bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein loop structure prediction with flexible stem geometries
Authors: Mönnigmann M. , Floudas C.A. 
Published: October 2005

AbstractThe structure prediction of loops with flexible stem residues is addressed in this article. While the secondary structure of the stem residues is assumed to be known, the geometry of the protein into which the loop must fit is considered to be unknown in our methodology. As a consequence, the compatibility of the loop with the remainder of the protein is not used as a criterion to reject loop decoys. The loop structure prediction with flexible stems is more difficult than fitting loops into a known protein structure in that a larger conformational space has to be covered. The main focus of the study is to assess the precision of loop structure prediction if no information on the protein geometry is available. The proposed approach is based on (1) dihedral angle sampling, (2) structure optimization by energy minimization with a physically based energy function, (3) clustering, and (4) a comparison of strategies for the selection of loops identified in (3). Steps (1) and (2) have similarities to previous approaches to loop structure prediction with fixed stems. Step (3) is based on a new iterative approach to clustering that is tailored for the loop structure prediction problem with flexible stems. In this new approach, clustering is not only used to identify conformers that are likely to be close to the native structure, but clustering is also employed to identify far‐from‐native decoys. By discarding these decoys iteratively, the overall quality of the ensemble and the loop structure prediction is improved. Step (4) provides a comparative study of criteria for loop selection based on energy, colony energy, cluster density, and a hybrid criterion introduced here. The proposed method is tested on a large set of 3215 loops from proteins in the PdbSelect25 set and to 179 loops from proteins from the Casp6 experiment. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Tension development length and lap splice design for reinforced concrete members
Authors: Darwin David 
Published: October 2005

AbstractThe key factors that govern development (anchorage) and splice performance of reinforcing bars in tension are described. The bond design provisions of the AASHTO (American Association of State Highway and Transportation Officials) LRFD (Load and Resistance Factor Design) Bridge Design Specifications, the American Concrete Institute Building Code Requirements for Structural Concrete (ACI 318‐05), ACI Committee 408, CEB‐FIP Model Code 1990, and Eurocode 2 are summarized and compared with test results. In terms of the key factors, the bond strength of bars not confined by transverse reinforcement is proportional to the concrete compressive strength to the ¼ power. The contribution of transverse reinforcement to bond strength increases with the area of the transverse reinforcement per bar and the relative rib area and diameter of the bar being developed or spliced and has been found to be proportional to the concrete compressive strength to a power between ¾ and 1.0. For deep members or for high‐slump (conventional and superplasticized) concrete, the effect of bar placement may be greater than accounted for in current design provisions. Of the five design procedures compared in this paper, those developed by ACI Committee 408 provide the best match with test results for both developed and spliced bars. For developed bars, the other four design procedures result in a high percentage of tests for which the test to calculated strength ratios (T/C) are less than 1.0, with the greatest percentage of low T/C values resulting from the AASHTO requirements. The relative safety of the latter four design procedures improves for lap splices. A provision in ACI 318‐05 that allows a 20% reduction in development and lap splice length for bars smaller than 19 mm appears to be unsafe and should be removed or modified.
Spectroscopic study of Eu3+ ions in heavy metal fluoride and oxide glasses
Authors: Pisarski W. A. 
Published: October 2005

AbstractTwo types of fluoride and oxide systems belonging to the heavy metal glass family have been studied. From absorption and emission spectra together with Judd–Ofelt analysis, spectroscopic parameters of Eu3+ ions in both optical systems were evaluated and compared. The new oxide glassy system based on PbO–B2O3–Al2O3–WO3 exhibits interesting spectroscopic properties of Eu3+ ions for application as a red‐emitting optical material. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Magnetism in n‐type GaMnN grown by molecular beam epitaxy
Authors: Van Nostrand J. E. , Albrecht J. D. , Claflin B. , Liu Y. , Nathan M. I. , Ruden P. P. 
Published: October 2005

AbstractWe investigate the magnetic properties of a strongly n‐type GaMnN alloy grown by molecular beam epitaxy. Transport, X‐ray diffraction, and magnetic characterizations are presented. The carrier concentration and mobility obtained by Hall effect measurements are nearly constant with respect to temperature over the entire temperature range from 4 K to 300 K. Magnetometry data indicates a transition temperature at approximately 170 K with hysteresis measurements indicating magnetic behavior at least to 300 K. The role of alloy microstructure is investigated using X‐ray diffraction and shows the possible presence of alternate phases giving rise to magnetization. In transport, we observe a linear Hall effect dependence on magnetic field strength. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Bulk and interface contributions to the optical second‐harmonic response of native‐oxide‐covered vicinal Si(111)
Authors: McGilp J. F. , Carroll L. 
Published: October 2005

AbstractThe optical second‐harmonic response of native‐oxide‐covered vicinal Si(111), offcut by 3° towards [$ \bar 1 $$ \bar 1 $2], is compared with previous work at the same wavelength on similar samples, but offcut by 5° in the opposite, [11$ \bar 2 $], direction. Sample rotation plots for sS, pS, sP and pP polarisation combinations are reported using 130 fs laser pulses of 765 nm wavelength, where mN indicates m‐polarised input and N‐polarised SH output. The two offcuts have different step geometries, but the same terrace structure at the Si/SiO2 interface. In addition, the bulk quadrupolar contributions from the two offcuts are related by simple geometric factors. By using these constraints, simultaneous fitting of eight rotation plots allows the bulk and interface contributions to be estimated. These results offer the possibility of more detailed investigation of bond hyperpolarisability models, which have been applied recently to the vicinal Si/SiO2 interface. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Frequency‐domain measurement of second harmonic phase
Authors: Carriles R. , An Y. Q. , Downer M. C. 
Published: October 2005

AbstractSecond harmonic (SH) phase is a potentially informative component of nonlinear optical interface characterization, but is often neglected because traditional SH phase measurement methods are very cumbersome. Frequency domain interferometric second harmonic (FDISH) generation enables rapid, accurate SH phase measurement without moving parts by exploiting the wide bandwidth of ultrashort laser pulses. We illustrate the versatility of FDISH through examples of SH phase measurements from GaAs, quartz and Si interfaces. SH phase variations with azimuthal angle and time, and amongst the three tensor components of the nonlinear susceptibility χ(2) of a Si(001)‐dielectric interface, are measured. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ab initio molecular orbital study of conformational properties of cyclohexyne, cycloheptyne, and cyclooctyne
Authors: Yavari Issa , Nasiri Farough , Djahaniani Hoorieh , Jabbari Arash 
Published: October 2005

AbstractThe structures and relative energies for the basic conformations of cyclohexyne (1), cycloheptyne (2), and cyclooctyne (3) have been calculated by the HF/6‐31G*, MP2/6‐31G*, and B3LYP/6‐31G* methods. The C2 symmetric twist conformer of 1 is calculated to be more stable than the planar C2v geometry. Ring inversion of the envelope conformation of 2 takes place via C2 symmetric twist transition state, which is 34.0 kJ mol−1 higher than the envelope form. The C2 symmetric chair conformation of 3 is calculated to be 11.7 kJ mol−1 more stable than the unsymmetrical twist‐boat (3‐TB) geometry. Interconversion of the chair conformation and 3‐TB takes place via an unsymmetrical transition state, which is 37.6 kJ mol−1 less stable than the chair form. Conformational racemization of the chiral 3‐TB takes place via the boat transition state. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Calculations of organic‐solvent dispersions of single‐wall carbon nanotubes
Authors: Torrens Francisco 
Published: October 2005

AbstractThe aqueous solubility Sw and 1‐octanol–(Po), cyclohexane–(Pch), and chloroform–(Pcf) water partition coefficients are calculated. The properties of single‐wall carbon nanotubes (SWNT) are related to the indices (n, m) designating the chiral vector. SWNTs are classified in zigzag (n, 0), armchair (n, n), and chiral (n, m). These properties permit classifying SWNTs according to (n, m). Correlations between (n2 + nm + m2)1/2, log Sw, log Po, log Pch, and log Pcf show that (n, m) are adequate indices. The (10,10) is the most abundant SWNT, presenting consistency between great kinetic stability, small Sw, and great {Po, Pch, Pcf}. The room temperature solubility of SWNTs is investigated in a variety of solvents, finding a class of non‐H‐bonding Lewis bases that provides good solubility. The investigated solvents are grouped into three classes. Five solvents, all featuring high electron‐pair donicity (β) and low H‐bond parameter (α) demonstrate the ability to form stable suspensions readily. SWNTs in some organic solvents are positively charged, while those in water–Triton X are negatively charged. This is explained on the basis of permittivity and electron affinity. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Pulmonary Resection for Non‐small‐cell Lung Cancer in Patients on Hemodialysis: Clinical Outcome and Long‐term Results
Authors: Ciriaco Paola , Casiraghi Monica , Melloni Giulio , Carretta Angelo , Libretti Lidia , Augello Giuseppe , Zannini Piero 
Published: October 2005

AbstractPatients on hemodialysis (HD) who undergo surgery represent a high risk group requiring careful perioperative management to avoid electrolyte imbalance and hemodynamic instability. The aim of the study was to analyze the postoperative outcome in terms of complications and survival of a group of patients on HD who had undergone pulmonary resection for non‐small cell lung cancer (NSCLC). Six patients on HD underwent seven pulmonary resections at our institution from 1998 to 2003. The underlying kidney disease was nephrosclerosis in two patients and glomerulonephritis in four. The mean levels of blood urea nitrogen and serum creatinine were 107 ± 11.5 mg/dl and 7.9 ± 0.64 mg/dl, respectively. The mean preoperative PO2 and FEV1 were 77.6 ± 2.4 mmHg and 2.4 ± 0.16 liters, respectively. The histologic diagnosis was squamous cell carcinoma in four cases and adenocarcinoma in three. One patient underwent two lung resections in 4 years for two primary lung cancers. Five patients underwent lobectomy, one underwent a wedge resection, and in one case pneumonectomy was performed after neoadjuvant chemotherapy. There was no operative mortality. Postoperatively, atrial fibrillation occurred in two patients associated with sputum retention in both, and two other patients had hyperkalemia (complication rate 57%). One patient died of cardiac complications 27 months after surgery. The remaining five patients are currently alive with no evidence of disease. Patients on HD who undergo lung resection have a high rate of postoperative complications. Although the underlying disease influences long‐term survival, radical lung resection in NSCLC patients is recommended in selected cases. Careful metabolic, hematologic, and pharmaceutical management is mandatory during the perioperative period.
Clinical and Radiologic Evaluation of Foramen of Morgagni Hernias and the Transthoracic Approach
Authors: Sırmalı Mehmet , Türüt Hasan , Gezer Suat , Fındık Göktürk , Kaya Sadi , Tastepe Ýrfan , Çetin Güven 
Published: October 2005

AbstractThe limited number of publications on repair of the foramen of Morgagni hernia concentrates mainly on the laparotomy approach. We present our experience with the transthoracic approach. Patients who were diagnosed as having a foramen of Morgagni hernia and were operated on via the transthoracic approach between December 1991 and June 2004 are reviewed retrospectively for their age, sex, presenting symptoms, and diagnostic and surgical procedures. Surgical repair was carried out via the transthoracic approach in all cases. Of the 24 patients who underwent transthoracic diaphragmatic repair of the defect, 16 were women and 8 were men, with an overall mean age of 55.1 years (range 42–69 years). In most cases the defect was on the right side; there was only one case of a left‐sided defect. The most common presenting symptoms were dyspnea and gastrointestinal discomfort; five (20.8%) patients were asymptomatic. In 21 cases (87.5%) the diagnoses were established radiologically. The defect was accessed surgically via a posterolateral thoracotomy. No postoperative morbidity or mortality was observed. The mean follow‐up was 8.3 years (14 months to 14 years), and no recurrence was noted. As important as the surgical repair of the foramen of Morgagni hernia itself is selection of the surgical approach so adhesions of the hernial sac from the surrounding tissues in the thoracic cavity are easily released. The transthoracic approach is amenable to safe primary repair of the defect and the release of adhesions, even in elderly and obese patients, in whom adhesions may be excessive.
Skin function parameters in intensive‐care patients
Authors: Fischer Matthias , Donath Christian , Radke Joachim , Marsch Wolfgang Ch. , Soukup Jens 
Published: October 2005

Background/purpose: The study was performed to investigate the transepidermal water loss (TEWL) and pH‐value in patients in intensive care.Methods: Forty intensive‐care patients (22 men, 18 women) were included in the study. TEWL and pH‐values were measured at admission, and after 24, 96 and 168 h. The areas of measurement were the forehead, the volar forearm, paraumbilical and the ventral thigh. The measurements were made under standardized environmental conditions according to the recommendations of the EMCO Group.Results: Elevated values were found on the forehead compared with the other skin areas examined. There was no significant change in mean TEWL‐values in any patient in the course of the study. There was also no significant influence of TEWL at the time of admission on the prognosis. The course analysis of the mean pH‐values, however, showed that patients who developed a systemic inflammatory response syndrome (SIRS) or sepsis during the further course had a higher pH‐value over the entire study period.Conclusion: TEWL and the pH of the skin surface could be measured at bedside in the intensive‐care unit and delivered reproducible results. These parameters appear, however, to be relevant only for subgroups of patients under intensive care.
Digital image enhancement for in vivo laser scanning microscopy
Authors: Gruber Martin J. , Wackernagel Alexandra , Richtig Erika , Koller Silvia , Kerl Helmut , Smolle Josef 
Published: October 2005

Background/purpose: In vivo confocal laser scanning microscopy (CLSM) is a new method that provides skin images in horizontal plane at a level of resolution that allows to view microanatomic structures. This study examines whether certain digital image‐processing steps can increase the visibility of various structures in CLSM.Study design: Fifty images were taken from normal skin of 25 probands, and 39 image enhancement procedures were created. Eight procedures that seemed to provide some quality enhancement were deliberately selected for further evaluation. Subsequently, a collection of random pairs of the original image and an image submitted to any of the eight selected procedures was rated by five independent observers.Results: In three of the eight procedures tested, the modified image was significantly preferred to the original image (χ2‐test,: P≤0.001). In particular, smoothing, shading correction, delineate and grey‐level normalization in various combinations were helpful in showing the characteristic honeycomb pattern, pigmented basal cell layer, cell borders and the nuclei more clearly.Conclusion: Digital image processing may help to increase visibility of in vivo CLSM images.
Age and skin structure and function, a quantitative approach (I): blood flow, pH, thickness, and ultrasound echogenicity
Authors: Waller Jeanette M. , Maibach Howard I. 
Published: October 2005

Background/purpose: The aging process has been studied with fervor recently, given our shifting demographics. Since age's effects are so manifest in skin's appearance, structure, mechanics, and barrier function, it is not surprising that much effort has been placed in research to better understand them. Quantitative measurements permitted by bioengineering have allowed us to objectively and precisely study aging skin. These overviews piece together the immense amounts of information that have emerged from recent technological advances in dermatological research in order to develop a unified understanding of the quantitative effects of age on the skin.Methods: We performed a literature on age‐related changes in blood flow, pH, skin thickness, and ultrasound imaging data, searching Pub‐med, Em‐Base, Science Citation Index, and the UCSF dermatological library's collection of books on the topic of aging skin.Results: Despite the many tools and techniques available for quantitative analysis of skin, age studies are often conflicting, especially in the areas of blood flow and skin thickness. Trends indicate that blood flow may decrease with age, especially in sites exposed to the environment. pH apparently varies little until the age of 70, after which it declines. Skin thickness data are difficult to interpret; while the stratum corneum is generally accepted to maintain its thickness during aging, dermal, epidermal, and whole skin thickness changes are controversial. Ultrasound reveals the appearance of a subepidermal low echogenic band that thickens with age, especially in environmentally exposed areas. Some studies also indicate the presence of an echogenic band in the lower dermis which thins with increased age. However, the whole dermis appears to become more echogenic in elderly people.Conclusion: Much remains to be done if we are to reach consensus on the effects of age on skin structure and function. Future studies would be benefited by increased standardization of skin sites tested, methodology, and increased sample size.
Fluorescence fibre‐optic confocal microscopy of skin in vivo: microscope and fluorophores
Authors: Suihko Christian , Swindle Lucinda D. , Thomas Steven G. , Serup Jørgen 
Published: October 2005

Background/aims: Fibre‐optic confocal imaging in vivo is a new approach in the assessment of human skin. The objective is to describe a novel instrument and its operation and use in combination with fluorophores.Methods: The Stratum® is a fibre‐optic fluorescence confocal microscope especially developed for the study of skin and mucous membranes. The system is flexible and any body site can be studied with a hand‐held scanner. The light source is a 488 nm argon ion laser. Horizontal (en face) images of the epidermis and outer dermis are produced with cellular resolution. Magnification is approximately 1000 × . Fluorescein sodium is routinely used as fluorophore (intradermal injection or application to the skin surface). This fluorophore is safe for human use in vivo, but other substances (rhodamine B, Acridine Orange, green fluorescent protein, curcumin) have also been studied.Results: The instrument produces sharp images of epidermal cell layers from the epidermal surface to the sub‐papillary dermis, with sub‐cellular resolution. The scanner is flexible in use. The technique of intradermal fluorophore injection requires some skill.Conclusions: We consider this fibre‐optic instrument a potentially important tool in skin research for non‐invasive optical biopsy of primarily the epidermis. Present use is focussed on research applications, where the fluorophore distribution in the skin may illustrate morphological changes in the epidermis.
Assemblages of soil macrofauna across a Scottish land‐use intensification gradient: influences of habitat quality, heterogeneity and area
Authors: EGGLETON PAUL , VANBERGEN ADAM J. , JONES DAVID T. , LAMBERT MATTHEW C. , ROCKETT CAROLE , HAMMOND PETER M. , BECCALONI JANET , MARRIOTT DOUGLAS , ROSS EMMA , GIUSTI ALESSANDRO 
Published: October 2005

SummaryLand‐use intensification strongly influences biodiversity by altering habitat heterogeneity, the distribution of habitat types and their extent. This study explores these effects within mixed semi‐natural/agricultural mosaic habitats in Scotland, examining the effect of land‐use intensification on the soil macrofauna at point (m2), landscape (km2) and regional (> 1 km2) scales.The soil macrofauna in six 1‐km2sampling areas (land‐use units; LUU) were sampled using a combined hand‐sorting and Winkler bag extraction technique. Within each LUU, 16 1‐m2samples were taken in each of 2 successive years. Each LUU had a mixture of land‐use types, representing an agricultural intensification gradient.The following hypotheses were tested: (i) the study area sustains a number of distinct habitats as defined by soil macrofaunal composition; (ii) a greater number of restricted range species are found in semi‐natural habitats; (iii) local (point) species density is related to habitat type; (iv) overall levels of species richness per habitat at regional scales are related to species‐area effects; and (v) landscape‐level species density is correlated with habitat heterogeneity.Initial analysis revealed five distinct habitat types: Caledonian forest (semi‐natural pine forest), closed canopy woodland (pine plantation and broadleaved woodland), riparian habitats (wet woodland and grassland), pasture (improved grassland) and arable (crop fields).As hypothesized, the Caledonian habitat contained a greater number of restricted‐range species than the other habitats. However, conifer plantations contained more restricted range species than expected, given their anthropogenic origin. Species density per m2was most strongly affected by habitat type. At the regional level, the size of the species pool was correlated with the size of habitat areas. There were more species overall in LUU with greater habitat heterogeneity.Synthesis and applications.Caledonian pine forests have high species densities and contain species of conservation value. Mixed conifer plantations also appear to have a surprisingly high invertebrate conservation value. In contrast, intensively managed agricultural habitats have low species densities and conservation value. Generally, mixed land‐use areas have higher species densities than single land‐use areas. This emphasizes the need for careful management of forest systems within the matrix of agricultural habitats to maximize landscape diversity.