bluuebunny/crossref_metadata_2025_split huggingface dataset:
Swell and Slanting-Fetch Effects on Wind Wave Growth
Authors: Ardhuin Fabrice , Herbers T. H. C. , Watts Kristen P. , van Vledder Gerbrant Ph , Jensen R. , Graber Hans C. 
Published: May 2007

AbstractWind-sea generation was observed during two experiments off the coast of North Carolina. One event with offshore winds of 9–11 m s−1 directed 20° from shore normal was observed with eight directional stations recording simultaneously and spanning a fetch from 4 to 83 km. An opposing swell of 1-m height and 10-s period was also present. The wind-sea part of the wave spectrum conforms to established growth curves for significant wave height and peak period, except at inner-shelf stations where a large alongshore wind-sea component was observed. At these short fetches, the mean wave direction θm was observed to change abruptly across the wind-sea spectral peak, from alongshore at lower frequencies to downwind at higher frequencies. Waves from another event with offshore winds of 6–14 m s−1 directed 20°–30° from shore normal were observed with two instrument arrays. A significant amount of low-frequency wave energy was observed to propagate alongshore from the region where the wind was strongest. These measurements are used to assess the performance of some widely used parameterizations in wave models. The modeled transition of θm across the wind-sea spectrum is smoother than that in the observations and is reproduced very differently by different parameterizations, giving insights into the appropriate level of dissipation. Calculations with the full Boltzmann integral of quartet wave–wave interactions reveal that the discrete interaction approximation parameterization for these interactions is reasonably accurate at the peak of the wind sea but overpredicts the directional spread at high frequencies. This error is well compensated by parameterizations of the wind input source term that have a narrow directional distribution. Observations also highlight deficiencies in some parameterizations of wave dissipation processes in mixed swell–wind-sea conditions.
Is Interleaving in the Agulhas Current Driven by Near-Inertial Velocity Perturbations?
Authors: Beal Lisa M. 
Published: May 2007

Abstract
Recent observations taken at a number of latitudes in the Agulhas Current reveal that the water mass structure on either side of its dynamical core is distinctly different. Moreover, interleaving of these distinct water masses is observed at over 80% of the stations occupied in the current, particularly within the subsurface density layer between tropical surface water and subtropical surface water masses, and within the intermediate layer between the Antarctic Intermediate Water and Red Sea water masses. Direct velocity measurements allow for a comparison between the characteristic vertical length scales of the Agulhas intrusions and those of velocity perturbations found throughout the current. It is found that the interleaving scales match those of the velocity perturbations, which are manifest as high-wavenumber vertical shear layers and are identified as near-inertial oscillations. Furthermore, the properties of the intrusions indicate that double diffusion is not an important process in their development: they are generally not associated with a density anomaly, their slope and thickness fall outside the predicted maxima for instability, and a strong horizontal shear field acts to separate water parcels more quickly than intrusions would be able to grow by double-diffusive processes. Instead, the position, thickness, and slope of Agulhas intrusions relative to the background salinity and density field suggest that they are forced by rotating inertial velocities, with subsequent growth possibly driven by small-scale baroclinic instabilities. However, not all the evidence points conclusively toward advectively driven intrusions. For instance, there is a discrepancy between the observed salinity anomaly amplitude and the predicted inertial displacement given the background salinity gradient, which deserves further examination. Hence, there is a future need for more pointed observations and perhaps the development of an analytical or numerical model to understand the exact nature of Agulhas intrusions.
Effect of Mesoscale Eddies on Subtropical Mode Water Variability from the Kuroshio Extension System Study (KESS)
Authors: Qiu Bo , Chen Shuiming , Hacker Peter 
Published: May 2007

Abstract
Forty-eight profiling floats have been deployed in the Kuroshio Extension (KE) region since May 2004 as part of the Kuroshio Extension System Study (KESS) project. By combining the float temperature–salinity measurements with satellite altimetry data, this study investigates the role played by mesoscale eddies in controlling the property changes in North Pacific Subtropical Mode Water (STMW). Following a 3-yr period of low eddy activity in 2002–04, the KE showed a transition to a high eddy kinetic energy state in 2005. This transition is the result of delayed oceanic response to the 2002 shift in the basin-scale surface wind forcing in connection with the Pacific decadal oscillation. The high eddy kinetic energy state of the KE is characterized by successive shedding of strong cold-core rings into the recirculation gyre, resulting from the interaction of the KE jet with the Shatsky Rise or the preexisting cutoff rings. By transporting northern-origin, high-potential-vorticity (PV) KE water into the recirculation gyre, the enhanced eddy activity affects STMW in two ways: first, it hinders the formation of deep winter mixed layer (hence the source for STMW) by modifying the upper-ocean stratification and, second, it provides a direct high-PV source to mix with the surrounding low-PV STMW. The eddies’ influence upon STMW is observed to be both significant in magnitude and efficient in time. Relative to 2004, the PV signal in the core of STMW was reduced by one-half in 2005, and this weakening of STMW’s intensity occurred within a period of less than 7 months. This result supports recent findings by the authors based on historical temperature data that the variability in STMW formation depends more sensitively on the dynamic state of the KE than on the overlying atmospheric conditions.
Economy and society: from Parsons through Habermas to semiotic institutionalism
Authors: Heiskala Risto 
Published: May 2007

English The great transformation to modernity made the economy the major organizing factor of the social synthesis, thus bringing forth the issue of the economy/society relationship as the central problem of modern social theory. This article deals with two broad approaches to this problem: Parsons's and Habermas's variants of structural-functionalism, on the one hand, and various currents of (neo)institutionalism, on the other. An attempt to synthesize the benefits of these conflicting approaches is made from the point of view of semiotic institutionalism. What emerges is a general theoretical framework, which is better equipped than the original structural-functionalist and institutionalist conceptions for the analysis of the economy/society relationship. French Les grandes transformations vers la modernité ont fait de l'économie le principal facteur organisateur de la synthèse sociale, portant sur le devant de la scène la question de la relation économie/société en tant que question centrale de la théorie sociale moderne. L'article s'intéresse à deux grandes approches de cette question: les variantes structuro-fonctionnalistes de Parsons et Habermas d'une part, et divers courants du (néo)institutionnalisme de l'autre. L'auteur s'efforce de faire la synthèse des points forts de ces deux approches conflictuelles du point de vue de l'institutionnalisme sémiotique. Il en émerge un cadre théorique général plus adapté que les conceptions structurofonctionnalistes et institutionnalistes à l'analyse de la relation économie/société.
Convergent origins, divergent destinations: sociology's contributions and connections to economics in a historical and interdisciplinary framework
Authors: Zafirovski Milan 
Published: May 2007

English This article explores selected significant instances of sociology's contributions and connections to economics. These contributions are framed and analyzed within a historical and interdisciplinary setting of the originally common or convergent roots (Enlightenment philosophical rationalism and liberalism) and early co-developments, and yet the subsequently (especially since the 1930s) divergent trajectories and destinations of sociology and economics. These contributions are divided into two general categories: theoretical-substantive and methodological-epistemological. Sociological analyses of market phenomena, societal development and institutions are adduced as examples of sociology's theoretical contribution to economics. Ideal-types, Verstehen, and sociology of knowledge exemplify its methodological contributions and connections to economics. The article aims to help bridge a gap in the current literature in which such contributions and connections of sociology to economics are rarely recognized and considered in favor of those in the opposite (“rational-choice”) direction. French L'article explore certains apports importants de la sociologie à l'économie et les interrelations entre les deux disciplines. Ces apports sont analysés dans une perspective historique et interdisciplinaire, des racines originellement communes ou convergentes des deux disciplines (le rationalisme philosophique des Lumières et le libéralisme) et de leur développement initial commun à leurs trajectoires et destinations par la suite - en particulier depuis les années trente - divergentes. Ces apports se répartissent en deux grandes catégories: théoriques-formels et méthodologiques-épistémologiques. Les analyses sociologiques des phénomènes de marché, du développement de la société et des institutions sont donnés en exemples de contributions théoriques de la sociologie à l'économie. Les types-idéaux, Verstehen, et la sociologie de la connaissance témoignent de son apport méthodologique à l'économie et de ses liens avec celle-ci. L'article a pour ambition de combler un vide dans la littérature qui n'atteste que rarement l'existence de tels apports de la sociologie à l'économie, en privilégiant plutôt à l'inverse les apports de l'économie à la sociologie ("choix rationnel").
Relating destabilizing regions to known functional sites in proteins
Authors: Dessailly Benoît H , Lensink Marc F , Wodak Shoshana J 
Published: May 2007

Abstract

Background
Most methods for predicting functional sites in protein 3D structures, rely on information on related proteins and cannot be applied to proteins with no known relatives. Another limitation of these methods is the lack of a well annotated set of functional sites to use as benchmark for validating their predictions. Experimental findings and theoretical considerations suggest that residues involved in function often contribute unfavorably to the native state stability. We examine the possibility of systematically exploiting this intrinsic property to identify functional sites using an original procedure that detects destabilizing regions in protein structures. In addition, to relate destabilizing regions to known functional sites, a novel benchmark consisting of a diverse set of hand-curated protein functional sites is derived.

Results
A procedure for detecting clusters of destabilizing residues in protein structures is presented. Individual residue contributions to protein stability are evaluated using detailed atomic models and a force-field successfully applied in computational protein design. The most destabilizing residues, and some of their closest neighbours, are clustered into destabilizing regions following a rigorous protocol. Our procedure is applied to high quality apo-structures of 63 unrelated proteins. The biologically relevant binding sites of these proteins were annotated using all available information, including structural data and literature curation, resulting in the largest hand-curated dataset of binding sites in proteins available to date. Comparing the destabilizing regions with the annotated binding sites in these proteins, we find that the overlap is on average limited, but significantly better than random. Results depend on the type of bound ligand. Significant overlap is obtained for most polysaccharide- and small ligand-binding sites, whereas no overlap is observed for most nucleic acid binding sites. These differences are rationalised in terms of the geometry and energetics of the binding site.

Conclusion
We find that although destabilizing regions as detected here can in general not be used to predict binding sites in protein structures, they can provide useful information, particularly on the location of functional sites that bind polysaccharides and small ligands. This information can be exploited in methods for predicting function in protein structures with no known relatives. Our publicly available benchmark of hand-curated functional sites in proteins should help other workers derive and validate new prediction methods.
Developmental biologists' choice of subjects approximates to a power law, with no evidence for the existence of a special group of 'model organisms'
Authors: Davies Jamie A 
Published: May 2007

Abstract
Background
This report describes an unexpected aspect of the structure and development of developmental biology research, rather than the development of a specific embryo. Descriptions of modern developmental biology emphasize investigators' concentration on a small number of 'model' organisms and it is assumed that a clear division exists between the attention paid to these 'model' organisms and that paid to other species. This report describes a quantitative analysis of the organisms that were the subjects of studies reported in developmental biology journals published in the years 1965, 1975, 1985, 1995 and 2005, chosen to represent five decades of modern developmental biology.

Results
The results demonstrate that the distribution of attention paid to different organisms has a smooth distribution that approximates to a scale-free power law, in which there is no clear discontinuity that divides organisms into 'models' and the rest. This is true for both individual years and for the aggregate of all years' data. In other systems (eg connections in the World Wide Web), such power-law distributions arise from mechanisms of preferential attachment ('the rich get richer'). Detailed analysis of the progress of different organisms over the years under study shows that, while preferential attachment may be part of the mechanism that generates the power law distribution, it is insufficient to explain it.

Conclusion
The smoothness of the distribution suggests that there is no empirical basis for dividing species under study into 'model' organisms and 'the rest', and that the widely-held view about organism choice in developmental biology is distorted.
Effects of lamivudine on serum albumin levels correlate with pretreatment HBV-DNA levels in cirrhotic patients
Authors: Nakamuta Makoto , Kotoh Kazuhiro , Enjoji Munechika , Kajiwara Eiji , Shimono Junya , Masumoto Akihide , Maruyama Toshihiro , Furusyo Norihiro , Nomura Hideyuki , Sakai Hironori , Takahashi Kazuhiro , Azuma Koichi , Shimoda Shinji , Tanabe Yuichi , Hayashi Jun 
Published: May 2007

Abstract

Background
Lamivudine treatment has been recently demonstrated to increase the serum albumin levels in cirrhotic patients with hepatitis B virus (HBV) infection, but the precise mechanism remains unclear. We hypothesized that the improvement of hypoalbuminemia by lamivudine may be attributable to the reduction of HBV replication itself, rather than to cessation of hepatitis. In order to confirm this hypothesis, in this study we evaluated factors which correlated with the increase in serum albumin levels. Fifty-four patients (Child-Pugh A/B/C, 35/9/10) with HBV-related liver cirrhosis who had been treated with lamivudine for more than 12 months were evaluated. We analyzed the correlation between the increase in serum albumin levels at month 12 after starting treatment (Δ-albumin) and various pretreatment variables. We also analyzed the correlation between Δ-albumin and the reduction in serum levels of HBV-DNA (Δ-HBV-DNA) or alanine aminotransferase (Δ-ALT) at month 12.

Results
The average Δ-albumin was 0.38 g/dL and only serum HBV-DNA levels before treatment correlated significantly with Δ-albumin. We also analyzed the correlation in patients whose alanine aminotransferase levels were normalized after 12 months so that the possible influence of breakthrough hepatitis could be excluded. Even among this subgroup of patients, there was no significant correlation between Δ-albumin and either pretreatment alanine aminotransferase levels or Δ-ALT. In contrast, in patients whose serum HBV-DNA was undetectable at month 12, we found a significant correlation between Δ-albumin and both pretreatment serum HBV-DNA levels and Δ-HBV-DNA.

Conclusion
Our results demonstrated that albumin levels are associated with pretreatment HBV-DNA but not with alanine aminotransferase levels.
Primary isolated extramedullary plasmacytoma of colon
Authors: Gupta Vishal , Nahak Brindaban , Sakhuja Puja , Agarwal Anil K , Kumar Nirmal , Mishra Pramod K 
Published: May 2007

Abstract

Background
Extramedullary plasmacytoma is an uncommon entity that most commonly involves nasopharynx or upper respiratory tract. Involvement of the gastrointestinal tract occurs in approximated 10% of cases. Isolated primary plasmacytoma of colon is rare and only 7 well documented cases have been reported in the literature.

Case presentation
We present a case of 42 year male who presented with diarrhea. Multiple colonic strictures were found on investigation. Colonoscopic biopsy was not helpful in making any specific diagnosis. Patient underwent subtotal colectomy. Isolated primary colonic plasmacytoma was found on histopathological examination.

Conclusion
Plasmacytoma is known to occur in extra osseous sites. Primary colonic plasmacytoma, however, is a rare clinical entity. Primary colonic plasmacytoma may have varying clinical presentations including multiple colonic strictures that may mimic colonic tuberculosis or inflammatory bowel disease. Although these cases are rare, treating physician as well as radiologist, and pathologist should be aware of this entity.
ngLOC: an n-gram-based Bayesian method for estimating the subcellular proteomes of eukaryotes
Authors: King Brian R , Guda Chittibabu 
Published: May 2007

AbstractWe present a method called ngLOC, an n-gram-based Bayesian classifier that predicts the localization of a protein sequence over ten distinct subcellular organelles. A tenfold cross-validation result shows an accuracy of 89% for sequences localized to a single organelle, and 82% for those localized to multiple organelles. An enhanced version of ngLOC was developed to estimate the subcellular proteomes of eight eukaryotic organisms: yeast, nematode, fruitfly, mosquito, zebrafish, chicken, mouse, and human.
Neurotoxicity From Oxaliplatin Combined With Weekly Bolus Fluorouracil and Leucovorin As Surgical Adjuvant Chemotherapy for Stage II and III Colon Cancer: NSABP C-07
Authors: Land Stephanie R. , Kopec Jacek A. , Cecchini Reena S. , Ganz Patricia A. , Wieand H. Samuel , Colangelo Linda H. , Murphy Kate , Kuebler J. Philip , Seay Thomas E. , Needles Burton M. , Bearden James D. , Colman Lauren K. , Lanier Keith S. , Pajon Eduardo R. , Cella David , Smith Roy E. , O'Connell Michael J. , Costantino Joseph P. , Wolmark Norman 
Published: May 2007

Purpose The randomized, multicenter, phase III protocol C-07 compared the efficacy of adjuvant bolus fluorouracil and leucovorin (FULV) versus FULV with oxaliplatin (FLOX) in stage II or III colon cancer. Definitive analysis revealed an increase in 4-year disease-free survival from 67.0% to 73.2% in favor of FLOX. This study compares neurotoxicity between the treatments. Patients and Methods Neurotoxicity was recorded for all patients using standard adverse event reporting. Patients at select institutions completed a neurotoxicity questionnaire through 18 months of follow-up. Results A total of 2,492 patients enrolled onto C-07 and 400 patients enrolled onto the patient-reported substudy. Mean patient-reported neurotoxicity was higher with oxaliplatin throughout the 18 months of study (P < .0001). During therapy, patients receiving oxaliplatin experienced significantly more hand/foot toxicity (eg, “quite a bit” of cold-induced hand/foot pain 26% FLOX v 2.6% FULV) and overall weakness (eg, moderate weakness in 27.4% FLOX v 16.2% FULV). At 18 months, hand neuropathy had diminished, but patients who received oxaliplatin experienced continued foot discomfort (eg, moderate foot numbness and tingling for 22.1% FLOX v 4.6% FULV). Observer-reported neurotoxicity was low grade and primarily neurosensory rather than neuromotor. Sixty-eight percent in the FLOX group v 8% in the FULV group had neurotoxicity at their first on-treatment assessment. Time to resolution was significantly longer for those receiving oxaliplatin, and continued beyond 2 years for more than 10% in the oxaliplatin group. Conclusion Oxaliplatin causes significant neurotoxicity. It is experienced primarily in the hands during therapy and in the feet during follow-up. In a minority of patients the neurotoxicity is long lasting.
Phase I-II Trial of Prone Accelerated Intensity Modulated Radiation Therapy to the Breast to Optimally Spare Normal Tissue
Authors: Formenti Silvia C. , Gidea-Addeo Daniela , Goldberg Judith D. , Roses Daniel F. , Guth Amber , Rosenstein Barry S. , DeWyngaert Keith J. 
Published: May 2007

Purpose To report the clinical feasibility of a trial of accelerated whole-breast intensity modulated radiotherapy, with the patient in prone position, optimally to spare the heart and lung. Patients and Methods Patients with stages I or II breast cancer, excised by breast conserving surgery with negative margins, were eligible for this institutional review board–approved prospective trial. Computed tomography simulation was performed with the patient prone on a dedicated breast board, in the exact position used for treatment. A dose of 40.5 Gy, delivered at 2.7 Gy in 15 fractions, was prescribed to the index breast with an additional concomitant boost of 0.5 Gy delivered to the tumor bed, for a total dose of 48 Gy to the lumpectomy site. Physics constraints consisted of limiting ≤ 5% of the heart volume to receive ≥ 18 Gy and ≤ 10% of the ipsilateral lung volume to receive ≥ 20 Gy. Results Between September 2003 and August 2005, 91 patients were enrolled on the study. Median length of follow-up was 12 months (range, 1 to 28 months). In all patients the technique was feasible and heart and lung sparing was achieved as prescribed by the protocol. Acute toxicities consisting mostly of reversible grades 1-2 skin dermatitis (67%) and fatigue (18%) occurred in 75 patients. One patient sustained a regional recurrence rapidly followed by distant metastases. Conclusion Accelerated whole breast intensity modulated radiotherapy in the prone position is feasible and it permits a drastic reduction in the volume of lung and heart tissue exposed to significant radiation.
High-performance Nanofiber-reinforeced Composite from All Bio-based Materials
Authors: Imai Naokichi , Kageyama Hiroshi , Uyama Hiroshi 
Published: May 2007

Abstract
An all bio-based polymer composite consisting of poly(l-lactic acid) nanofibers and network polymers of epoxidized soybean oil has been developed. The mechanical properties improved as compared with those of each solo material, and the composite showed relatively good transparency.
Thin Film of a Spin Crossover Complex [Fe(dpp)2](BF4)2
Authors: Matsuda Masaki , Tajima Hiroyuki 
Published: May 2007

Abstract
Thin film of a spin crossover complex [Fe(dpp)2](BF4)2 (dpp = 2,6-di(pyrazollyl)pyridine) has been fabricated by a spin-coating method. The obtained film exhibits spin transition at around 260 K. The absorption spectra and the electrical resistance change with the spin transition. These phenomena are reproducible through both cooling and heating process.