bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic α‐helices: Conformations that do not conform
Authors: Sandhu Kuljeet Singh , Dash Debasis 
Published: April 2007

AbstractStructural transitions are important for the stability and function of proteins, but these phenomena are poorly understood. An extensive analysis of Protein Data Bank entries reveals 103 regions in proteins with a tendency to transform from helical to nonhelical conformation and vice versa. We find that these dynamic helices, unlike other helices, are depleted in hydrophobic residues. Furthermore, the dynamic helices have higher surface accessibility and conformational mobility (P‐value = 3.35e‐07) than the rigid helices. Contact analyses show that these transitions result from protein‐ligand, protein‐nucleic acid, and crystal‐contacts. The immediate structural environment differs quantitatively (P‐value = 0.003) as well as qualitatively in the two alternate conformations. Often, dynamic helix experiences more contacts in its helical conformation than in the nonhelical counterpart (P‐value = 0.001). There is differential preference for the type of short contacts observed in two conformational states. We also demonstrate that the regions in protein that can undergo such large conformational transitions can be predicted with a reasonable accuracy using logistic regression model of supervised learning. Our findings have implications in understanding the molecular basis of structural transitions that are coupled with binding and are important for the function and stability of the protein. Based on our observations, we propose that several functionally relevant regions on the protein surface can switch over their conformation from coil to helix and vice‐versa, to regulate the recognition and binding of their partner and hence these may work as “molecular switches” in the proteins to regulate certain biological process. Our results supports the idea that protein structure–function paradigm should transform from static to a highly dynamic one. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Building an eco‐industrial park as a public project in South Korea. The stakeholders' understanding of and involvement in the project
Authors: Kim Heungsoon 
Published: April 2007

AbstractThis study aims to investigate the actual development of an eco‐industrial park (EIP) in South Korea by employing a case study approach and deals with a pilot eco‐industrial park project in the Macheon Industrial Park of Jinhae, Gyeongnam, in the south of Korea. This paper reviews the stakeholders' understanding of EIPs. Furthermore, research was conducted on the barriers to the actual promotion of the project in South Korea. First, stakeholders' understanding of EIPs is identified as being self‐interested. The need for EIPs is mostly found in responding to civil complaints and pollutants resulting from the industrial park. However, the need is quite different from the original intention of EIPs. As a result, the project unsuccessfully deals with the needs of the stakeholders because of technical, economic, and social obstacles. Second, support from the public sector for the project seems quite inadequate. The public sector appears to lack the proper policy means and will to actualize the project. In conclusion, the Korean government needs to participate more actively in the project than it currently is doing. Copyright © 2007 John Wiley & Sons, Ltd and ERP Environment.
Using system dynamics modeling to understand the impact of social change initiatives
Authors: Hirsch Gary B. , Levine Ralph , Miller Robin Lin 
Published: April 2007

AbstractCommunity psychologists have a long history of interest in understanding social systems and how to bring about enduring positive change in these systems. However, the methods that community psychologists use to anticipate and evaluate the changes that result from system change efforts are less well developed. In the current paper, we introduce readers to system dynamics modeling, an action research approach to studying complex systems and the consequences of system change. We illustrate this approach by describing a system dynamics model of educational reform. We provide readers with an introduction to system dynamics modeling, as well as describe the strengths and limitations of the approach for application to community psychology.
Pre-operative nutritional status does not alter the metabolic response to major gastrointestinal surgery in patients with oesophageal cancer
Authors: Bisschop Peter H. , Klein Samuel , Ackermans Mariëtte T. , Patterson Bruce W. , Endert Erik , van Lanschot Jan J. B. , Romijn Johannes A. , Sauerwein Hans P. 
Published: April 2007

Malnutrition is associated with an increased incidence of perioperative morbidity and mortality. To evaluate the effect of malnutrition on the metabolic and inflammatory response to surgery in patients with oesophageal cancer, we studied the effects of oesophagectomy in six patients with major (13·9 (se 1·3) %) weight loss and five patients with minor (0·7 (se 0·6) %) weight loss in the 6 months before to surgery. Rates of appearance (Ra) of glucose, glycerol, leucine and urea were determined by stable isotopically labelled tracer infusion before and after surgery. C-reactive protein was measured as an inflammation marker. BMI was lower in the patients with major weight loss than those with minor weight loss (20·3 (se 0·7) and 24·9 (se 1·5) kg/m2, P = 0·02). With the exception of greater glucose Ra in the major weight loss than minor weight loss subjects (11·1 (se 0·3) v. 9·5 (se 0·3) μmol/kg per min, P = 0·01), there were no differences in substrate kinetics before surgery between groups. Surgery increased glucose Ra, leucine Ra and urea Ra by 41, 24 and 58 %, respectively, in the total group. Changes in substrate kinetics in response to surgery were not different between patients with major and minor weight loss. Surgery increased C-reactive protein concentrations to a comparable extent in both groups. In conclusion, major upper gastrointestinal tract surgery in patients with oesophageal cancer elicits a catabolic response, characterized by increased inflammation, glucose production and protein breakdown. However, this catabolic response does not seem to be influenced by pre-operative nutritional status.
A dietary pattern rich in olive oil and raw vegetables is associated with lower mortality in Italian elderly subjects
Authors: Masala Giovanna , Ceroti Marco , Pala Valeria , Krogh Vittorio , Vineis Paolo , Sacerdote Carlotta , Saieva Calogero , Salvini Simonetta , Sieri Sabina , Berrino Franco , Panico Salvatore , Mattiello Amalia , Tumino Rosario , Giurdanella Maria C. , Bamia Christina , Trichopoulou Antonia , Riboli Elio , Palli Domenico 
Published: April 2007

Dietary habits play an important role in healthy ageing. We have investigated the role of dietary patterns on overall mortality in a large series of Italian elderly, recruited in five EPIC cohorts in Northern (Varese and Turin), Central (Florence) and Southern Italy (Naples and Ragusa).A total of 5611 subjects (72·6 % women) aged 60 years or older, enrolled in 1993–1998, were prospectively followed (median 6·2 years), with 152 deaths (98 women). Four major dietary patterns were identified by using an exploratory factor analysis based on dietary information collected at enrolment. The associations between these dietary patterns and overall mortality were evaluated by Cox models adjusted for potential confounders. The ‘Olive Oil & Salad’ pattern, characterised by a high consumption of olive oil, raw vegetables, soups and poultry, emerged as being inversely associated with overall mortality in both crude and adjusted models. After adjustment for gender, age and caloric intake, overall mortality was reduced by approximately 50 % in the highest quartile and a significant trend emerged (P = 0·008). This association persisted after adjusting for several additional confounders (hazard ratio (HR) 0·50; 95 % CI 0·29, 0·86; P for trend = 0·02). An association of the ‘Pasta & Meat’ pattern (characterised by pasta, tomato sauce, red meat, processed meat, added animal fat, white bread and wine) with increased overall mortality was also suggested, but only for the highest quartile in a multivariate model. Dietary recommendations aimed at the Italian elderly population should support a dietary pattern characterised by a high consumption of olive oil, raw vegetables and poultry.
Exogenous nucleic acids and nucleotides are efficiently hydrolysed and taken up as nucleosides by intestinal explants from suckling piglets
Authors: Gil Angel , Gómez-León Carmen , Rueda Ricardo 
Published: April 2007

Human milk is a rich source of RNA, free nucleotides (NT) and nucleosides (NS). To determine the uptake of different NS sources by the intestinal epithelium, jejunal explants from suckling piglets were cultured in a medium supplemented with a mixture of NS (adenosine, cytidine, guanosine, inosine, uridine; 10 mg/l each), a mixture of five NT (AMP, CMP, GMP, IMP, UMP; 7 mg/l each) or RNA (60 mg/l), respectively. Aliquots from the media were taken at different times (0·5, 2, 5, 15, 30, 60, 180 min). NS and NT concentrations were analysed in the different supernatants at those periods using solid-phase extraction followed by HPLC. When explants were cultured in the presence of NS the concentration of these compounds, excepting cytidine, rapidly decreased, suggesting that they are efficiently taken up. When explants were incubated in the presence of NT, the total concentration of these compounds decreased while the total concentration of NS increased, suggesting that enterocytes efficiently hydrolyse NT into NS. Likewise, when explants were incubated in the presence of RNA, the total concentration of both NT and NS increased, indicating that intestinal explants are able to hydrolyse RNA to NT and then to NS in the absence of luminal enzymes. In conclusion, the jejunum of piglets at weaning is able to hydrolyse RNA and free NT to NS, and NS, excepting cytidine, are efficiently taken up by the small intestine. These results suggest that the current concentration of NT used to supplement infant formulas should be reconsidered.
The “Rout of Monsters” in Cornus
Authors: Wentersdorf Karl P. 
Published: April 2007

In his entertainment A Mask Presented at Ludlow‐Castle, 1634, Milton describes the followers of the “foul inchanter” Comus, son of Circe by Bacchus, as a “rout of Monsters” who have been transformed, by a metamorphosis of their heads,Into som brutish form of Woolf, or Bear, Or Ounce, or Tiger, Hog, or bearded Goat, All other parts remaining as they were.
Progress Report on Long Period Seismographs
Authors: Benioff Hugo , Press Frank 
Published: April 2007

Summary
Long period seismograph systems in operation in Pasadena are described. Extension of the group velocity curves for mantle Rayleigh waves and G-waves, the detection of these waves from earthquakes in the magnitude range , and the recording of unusual body waves with unsuspected long period components are among the results which have been achieved.
Caustics Produced by Waves Through the Earth's Core
Authors: Gutenberg B. 
Published: April 2007

Summary
Caustics produced by SKP, PKS, PKP and other phases through the Earth's core are investigated. No impulses from diffracted waves with periods of two seconds or more have been found beyond five degrees from caustics. Short waves preceding the main PKIKP-phase at distances between 125° and 140° probably have their deepest point in or near a transition zone between the liquid outer and the probably solid inner core and it is unlikely that they are related to the caustic of PKP near 145° although their travel-time curves end near this caustic. The observed range of long-period waves diffracted beyond the caustics of several phases is smaller than the maximum range calculated by Jeffreys.
On the Chemical Composition of the Outer Core
Authors: MacDonald Gordon J. F. , Knopoff Leon 
Published: April 2007

Summary
The average composition of the Earth is assumed to be the same as that of the chondritic meteorites. This assumption is consistent with the present rate of heat production in the Earth. A core made up solely of iron-nickel is inconsistent with the chondritic model unless the ratio of the abundances of (Fe+ Mg)/Si is unity in the mantle. The condition (Fe + Mg)/Si = 1 requires that a major part of the mantle be made of material having the composition of pyroxene or pyroxene-garnet (eclogite). If the mantle is assumed to be made up of a 400 km shell of the composition of eclogite underlain by a material of dunite composition, the chondritic model requires a core of composition (Fe, Ni)1.6Si.
The representative atomic number (Ẑ) has been introduced to characterize compounds at moderately high pressures. From asymptotic relations in the Thomas-Fermi-Dirac model, a basis is formed for the computation of Ẑ. Bullen's density distribution gives Ẑ for the outer core of about 22. The representative atomic number of Fe1.6Si is 22.8. The composition of the core deduced from equation of state arguments is thus consistent with the chondritic model of the Earth.
The electrical conductivity of (Fe, Ni)1.6Si should be a third to a tenth that of pure iron for conditions obtained in the core. Such a conductivity is consistent with the requirements of the dynamo theory of the magnetic field.
A New Determination of the Differences in Gravity between the N.P.L. Teddington and the South African Fundamental and Secondary Stations
Authors: Gough D. I. 
Published: April 2007

Summary
Observations have been made with the Cambridge pendulum apparatus at the British Fundamental gravity station at the N.P.L. Teddington, at the South African Fundamental gravity station at Johannesburg, and at the South African secondary stations at Pretoria and Mowbray. Two pendulums were exposed to mercury during the project. The remaining four, namely I A, I B, I C and VI A, give for the mean gravity differences
Teddington-Mowbray = 1.5495 ± 0.0001 cm/s2 Teddington-Johannesburg = 2.6472 ± 0.0003 cm/s2 Teddington-Pretoria = 2.5672 ± 0.0003 cm/s2 whence, adopting g = 981.1963 cm/s2 at Teddington, g = 979.6468 cm/s2 at Mowbray 978.5491 at Johannesburg 978.6291 at Pretoria.
These values agree well with the determinations of 1948-9 by Hales and Gough.
Spontaneous Magnetization Curves and Curie Points of Cation Deficient Titanomagnetites
Authors: Stephenson A. 
Published: April 2007

Summary
Spontaneous magnetization curves J(T) and Curie points of cation deficient titanomagnetites have been calculated by using a molecular field approximation which has been successful in explaining quantitatively the P type behaviour of some stoichiometric titanomagnetites and the variation with composition of the Curie points. In extending this to the case of cation deficient titanomagnetites it is shown that, depending on cation distribution, these can have N type J(T) curves with compensation temperatures up to about 450°C and that others can have J(T) curves unlike the Q, P, L and N types of Néel.
Mucinous carcinoma of the breast: further characterization of its three subtypes
Authors: COADY A. T. , SHOUSHA S. , DAWSON P. M. , MOSS M. , JAMES K. R. , BULL T. B. 
Published: April 2007

Nineteen cases of mucinous carcinoma of the breast were studied. Twelve tumours were of the pure type, and seven were mixed. All had abundant neutral and acidic mucin, and stained strongly with CAM 5.2. Of the 12 pure mucinous tumours, six were devoid of argyrophilic granules and were S‐100 negative, and only one was CEA positive. All six patients are alive with no evidence of recurrence (mean follow‐up 42 months). The other six pure mucinous tumours were rich in argyrophilic granules. Five of these showed S‐100 positivity and all were CEA positive. One patient developed local recurrence and one died of myocardial infarction with no evidence of tumour recurrence (mean follow‐up 80 months). Of the seven mixed tumours, only one contained an occasional cell with argyrophilic granules and four had variable degrees of CEA positivity. Two patients died and one developed bony metastasis (mean follow‐up 40 months).Our findings emphasise the microscopic and prognostic differences between the three subtypes of mucinous carcinoma of the breast, and support the concept of dividing pure mucinous tumours into two distinct subtypes. We suggest that the latter subtyping can be qualitatively made on the basis of the presence or absence of argyrophilic granules in the tumour cells.
Combined immunohistochemical study of tissue polypeptide antigen and cancer antigen 125 in human ovarian tumours
Authors: GHAZIZADEH M. , SASAKI Y. , OGURO T. , AIHARA K. , TENJIN H. , ARAKI T. 
Published: April 2007

An indirect immunoperoxidase method was used to study the expression of tissue polypeptide antigen (TPA) and cancer antigen 125 (CA 125) in 47 benign and malignant ovarian tumours. Tissue polypeptide antigen and CA 125 antigen were expressed respectively in 22 (73%) and 16 (53%) of the 30 adenocarcinomas and in five (29%) and four (23%) of the 17 benign tumours. Co‐expression of TPA and CA 125 antigen occurred in 12 (40%) malignant and four (23%) benign tumours. Ultrastructurally, TPA and CA 125 antigens were located at the cell surface and microvillous surfaces.Evaluation of combined TPA and CA 125 antigen results revealed a remarkable improvement in the positivity rate and a significant decrease (P<0.05) in the negativity rate of ovarian carcinomas as compared with the result of each one separately. These findings provide complementary evidence for the previous results on the plasma levels of TPA and CA 125 antigen and suggest that specific combinations of tumour markers may be more effective for the diagnosis and monitoring of ovarian carcinomas, than the use of any single marker.
Immunolocalization of urokinase‐type plasminogen activator in adenomas and carcinomas of the colorectum
Authors: SIER C.F.M. , FELLBAUM C. , VERSPAGET H.W. , SCHMITT M. , GRIFFIOEN G. , GRAEFF H. , HÖFLER H. , LAMERS C.B.H.W. 
Published: April 2007

Carcinogenesis in the human colon is associated with a marked increase in the tissue content of the urokinase‐type plasmmogen activator (u‐PA). This study was performed to determine the type of cells responsible for the u‐PA increase in carcinomas of the colon and in their precursor lesions, the adenomas, by immunohistological evaluation applying monoclonal antibody 3689 directed to the β‐chain of u‐PA.Normal intestinal mucosa (n= 17) showed hardly any staining of u‐PA, but some lamina propria cells were faintly positive. Carcinomas (n= 17) and adenomas (n= 16) showed a considerable and comparable staining intensity of u‐PA in neoplastic columnar epithelial cells, and this staining was found to be diffuse and cytoplasmic. In a majority of the neoplastic tissues the u‐PA staining was found to be patchy and not related to known risk markers of malignancy such as dysplasia in the adenomas, or to prognostic determinants such as Dukes' classification or differentiation in the carcinomas. The observation of strong u‐PA positive lamina propria cells in adenomas but infrequently observed in normal mucosa and carcinomas was noteworthy. u‐PA staining intensity of the tissue sections was found to correlate well with the u‐PA antigen level in the tissue extracts determined by ELISA (r= 0.52, P= 0.0001) but poorly with the u‐PA activity determined enzymatically (r= 0.28, P= 0.05).In conclusion, the u‐PA increase in neoplasia of the human colon can be attributed to an increased diffuse cytoplasmic content of u‐PA in neoplastic columnar epithelial cells.
A comparative study of proliferation indices and ploidy in dysplastic naevi and malignant melanomas using flow cytometry
Authors: SLATER S.D. , COOK M.G. , FISHER C. , WRIGHT N.A.W. , FOSTER C.S. 
Published: April 2007

Cell proliferation indices and DNA content have been determined in 18 intradermal naevi, 40 dysplastic naevi and 16 superficial malignant melanomas (<0.76 mm depth of invasion) using flow cytometry. In this study, proliferation indices of intradermal naevi and dysplastic naevi were not significantly different from eachother. Abnormalities of DNA ploidy were not identified in the intradermal naevi or dysplastic naevi; whereas three of the malignant melanomas were aneuploid. In addition, cellular proliferation was increased within the group of malignant melanomas, in comparison with the naevi.This study has found no evidence to indicate that sporadic dysplastic naevi were more likely than intradermal naevi to transform to malignant melanoma, when objective criteria were employed. However, dysplastic naevi could be distinguished from some early malignant melanomas by absence of aneuploidy and by low cell proliferation indices.
Phenotyping of T‐cell lymphomas in paraffin sections–which antibodies?
Authors: CABEÇADAS J.M. , ISAACSON P.G. 
Published: April 2007

Five antibodies, MT1 (CD43), UCHL1 (CD45RO), OPD4, poly‐CD3 and βF1, were assessed for their reactivity with 50 archival cases of T‐cell lymphoma in formalin‐fixed paraffin‐embedded tissue. All cases had been previously characterized as T‐cell lymphomas, and the histological types included 14 cases of small cerebriform lymphoma, six cases of angioimmunoblastic lymphadenopathy‐like T‐cell lymphoma, four cases of T‐zone lymphoma, five cases of pleemorphic small cell lymphoma, 12 cases of pleomorphic medium and large cell lymphoma, four cases of anaplastic large cell lymphoma, two cases of T‐lymphoblastic lymphoma and three cases of enteropathy‐associated T‐cell lymphoma.UCHL1 and MT1 showed reactivity with the highest percentage of cases (94 and 86% respectively) but lack absolute specificity for T‐cells, especially in high‐grade lymphomas. Poly‐CD3 is highly specific for T‐cells, and stained neoplastic cells in almost 80% of the cases. βF1 stained the lowest percentage of cases (40%). UCHL1 and poly‐CD3 together identified 98% of cases, and this combination is recommended for the diagnosis of T‐cell lymphomas in paraffin sections.
Primary liver lymphoma associated with primary biliary cirrhosis
Authors: GOLDIN R. , SAYER J. , WILKINS M. , PRICE† P. , THOMAS H. 
Published: April 2007

We describe a case of a primary polymorphic centroblastic–centrocytic B‐cell lymphoma of the liver developing in a patient with primary biliary cirrhosis—an association which has not previously been reported.We would like to thank Dr C.Fisher, Department of Histopathology, The Royal Marsden Hospital, Fulham Road, London. UK, for his expert help with this case.