bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast and automated functional classification with MED‐SuMo: An application on purine‐binding proteins
Authors: Doppelt‐Azeroual Olivia , Delfaud François , Moriaud Fabrice , de Brevern Alexandre G. 
Published: February 2010

AbstractLigand–protein interactions are essential for biological processes, and precise characterization of protein binding sites is crucial to understand protein functions. MED‐SuMo is a powerful technology to localize similar local regions on protein surfaces. Its heuristic is based on a 3D representation of macromolecules using specific surface chemical features associating chemical characteristics with geometrical properties. MED‐SMA is an automated and fast method to classify binding sites. It is based on MED‐SuMo technology, which builds a similarity graph, and it uses the Markov Clustering algorithm. Purine binding sites are well studied as drug targets. Here, purine binding sites of the Protein DataBank (PDB) are classified. Proteins potentially inhibited or activated through the same mechanism are gathered. Results are analyzed according to PROSITE annotations and to carefully refined functional annotations extracted from the PDB. As expected, binding sites associated with related mechanisms are gathered, for example, the Small GTPases. Nevertheless, protein kinases from different Kinome families are also found together, for example, Aurora‐A and CDK2 proteins which are inhibited by the same drugs. Representative examples of different clusters are presented. The effectiveness of the MED‐SMA approach is demonstrated as it gathers binding sites of proteins with similar structure‐activity relationships. Moreover, an efficient new protocol associates structures absent of cocrystallized ligands to the purine clusters enabling those structures to be associated with a specific binding mechanism. Applications of this classification by binding mode similarity include target‐based drug design and prediction of cross‐reactivity and therefore potential toxic side effects.
IR reflection, attenuated total reflection, and Raman scattering of porous polar III–V semiconductors
Authors: Dmitruk Nicholas , Barlas Tetyana , Dmitruk Igor , Kutovyi Sergiy , Berezovska Natalia , Sabataityte Julija , Simkiene Irena 
Published: February 2010

AbstractOptical properties of porous III–V compounds (GaAs, GaP, InP) in the far infrared (IR) reststrahlen region have been studied by IR reflection and attenuated total reflection (ATR). Comparison of obtained data with Raman scattering (RS) spectra have been performed. Porous layers on III–V compounds wafers were obtained by electrochemical etching. Morphology of porous layers was investigated by methods of atomic force microscopy (AFM) and scanning electron microscopy (SEM), including cross‐section measurements. The ATR measurements allow to study dispersion and damping of surface phonon polaritons (SPPs) in λ = 20–50 µm spectral region. The ATR measurements were carried out in Otto geometry under frequency‐scanning regime at several constant angles of incidence of light. The reflection spectra of porous samples demonstrate change of the reststrahlen band shape due to direct excitation of surface polaritons. It was enabled to excite mixed plasmon–phonon surface modes for semiconductors with free electron concentrations of 1017–1018 cm−3. Frequencies of bulk TO‐, LO‐phonons, surface phonons, and coupled plasmon–phonon modes in the case of high doped semiconductors have been obtained and compared for three spectroscopic methods – reflectance, ATR, and RS.
Pressure‐induced superconductivity in CePd5Al2 and CeRhGe2, new family of heavy fermion superconductors
Authors: Honda Fuminori , Yoshiuchi Shingo , Hirose Yusuke , Nakamura Taichi , Yamamoto Etsuji , Tateiwa Naoyuki , Haga Yoshinori , Takeuchi Tetsuya , Settai Rikio , Ōnuki Yoshichika 
Published: February 2010

AbstractAntiferromagnets CePd5Al2 and CeRhGe2 with the quasi‐two dimensional electronic state have been found to become superconductive by measuring the electrical resistivity under pressure. In these compounds, the Néel temperature decreases at high pressure and becomes approximately zero at critical pressure Pc = 9 GPa in CePd5Al2 and Pc = 7 GPa in CeRhGe2. Superconductivity was observed around Pc. In CePd5Al2, the upper critical field Hc2 is found to be highly anisotropic among H || [001] and [100], reflecting nearly cylindrical Fermi surfaces along the tetragonal [001] direction.
Structure and dynamics of the convective boundary layer on Mars as inferred from large‐eddy simulations and remote‐sensing measurements
Authors: Spiga A. , Forget F. , Lewis S. R. , Hinson D. P. 
Published: February 2010

AbstractThe structure of the Martian convective boundary layer (BL) is decribed by means of a novel approach involving both modelling and data analysis. Mars Express radio‐occultation (RO) temperature profiles are compared to large‐eddy simulations (LESs) performed with the Martian mesoscale model. The model combines the Martian radiative transfer, soil and surface layer schemes designed at Laboratoire de Météorologie Dynamique (LMD) with the most recent version of the Weather Research and Forecast (WRF) fully compressible non‐hydrostatic dynamical core. The key roles of the vertical resolution and, to lesser extent, of the domain horizontal extent have been investigated to ensure the robustness of the LES results. The dramatic regional variations of the BL depth are quantitatively reproduced by the Martian LES. Intense BL dynamics are found to underlie the measured depths (up to 9 km): vertical speed up to 20 m s−1, heat flux up to 2.7 K m s−1 and turbulent kinetic energy up to 26 m2 s−2. Under specific conditions, both the model and the measurements show a distinctive positive correlation between surface topography and BL depth. Our interpretation is that, in the tenuous CO2 Martian near‐surface environment, the daytime BL is to first order controlled by the infrared radiative heating, fairly independent of elevation, which implies a simple correlation between the BL potential temperature and the inverse pressure (‘pressure effect’). No prominent ‘pressure effect’ is in action on Earth where sensible heat flux dominates the BL energy budget. Both RO observations and numerical simulations confirm the terrain‐following behaviour of near‐surface temperature on Mars induced by the dominant radiative influence. The contribution of the Martian sensible heat flux is not negligible and results in a given isotherm in the BL being comparatively closer to the ground at higher surface elevation. The strong radiative control of the Martian convective BL implies a generalised formulation for the BL dimensionless quantities. Based on this formulation and the variety of simulated BL depths by the LES, new similarity relationships for the Martian convective BL in quasi‐steady midday conditions are derived. Rigorous comparisons between the Martian and terrestrial BL and fast computations of the mean Martian BL turbulent statistics are now made possible by such similarity laws. Copyright © 2010 Royal Meteorological Society
Frequency Characteristics of 1‐D Periodic Structures with Tapered Microstrip Lines
Authors: Matsushita Kenji , Fukuda Makoto 
Published: February 2010

AbstractThe electromagnetic bandgap (EBG) structure is a kind of photonic crystal that can be used in microwave and millimeter‐wave frequency regions. In this paper, we present the analysis and design of two types of periodic structure circuit with one‐dimensional (1‐D) EBG structures using alternately arranged, linear, tapered microstrip line (MSL) elements. In order to design the circuits, we calculated their frequency characteristics on the basis of transmission line models. First, we found an ABCD matrix using a model consisting of very short, series‐connected MSL elements. Thereafter, we converted these ABCD matrices into S matrices. Based on the theoretical analyses, we fabricated two types of circuits on printed circuit boards (PCBs) and evaluated their frequency characteristics. The results of evaluation showed that one of the circuits had a stopband of 2 GHz bandwidth and the other had a passband in the center of the stopband. The measured and calculated results were found to be in good agreement. Copyright © 2010 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Hemodynamic Effects of Combined Therapy Using Partial Splenic Embolization and Transjugular Retrograde Obliteration for Gastric Varices with Gastrorenal Shunt
Authors: Chikamori Fumio , Inoue Atsushi , Okamoto Hiroshi , Kuniyoshi Nobutoshi , Kawashima Takahiko , Takase Yasuhiro 
Published: February 2010

AbstractBackgroundThe purpose of the present study was to investigate the short‐term effects of combined therapy using partial splenic embolization (PSE) and transjugular retrograde obliteration (TJO) on the portal hemodynamics of gastric varices with a gastrorenal shunt.Patients and MethodsSixteen patients with gastric varices and a gastrorenal shunt were included in this study. Partial splenic embolization was applied 2 weeks before TJO. The portal blood flow was measured by an ultrasonic duplex Doppler system, and the wedged hepatic venous pressure (WHVP) was measured by hepatic venous catheterization, before and after the combined therapy.ResultsThe complete obliteration of the gastrorenal shunt and gastric varices was revealed by retrograde shuntography and computed tomography after TJO in all cases. The WHVP before and just after PSE was 23 ± 7 and 19 ± 7 mmHg, respectively, showing a significant change (P < 0.01). The WHVP before and the day after TJO was 20 ± 5 mmHg and 22 ± 6 mmHg, respectively, showing a significant change (P < 0.01). There was no significant difference between the WHVP before and after the combined therapy. The portal venous flow volume before and after the combined therapy were 514 ± 146 and 512 ± 161 ml/min, respectively, showing no significant change. However, the splenic venous flow volume before and after the combined therapy was 319 ± 131 and 179 ± 113 ml/min, respectively, showing a significant change (P < 0.05).ConclusionsThe WHVP did not change after the combined therapy of PSE and TJO. Partial splenic embolization contributed to protecting portal congestion after TJO. We conclude that the combined therapy using PSE and TJO is an effective treatment for gastric varices from the portal hemodynamic point of view.
Regulatory T Cells in Peripheral Blood, Lymph Node, and Thyroid Tissue in Patients with Medullary Thyroid Carcinoma
Authors: Müller S. , Poehnert D. , Müller J. A. , Scheumann G. W. F. , Koch M. , Lück R. 
Published: February 2010

AbstractBackgroundImmunological response of the human body is controlled by the suppressive characteristics of regulatory T cells (Tregs). In various diseases a change in the number of Tregs is evident. For example, whereas Tregs are reduced in auto‐immunological processes, an increase of Tregs is found with various malignant tumors. Regarding medullary thyroid carcinoma (MTC) no such studies have been performed to date.MethodsExpression of CD4 and CD25 in CD45+ leukocytes from blood and lymph nodes was studied by flow cytometry in patients with MTC and patients with benign goiter. We also examined the marker forkhead box P3 (FoxP3), an intracellular transcription factor, which is supposed to be the most specific marker for Tregs. Immunohistochemical staining for FoxP3 was performed on lymph node and thyroid tissue.ResultsThe number of FoxP3+ lymphocytes in peripheral blood was significantly higher in patients with MTC than in controls (p = 0.02). This result was confirmed immunohistochemically in lymph node and thyroid tissue, as well as in carcinoma tissue. No difference in CD4+CD25+ lymphocytes was observed between the two groups. After clinical staging (International Union against Cancer—UICC—stages) of MTC patients, triplication of FoxP3+ lymphocytes could be observed from MTC < UICC II to MTC > UICC II.ConclusionsAn increase of FoxP3+ lymphocytes could be shown in peripheral blood of patients with MTC but not in patients with benign goiter; this increase also correlates with findings in lymph nodes and thyroid gland. The number of FoxP3+ cells correlated with the patients’ prognosis. Therefore, FoxP3+ lymphocytes are a good diagnostic criterion for malignancy in patients with medullary thyroid carcinoma, and their presence at staging may influence therapeutic decisions.
Role of nasal muscles in nasal valve collapse
Authors: Aksoy Fadlullah , Veyseller Bayram , Yıldırım Yavuz Selim , Acar Hürtan , Demirhan Hasan , Özturan Orhan 
Published: February 2010

ObjectiveThis study was performed to determine the role of nasal muscle function in patients with dynamic or static nasal valve collapse by comparing the electromyographic activities of nasal muscles in healthy individuals.Study DesignCross‐sectional clinical study.SettingTertiary referral center.Subjects and MethodsTwenty adult patients with dynamic nasal valve collapse, 18 patients with unilateral static nasal valve stenosis (septum deviation), and 20 healthy adults were included in the study. The activity of their nasal muscles was measured by surface electromyography (EMG), and the results were compared for the patient and control groups.ResultsNo abnormal finding was found in any of the nasal muscles of the control group. In the majority of patients with dynamic nasal valve pathology, statistically significant functional disorders were detected in the m dilator naris anterior and m nasalis transversalis muscles compared with the controls. During inspiration and expiration in patients with static nasal valve pathology, some revealed muscular abnormities during inspiration. Normal muscle activation was observed in all of the patients during expiration.ConclusionDetermination of agents involved in pathologies of the nasal valve region is necessary for planning appropriate treatment. The role of nasal muscles in dynamic nasal valve pathologies, which has not been previously recognized, should be considered. A more effective and adequate solution for the nasal sidewalls than static pathologies should be considered in these patients by taking into account the muscular activity disorders detected by EMG at the stage of surgical treatment.
Erratum: Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems
Authors: Atamna-Ismaeel Nof , Sabehi Gazalah , Sharon Itai , Witzel Karl-Paul , Labrenz Matthias , Jürgens Klaus , Barkay Tamar , Stomp Maayke , Huisman Jef , Beja Oded 
Published: February 2010

Abstract
Correction to: The ISME Journal (2008) 2, 656–662; doi:10.1038/ismej.2008.27 Since the publication of this paper, the authors have noticed an error in Table 2. The correct table is shown below. The authors would like to apologize for any inconvenience this may have caused.
Vitronectin binds to the head region of Moraxella catarrhalis ubiquitous surface protein A2 and confers complement‐inhibitory activity
Authors: Singh Birendra , Blom Anna M. , Unal Can , Nilson Bo , Mörgelin Matthias , Riesbeck Kristian 
Published: February 2010

SummaryThe serum resistance of the common respiratory pathogen Moraxella catarrhalis is mainly dependent on ubiquitous surface proteins (Usp) A1 and A2 that interact with complement factor 3 (C3) and complement inhibitor C4b binding protein (C4BP) preventing the alternative and classical pathways of the complement system respectively. UspA2 also has the capacity to attract vitronectin that in turn binds C9 and hereby inhibits membrane attack complex (MAC) formation. We found UspA2 as a major vitronectin binding protein and hence the UspA2/vitronectin interaction was studied in detail. The affinity constant (KD) for vitronectin binding to UspA2 was 2.3 × 10−8 M, and the N‐terminal region encompassing residues UspA2 30–170 bound vitronectin with a KD of 7.9 × 10−8 M. Electron microscopy verified that the active binding domain (UspA230–177) was located at the head region of UspA2. Experiments with recombinantly expressed vitronectin also revealed that UspA230–177 bound to the C‐terminal region of vitronectin residues 312–396. Finally, when human serum was pre‐incubated with UspA2, bacteria showed significantly less serum resistance. Our study directly reveals the binding mode between the N‐terminal domain of UspA2 and the C‐terminal part of vitronectin and thus sheds light upon the mechanism of M. catarrhalis‐dependent serum resistance.
Optical methods for measurement of fatigue crack closure: moiré interferometry and digital image correlation
Authors: NOWELL D. , PAYNTER R. J. H. , DE MATOS P. F. P 
Published: February 2010

ABSTRACTThis paper describes three different optical techniques for the measurement of in‐plane displacements close to the crack tip which can then be used to determine the presence of crack closure in propagating fatigue cracks. Conventional temporal phase shifting moiré interferometry is described first, followed by an improvement to this technique, load sequence phase stepping, which allows data to be collected much more frequently during a load cycle. Finally, more recent measurements using digital image correlation are reported. Results from all three techniques are compared and the advantages and disadvantages of each approach are discussed.
Cardiovascular Disease Is Associated with Greater Incident Dehydroepiandrosterone Sulfate Decline in the Oldest Old: The Cardiovascular Health Study All Stars Study
Authors: Sanders Jason L. , Boudreau Robert M. , Cappola Anne R. , Arnold Alice M. , Robbins John , Cushman Mary , Newman Anne B. 
Published: February 2010

OBJECTIVES: To describe cross‐sectional and longitudinal associations with dehydroepiandrosterone sulfate (DHEAS) and change in DHEAS with age.DESIGN: Longitudinal cohort study.SETTING: Pittsburgh, Pennsylvania.PARTICIPANTS: Cardiovascular Health Study All Stars study participants assessed in 2005/06 (N=989, mean age 85.2, 63.5% women, 16.5% African American).MEASUREMENTS: Health characteristics were assessed in 2005/06 according to DHEAS level, mean DHEAS and DHEAS change across age categories were tested, and linear and logistic regression was used to identify factors present in 1996/97 associated with continuous and categorical DHEAS change.RESULTS: Mean ± standard deviation DHEAS was 0.555 ± 0.414 μg/mL in 1996/97 and 0.482 ± 0.449 μg/mL in 2005/06 for women and 0.845 ± 0.520 μg/mL in 1996/97 and 0.658 ± 0.516 μg/mL in 2005/06 for men. In 2005/06, DHEAS was lower in women and subjects with cardiovascular disease (CVD) and chronic pulmonary disease and higher for African Americans and subjects with hypertension and high cholesterol. Mean DHEAS change was greater in men (−0.200 μg/mL) than in women (−0.078 μg/mL) (P<.001). Each 1‐year increase in age attenuated the effect of male sex by 0.01 μg/mL (P=.009), abolishing the sex difference in DHEAS change by age 79. Presence of CVD before the study period was associated with greater absolute DHEAS change (β=−0.04 μg/mL, P=.04) and with the fourth quartile of DHEAS change versus the first to third quartiles (odds ratio=1.46, 95% confidence interval=1.03–2.05).CONCLUSION: DHEAS change continues into very old age, is not homogenous, is affected by sex, and is associated with prevalent CVD. Future studies should investigate factors that might accelerate DHEAS decline.
Constraints on intragroup stellar mass from hostless Type Ia supernovae
Authors: McGee Sean L. , Balogh Michael L. 
Published: February 2010

Abstract
We probe the diffuse stellar mass in a sample of 1401 low-redshift galaxy groups (1013–1014h−1 M⊙) by examining the rate of hostless Type Ia supernovae (SNe Ia) within the groups. We correlate the sample of confirmed SNe Ia from the Sloan Digital Sky Survey SN survey with the positions of our galaxy groups, as well as with the resolved galaxies within them. We find that 19 of the 59 SNe Ia within the group sample have no detectable host galaxy, with another three ambiguous instances. This gives a robust upper limit that a maximum of 2.69+1.58−1.34 per cent of the group's total mass arises from diffuse stars in the intragroup medium. After correcting for a contribution from ‘prompt’ SNe occurring within galaxies, and including a contribution from those which arise in dwarf galaxies below our photometric limit, we find that only 1.32+0.78−0.70 per cent of the group's total mass is likely in the form of diffuse stellar mass. Combining this result with the galaxy stellar mass functions of Yang, Mo and van den Bosch, we find that 47+16−15 per cent of the stellar mass in our groups is in the form of diffuse light, so that stars make up a fraction 0.028+0.011−0.010 of the total group mass. Galaxy groups appear to be very efficient in disrupting stellar mass into a diffuse component; however, stars still make up a small fraction of the group mass, comparable to that seen in rich clusters. This remains a challenge to galaxy formation models.
Microperimetric changes after intravitreal bevacizumab injection for exudative age‐related macular degeneration
Authors: Ozdemir Hakan , Karacorlu Murat , Senturk Fevzi , Karacorlu Serra Arf , Uysal Omer 
Published: February 2010

Abstract.Purpose:  To evaluate the effect of intravitreal bevacizumab on macular function in the cases of exudative age‐related macular degeneration (AMD).Methods:  A total of 21 eyes of 21 patients with exudative AMD were included in this study. In each eye, at baseline and 1, 3 and 6 months after intravitreal bevacizumab injection, logMAR visual acuity, central 4° macular sensitivity, absolute scotoma size, fixation stability and fixation location by MP‐1 microperimetry and optical coherence tomography (OCT) foveal morphologic changes were assessed. After the initial treatment phase which included three consecutive injections, the decision to re‐treat was based on OCT and clinical findings. Subsequent injections could be administered at least 1 month after the previous injection period according to the OCT‐guided treatment regimen.Results:  Mean retinal sensitivity within central 4° (12 points) area had increased from 3.69 ± 3.44 dB at baseline to 7.16 ± 3.27 dB at month 6. In all controls after the treatment, there was significant increase in logMAR visual acuity (p < 0.001) and MP‐1 retinal sensitivity (p < 0.001). Mean absolute scotoma in test point location had decreased significantly from 12 of the 76 applied test point locations measured at baseline to five test point locations (−7 test point locations; p < 0.001) at month 6 showing statistical significance. Fixation properties had preserved in all patients 6 months after intravitreal bevacizumab treatment.Conclusion:  Intravitreal bevacizumab therapy induced a significant increase in mean retinal sensitivity and significant decrease in mean absolute scotoma size during 6 months. The MP1 microperimetry proved to be a valuable tool in the evaluation of functional benefit of exudative AMD therapy with intravitreal bevacizumab.