ng/mL (P = .006), and distance from the anal verge >5 cm (P = .035) were associated significantly with lower downstaging rates. The results from a multivariate logistic regression analysis indicated that greater circumferential extent of tumor (odds ratio [OR], 0.43; P = .033) independently predicted a lower pathologic CR rate. The multivariate logistic regression analysis also indicated that greater circumferential extent of tumor (OR, 0.49; P = .020) and greater distance from the anal verge (OR, 0.46; P = .010) independently predicted a lower downstaging rate.CONCLUSIONSCircumferential extent of tumor, CEA level, and distance from the anal verge predicted for the pathologic response to preoperative chemoradiation for patients with rectal cancer. Therefore, these factors may be used to predict outcomes for patients, to develop risk‐adapted treatment strategies, and to target patients who participate in trials of newer therapies. Cancer 2007. © 2007 American Cancer Society.
Clinicopathologic features and BRAFV600E mutation analysis in cutaneous metastases from well‐differentiated thyroid carcinomas
Authors: Erickson Lori A. , Jin Long , Nakamura Nobuki , Bridges Alina G. , Markovic Svetomir N. , Lloyd Ricardo V. 
Published: March 2007

AbstractBACKGROUNDCutaneous metastases from well‐differentiated thyroid carcinomas are rare and are usually identified in patients with widely disseminated disease. Occasionally, thyroid carcinomas can present as cutaneous metastases for which the primary site needs to be determined. Papillary thyroid carcinomas (PTCs) commonly have BRAFV600E mutation. A series of 16 cutaneous metastases were analyzed from well‐differentiated thyroid carcinomas to learn more about the clinicopathologic features and BRAFV600E mutation status.METHODSEleven cases of PTC and 5 of follicular thyroid carcinoma (FTC) metastatic to the skin were evaluated. All cutaneous metastases were studied histologically and with thyroglobulin and thyroid transcription factor immunostains. All tumor samples were analyzed for mutations at nucleotide 1799 in exon 15 of the BRAF gene.RESULTSTwo patients with FTC presented with cutaneous metastases. Fourteen of 16 patients died of disease and 2 were alive with disease at follow‐up. The histologic features of the cutaneous metastases were generally characteristic of the primary tumor; however, 2 of the 11 PTC metastases demonstrated cytoplasmic clearing not typical of classic PTC. BRAFV600E mutation (T1799A) was detected in 5 of 11 cases of PTC and in none of the 5 FTCs.CONCLUSIONSCutaneous metastases from PTC may show prominent clear cell change requiring differentiation from clear cell hidradenoma, clear cell dermatofibroma, malignant melanoma with prominent clear cell change, and cutaneous metastasis from renal cell carcinoma. BRAFV600E mutation is identified in a subset of cutaneous metastases from PTC. Cutaneous metastases from PTC and FTC are associated with a very poor prognosis. Cancer 2007. © 2007 American Cancer Society.
Controlled Aggregation of Functionalized Gold Nanoparticles with a Novel Conjugated Oligomer
Authors: Liu Xiaofeng , He Xiaorong , Jiu Tonggang , Yuan Mingjian , Xu Jialiang , Lv Jing , Liu Huibiao , Li Yuliang 
Published: March 2007

AbstractA new route is developed to control the self‐assembly of gold nanoparticles (AuNPs) functionalized with a novel pyridyl‐ended porphyrin–oligo(p‐phenylene vinylene) conjugated oligomer (P–OPV–Py) into branched‐rods, chain‐networks, uniform fractal‐like Au clusters, and larger nanoparticles. The techniques of optical spectroscopy, transmission electron microscopy (TEM) and dynamic light scattering (DLS) are used to characterize the self‐assembly in various solvent systems (pure toluene, CHCl3/toluene, THF/toluene and n‐butanol/toluene). A combination of the ligand/AuNPs molar ratio and relative concentration serves as the driving force to control the size and shape of P–OPV–Py capped AuNPs.
International Society for Analytical Cytology Biosafety Standard for Sorting of Unfixed Cells
Authors: Schmid Ingrid , Lambert Claude , Ambrozak David , Marti Gerald E. , Moss Delynn M. , Perfetto Stephen P. 
Published: March 2007

AbstractBackground:Cell sorting of viable biological specimens has become very prevalent in laboratories involved in basic and clinical research. As these samples can contain infectious agents, precautions to protect instrument operators and the environment from hazards arising from the use of sorters are paramount. To this end the International Society of Analytical Cytology (ISAC) took a lead in establishing biosafety guidelines for sorting of unfixed cells (Schmid et al., Cytometry 1997;28:99–117). During the time period these recommendations have been available, they have become recognized worldwide as the standard practices and safety precautions for laboratories performing viable cell sorting experiments. However, the field of cytometry has progressed since 1997, and the document requires an update.Methods:Initially, suggestions about the document format and content were discussed among members of the ISAC Biosafety Committee and were incorporated into a draft version that was sent to all committee members for review. Comments were collected, carefully considered, and incorporated as appropriate into a draft document that was posted on the ISAC web site to invite comments from the flow cytometry community at large. The revised document was then submitted to ISAC Council for review. Simultaneously, further comments were sought from newly‐appointed ISAC Biosafety committee members.Results:This safety standard for performing viable cell sorting experiments was recently generated. The document contains background information on the biohazard potential of sorting and the hazard classification of infectious agents as well as recommendations on (1) sample handling, (2) operator training and personal protection, (3) laboratory design, (4) cell sorter set‐up, maintenance, and decontamination, and (5) testing the instrument for the efficiency of aerosol containment.Conclusions:This standard constitutes an updated and expanded revision of the 1997 biosafety guideline document. It is intended to provide laboratories involved in cell sorting with safety practices that take into account the enhanced hazard potential of high‐speed sorting. Most importantly, it states that droplet‐based sorting of infectious or hazardous biological material requires a higher level of containment than the one recommended for the risk group classification of the pathogen. The document also provides information on safety features of novel instrumentation, new options for personal protective equipment, and recently developed methods for testing the efficiency of aerosol containment. Published 2007 Wiley‐Liss, Inc.
Dynamic centrifuge testing of a cantilever retaining wall
Authors: Ortiz L. A. , Scott R. F. , Lee J. 
Published: March 2007

AbstractTwo correctly‐scaled model cantilever retaining walls of different stiffnesses were tested under dynamic loading conditions in a centrifuge. A medium‐dense fine sand was retained with a range of backfill slopes. For the centrifuge model, an earthquake‐generating mechanism was designed to produce seismic shaking equivalent to that generated at ground surface in the epicentral area of an earthquake of approximate magnitude 5–5. The response of the model retaining walls to the input dynamic motion was measured by strain gauges, pressure transducers and accelerometers. From the measurements plots were constructed of moment, shear, pressure and displacement over the height of the walls as a function of time. The results are compared with calculations based on the quasi‐static Mononobe‐Okabe theory. Although the calculated resultant force is in reasonable agreement with the experiments, the moments can be substantially different. Residual values of all parameters at the end of shaking are considerably greater than the initial static values. It is recommended that dynamic behaviour be incorporated in the earthquake design of retaining walls.
Effect of radiation damping on earthquake response of pile‐supported offshore platforms
Authors: Nogami Toyoaki , Idriss I. M. , Power M. S. , Chang C.‐Y. 
Published: March 2007

AbstractAn economical approach was developed to examine the effect of radiation damping on earthquake response of pilesupported offshore platforms. Parameteric studies were conducted to evaluate the effects of radiation damping on response. Various features of this effect were found for pile head stiffnesses, and responses of platforms subjected to harmonic and earthquake excitations.
Building over faults: A procedure for evaluating risk
Authors: Berrill J. B. 
Published: March 2007

AbstractThis paper examines the risk from fault offset to a building constructed over the surface trace of a fault. An expression relating the magnitude of surface offset to its return period is derived using classical seismic hazard analysis. The risk from fault offset is compared with that due to ground shaking by comparing offsets and MM intensities with equal likelihoods of occurrence. The comparison of risks is useful since it enables risk from fault movement to be related to levels of community acceptance as expressed in building codes for design against ground shaking effects. Relative risk is independent of fault activity rate, but does depend on regional constants, principally those describing the attenuation of MM intensities. For a site over an isolated fault in the Wellington, New Zealand region the risk of damage from fault rupture appears to be about equal to that from ground shaking for buildings with poor earthquake resistance (e.g. unreinforced masonry structures). But for structures designed to have some resistance to ground shaking, the risk due to fault rupture is considerably greater than that due to ground shaking.
Effect of topography and subsurface inhomogeneities on seismic SV waves
Authors: Ohtsuki Akira , Harumi Kasaburo 
Published: March 2007

AbstractThe effect of topography and subsurface inhomogeneity on surface motion is investigated in the case of incident SV waves. Several types of topography, such as a cliff, a cliff with a soft layer and filled land, are considered. Computations are made using a new method combining a particle model with a finite element method. The accuracy of this method is discussed through comparisons with Wong's solutions, which are in good agreement. It is found that the surface displacement is very much influenced by surface irregularities when the incident wavelengths are comparable to the size of the topographic features. Rayleigh waves are strongly produced in the neighbourhoods of the slopes of a cliff and a cliff with a soft layer, the latter being a cliff adjacent to and covered at its foot by a soft layer. Thus, a zone of large amplification takes place near a slope, combining incident SV waves and Rayleigh waves. A large displacement also occurs at the upper corner of the slope. In filled land, vertical and horizontal displacements are produced, which are 3 times larger than those at a distance. The present results are considered to be significant from the viewpoint of engineering seismology.
Response of a nuclear power plant on aseismic bearings to horizontally propagating waves
Authors: Wolf John P. , Obernhuber Pius , Weber Benedikt 
Published: March 2007

AbstractThe nuclear island of Koeberg with a large basemat, a non‐linear base isolation effective in the horizontal direction only, founded on rock, is analysed for inclined body waves and for a combination of surface and body waves associated with prescribed horizontal and vertical components of the control motion.When compared to vertical incidence, an additional rocking component arises, generated by the horizontally propagating vertical component. As the aseismic bearings do not isolate against this rocking component, the corresponding horizontal response bears comparison with that of a conventional structure. The ratio of the response for horizontally propagating waves and that for vertically incident waves is thus considerably larger for the base‐isolated structure than for a conventional one. However, the actual design incorporating other loading cases is affected much less.