bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detailed characterization of stellar high energy (FUV/EUV/X-ray) radiation fields during protoplanetary system formation
Authors: Brown Alexander 
Published: February 2010

AbstractYoung stars undergoing the conversion of pre-main-sequence circumstellar disks into protoplanetary systems are strong sources of high energy (FUV/EUV/X-ray) radiation that controls the physical and chemical processes in their circumstellar environment out to hundreds of AU from the star. The high energy radiation resulting from magnetic activity and accretion onto the central star controls the thermal structure of disks, the formation process of planetesimals, and the photoexcitation and photoionization of protoplanets and young planetary atmospheres. Modeling of the dust and gas evolution requires an accurate understanding of the local radiation field throughout the ultraviolet (UV) and X-ray spectral regions, even those parts of the spectrum that are impossible to observe from Earth.Our current research efforts are directed towards developing a better understanding of UV (using HST and FUSE) and X-ray (using Chandra, XMM-Newton, and Swift) stellar activity and the resulting radiation fields during pre-main-sequence evolution from ages of a few to several hundred million years. These studies include extensive UV and X-ray spectral sampling of individual stars in nearby star formation regions and the various moving groups of the Local Association, including our HST Cycle 17 Large Project (GO-11616), which is using 111 HST orbits to observe 32 T Tauri stars with the COS UV spectrograph. Most young stars are well over 100 pc from the Sun and are consequently hard to observe in the UV and X-ray regions at even moderate spectral resolution. However, members of the Local Association, whose ages range from 7 Myr to a few hundred Myr, surround the Sun at distances of 50 pc or less and permit the detailed study of the later stages of the early evolution of stellar activity when gas giant and terrestrial protoplanets are forming. We illustrate our methodology using the 12 Myr old early-M dwarf AU Mic, which possesses a striking dust debris disk, as an example.
Biological damage due to photospheric, chromospheric and flare radiation in the environments of main-sequence stars
Authors: Cuntz Manfred , Guinan Edward F. , Kurucz Robert L. 
Published: February 2010

AbstractWe explore the biological damage initiated in the environments of F, G, K, and M-type main-sequence stars due to photospheric, chromospheric and flare radiation. The amount of chromospheric radiation is, in a statistical sense, directly coupled to the stellar age as well as the presence of significant stellar magnetic fields and dynamo activity. With respect to photospheric radiation, we also consider detailed synthetic models, taking into account millions or hundred of millions of lines for atoms and molecules. Chromospheric UV radiation is increased in young stars in regard to all stellar spectral types. Flare activity is most pronounced in K and M-type stars, which also has the potential of stripping the planetary atmospheres of close-in planets, including planets located in the stellar habitable zone. For our studies, we take DNA as a proxy for carbon-based macromolecules, guided by the paradigm that carbon might constitute the biochemical centerpiece of extraterrestrial life forms. Planetary atmospheric attenuation is considered in an approximate manner.
Synchronous manifestation of 160-min pulsations of the ground pressure and Z-component of geomagnetic field at Moscow, Apatity, Oulu, Yakutsk and Tixie
Authors: Timofeev V. Ye. , Baishev D. G. , Miroshnichenko L. I. , Samsonov S. N. , Skryabin N. G. 
Published: February 2010

AbstractOscillations of the ground pressure and Z-component of geomagnetic field with a period of 160-min in December 2003 and March 2004 have been studied by regular measurements carried out over the territory of Europe and Siberia. As the analysis has shown, in December 2003 these specific oscillations are manifested synchronously from Europe up to Siberia, preferentially in the form of ‘packages’ (‘quanta’) consisting of two-five pulses. Their average amplitudes in December 2003 are of 0.0115±0.0023 mb in the ground pressure and of 0.323±0.070 nT in the Z-component. We suppose that the 160-min pulsations in those both terrestrial parameters represent the effect of a gravitational wave of the same period coming from the Galaxy center.
Surveying RFI for a new Brazilian Solar Spectroscope site
Authors: Cecatto José R. , Albuquerque Paulo C. G. , Vila Ivan O. G. , Cassiano Alan B. , Strauss César , Fernandes Francisco C. R. 
Published: February 2010

AbstractBrazilian Solar Spectroscope (BSS) carry out high time (0.01–0.1 s) resolution solar spectral investigations within the frequency range 1–2.5 GHz on a daily basis. At the moment, a new site is imposed to this facility. This site change became necessary due to both factors: the growing level of radio frequency interference (RFI) signals at actual site and requirements of rising up a new building at the BSS antenna location. We present results of RFI signals search at INPE-Cachoeira Paulista area as purpose to define a new BSS site.
The Indian National Large Solar Telescope (NLST)
Authors: Hasan S. S. 
Published: February 2010

AbstractThe Indian National Large Solar Telescope (NLST) will be a state-of-the-art 2-m class telescope for carrying out high resolution studies of the solar atmosphere. Sites in the Himalayan region at altitudes greater than 4000-m that have extremely low water vapor content and are unaffected by monsoons are under evaluation. This project is led by the Indian Institute of Astrophysics and has national and international partners.NLST is an on-axis alt-azimuth Gregorian multi-purpose open telescope with the provision of carrying out night time stellar observations using a spectrograph. The telescope utilizes an innovative design with low number of reflections to achieve a high throughput and low instrumental polarization. High order adaptive optics is integrated into the design that works with a modest Fried's parameter of 7-cm to give diffraction limited performance. The telescope will be equipped with a suite of post-focus instruments including a high resolution spectrograph and a polarimeter. A detailed concept design of the telescope is presently being finalized and fabrication is expected to begin in 2010 with first light in 2014.
Der Einfluss des Ernährungswissens auf Nahrungsmittelpräferenzen bei Kindern
Authors: Hartmann Andrea Sabrina , Michael Tanja , Munsch Simone 
Published: February 2010

Adipöse Kinder zeigen stärkere Präferenzen für und einen größeren Konsum fetthaltiger Nahrungsmittel. Die aktuelle Studie untersucht, ob Ernährungswissen die Präferenz für Nahrungsmittel beeinflusst. 59 Kinder nahmen an der experimentellen Untersuchung teil, in der Comicfiguren als konditionierte Reize und Nahrungsmittelbilder als unkonditionierte Reize dienten. Relative Präferenzen für die Comicfiguren wurden vor und nach gepaarter Präsentation und das Ernährungswissen mittels Fragebogen erfasst. Das Ernährungswissen scheint die Veränderung der Präferenzen zu beeinflussen. Vor allem die Veränderung der Präferenz für die mit dem fettarmen Nahrungsmittel gepaarte Comicfigur kann dadurch vorhergesagt werden. Ernährungswissen scheint die Attraktivität des fettarmen Nahrungsmittels zu steigern und somit Präferenz für das Nahrungsmittel zu beeinflussen. Es ist daher von Relevanz, dass in Interventionen bei kindlicher Adipositas über gesunde Ernährung aufgeklärt wird. Zukünftige Forschung soll weitere potentielle Einflussvariablen untersuchen.
MHC Restriction of V-V Interactions in Serum IgG
Authors: Leung Earnest , Hoffmann Geoffrey 
Published: February 2010

AbstractAccording to Jerne’s idiotypic network hypothesis, the adaptive immune system is regulated by interactions between the variable regions of antibodies, B cells, and T cells. The symmetrical immune network theory is based on Jerne’s hypothesis, and provides a basis for understanding many of the phenomena of adaptive immunity. The theory includes the postulate that the repertoire of serum IgG molecules is regulated by T cells, with the result that IgG molecules express V region determinants that mimic V region determinants present on suppressor T cells. In this paper we describe rapid binding between purified murine serum IgG of H-2b and H-2d mice and serum IgG from the same strain and from MHC-matched mice, but not between serum IgG preparations of mice with different MHC genes. We interpret this surprising finding in terms of a model in which IgG molecules are selected to have both anti-anti-self MHC and anti-anti-anti-self MHC specificity.
The power of protein interaction networks for associating genes with diseases
Authors: Navlakha Saket , Kingsford Carl 
Published: February 2010

Abstract
Motivation: Understanding the association between genetic diseases and their causal genes is an important problem concerning human health. With the recent influx of high-throughput data describing interactions between gene products, scientists have been provided a new avenue through which these associations can be inferred. Despite the recent interest in this problem, however, there is little understanding of the relative benefits and drawbacks underlying the proposed techniques.
Results: We assessed the utility of physical protein interactions for determining gene–disease associations by examining the performance of seven recently developed computational methods (plus several of their variants). We found that random-walk approaches individually outperform clustering and neighborhood approaches, although most methods make predictions not made by any other method. We show how combining these methods into a consensus method yields Pareto optimal performance. We also quantified how a diffuse topological distribution of disease-related proteins negatively affects prediction quality and are thus able to identify diseases especially amenable to network-based predictions and others for which additional information sources are absolutely required.
Availability: The predictions made by each algorithm considered are available online at http://www.cbcb.umd.edu/DiseaseNet
Contact: carlk@cs.umd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SPICi: a fast clustering algorithm for large biological networks
Authors: Jiang Peng , Singh Mona 
Published: February 2010

Abstract
Motivation: Clustering algorithms play an important role in the analysis of biological networks, and can be used to uncover functional modules and obtain hints about cellular organization. While most available clustering algorithms work well on biological networks of moderate size, such as the yeast protein physical interaction network, they either fail or are too slow in practice for larger networks, such as functional networks for higher eukaryotes. Since an increasing number of larger biological networks are being determined, the limitations of current clustering approaches curtail the types of biological network analyses that can be performed.
Results: We present a fast local network clustering algorithm SPICi. SPICi runs in time O(V log V+E) and space O(E), where V and E are the number of vertices and edges in the network, respectively. We evaluate SPICi's performance on several existing protein interaction networks of varying size, and compare SPICi to nine previous approaches for clustering biological networks. We show that SPICi is typically several orders of magnitude faster than previous approaches and is the only one that can successfully cluster all test networks within very short time. We demonstrate that SPICi has state-of-the-art performance with respect to the quality of the clusters it uncovers, as judged by its ability to recapitulate protein complexes and functional modules. Finally, we demonstrate the power of our fast network clustering algorithm by applying SPICi across hundreds of large context-specific human networks, and identifying modules specific for single conditions.
Availability: Source code is available under the GNU Public License at http://compbio.cs.princeton.edu/spici
Contact: mona@cs.princeton.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes
Authors: Muffato Matthieu , Louis Alexandra , Poisnel Charles-Edouard , Crollius Hugues Roest 
Published: February 2010

Abstract
Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.
Availability: Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus while data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus
Contact: hrc@biologie.ens.fr
ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules
Authors: Loriot Sébastien , Cazals Frédéric , Bernauer Julie 
Published: February 2010

Abstract
Summary: The ever increasing number of structural biological data calls for robust and efficient software for analysis. Easy Structural Biology Template Library (ESBTL) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric constructions and analyses. The parser and data model provided by this ready-to-use include-only library allows adequate treatment of usually discarded information (insertion code, atom occupancy, etc.) while still being able to detect badly formatted files. The template-based structure allows rapid design of new computational structural biology applications and is fully compatible with the new remediated PDB archive format. It also allows the code to be easy-to-use while being versatile enough to allow advanced user developments.
Availability: ESBTL is freely available under the GNU General Public License from http://esbtl.sf.net. The web site provides the source code, examples, code snippets and documentation.
Contact: julie.bernauer@inria.fr
N‐terminal pro‐brain natriuretic peptide from fresh urine for the biochemical detection of heart failure and left ventricular dysfunction
Authors: Jungbauer Carsten G. , Buchner Stefan , Birner Christoph , Resch Markus , Heinicke Norbert , Debl Kurt , Buesing Monika , Biermeier Daniela , Schmitz Gerd , Riegger Günter , Luchner Andreas 
Published: February 2010

AimsPlasma N‐terminal pro‐brain natriuretic peptide (NT‐proBNP) is a strong biochemical marker of heart failure and left ventricular dysfunction (LVD). Due to renal arterio‐venous clearance of NT‐proBNP and the correlation of plasma concentrations with renal function, we hypothesized that NT‐proBNP may have potential as a urinary marker. The objective of this study was to assess urinary concentrations of NT‐proBNP and to identify the predictive value of urinary NT‐proBNP for detecting LVD and heart failure.Methods and resultsN‐terminal pro‐brain natriuretic peptide (Elecsys proBNP®, Roche) was assessed simultaneously in fresh spot urine and plasma from 191 individuals. In patients with heart failure (n = 149), urinary and plasma NT‐proBNP concentrations were positively correlated (r = 0.79, P < 0.001), but urinary NT‐proBNP was significantly lower than plasma NT‐proBNP (42 ± 25 vs. 1389 ± 325 pg/mL, P < 0.001). Upon receiver operating curve analysis, urinary NT‐proBNP detected LV dysfunction (ejection fraction <40%) with a sensitivity of 91% and a specificity of 98% at a cutpoint of 22 pg/mL [area under the curves (AUC) 0.98]. At the same cutpoint, symptomatic heart failure (NYHA‐class > 2) was detected with a sensitivity of 97% and specificity of 98% (AUC 0.99) and clinical signs of fluid retention were detected with a sensitivity and specificity of 98% each (AUC 0.99).ConclusionN‐terminal pro‐brain natriuretic peptide concentrations were markedly lower in the urine than in the plasma. However, urinary NT‐proBNP levels increased stepwise with the severity of heart failure and LVD, and therefore yielded satisfactory predictive values for the detection of significant LVD and symptomatic heart failure. Measurement of urinary NT‐proBNP is a novel, promising, and simple method for the biochemical detection of heart failure.
Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays
Authors: Lee Charlie Wah Heng , Koh Chee Wee , Chan Yang Sun , Aw Pauline Poh Kim , Loh Kuan Hon , Han Bing Ling , Thien Pei Ling , Nai Geraldine Yi Wen , Hibberd Martin L. , Wong Christopher W. , Sung Wing-Kin 
Published: February 2010

ABSTRACT
In April 2009, a new influenza A (H1N1 2009) virus emerged that rapidly spread around the world. While current variants of this virus have caused widespread disease, particularly in vulnerable groups, there remains the possibility that future variants may cause increased virulence, drug resistance or vaccine escape. Early detection of these virus variants may offer the chance for increased containment and potentially prevention of the virus spread. We have developed and field-tested a resequencing kit that is capable of interrogating all eight segments of the 2009 influenza A(H1N1) virus genome and its variants, with added focus on critical regions such as drug-binding sites, structural components and mutation hotspots. The accompanying base-calling software (EvolSTAR) introduces novel methods that utilize neighbourhood hybridization intensity profiles and substitution bias of probes on the microarray for mutation confirmation and recovery of ambiguous base queries. Our results demonstrate that EvolSTAR is highly accurate and has a much improved call rate. The high throughput and short turn-around time from sample to sequence and analysis results (30 h for 24 samples) makes this kit an efficient large-scale evolutionary biosurveillance tool.
Epidemiological survey of foot diseases in Japan: Results of 30 000 foot checks by dermatologists
Authors: WATANABE Shinichi , HARADA Takashi , HIRUMA Masataro , IOZUMI Ken , KATOH Takuro , MOCHIZUKI Takashi , NAKA Wataru ,   JAPAN FOOT WEEK GROUP
Published: February 2010

AbstractThere has been no epidemiological survey of foot diseases in Japan. In this study we determined the prevalence of foot diseases, especially tinea pedis (TP) and tinea unguium (TU) in Japan. We conducted a randomized survey of outpatients who visited a dermatologist during the third week of May in 1999, 2000 and 2006. The most frequently reported condition was “fungal infection” in 8737 (40.0%) of 21 820 patients in 1999/2000, and 3848 (49.4%) of 7783 patients in 2006. The patients who visited a dermatologist for reasons other than superficial fungal infection but were diagnosed with TP or TU comprised 18.6% of the study population in 2000 and 24.1% in 2006. Of the patients with TP or TU, 63.2% used topical medication only. This survey showed that often patients are not aware of fungal infections and that their treatment is sometimes insufficient. Dermatologists should actively examine and treat patients with TP and TU.
Association of human leukocyte antigen class II alleles with pemphigus vulgaris in a Turkish population
Authors: TUNCA Mustafa , MUSABAK Ugur , SAGKAN Rahşan Ilikci , KOC Erol , AKAR Ahmet 
Published: February 2010

AbstractPemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles. Human leukocyte antigen (HLA) subtypes vary with racial/ethnic backgrounds. The purpose of this study was to determine the association of HLA class II alleles and haplotypes with PV in Turkish patients. Twenty‐five patients with PV and 113 healthy transplant donors were genotyped for HLA class II alleles. HLA DNA typing was performed by the polymerase chain reaction/sequence specific primer method. The frequency of HLA DRB1*04 allele was 68.00% in patients compared to 30.97% in controls (P = 0.0012) and the frequency of HLA DRB1*14 allele was 32.00% in the patient group compared to 8.85% in the control group (P = 0.0054). Also, the frequency of HLA DRB1*04/DQB1*03 and HLA DRB1*14/DQB1*05 haplotypes in PV patients was significantly higher than controls (32.0% vs 6.2%, χ2 = 28.142, P < 0.001; and 16% vs 2.7%, χ2 = 15.143, P = 0.001, respectively). A preventive allele or haplotype for the manifestation of PV has not been identified in this study. Our findings suggest that HLA DRB1*04 and DRB1*14 alleles, and HLA DRB1*04/DQB1*03 and HLA DRB1*14/DQB1*05 haplotypes are genetic markers for general susceptibility to PV in the Turkish population.
Risk factors associated with having psoriatic arthritis in patients with cutaneous psoriasis
Authors: TEY Hong Liang , EE Hock Leong , TAN Andy SL , THENG Thiam Seng , WONG Su Ni , KHOO Shih Wee 
Published: February 2010

AbstractThe aim of this study was to determine if the following characteristics were associated with the presence of psoriatic arthritis in a sample of psoriasis patients: race, family history of psoriasis and psoriatic arthritis, age of onset of psoriasis, smoking, alcohol consumption and the maximum body surface area (BSA) affected by psoriasis. This was a case–control study involving 400 psoriasis patients who attended the Psoriasis and Photo‐medicine clinic in the National Skin Center of Singapore over a 1‐year period. Cases were psoriasis patients with psoriatic arthritis while controls were psoriasis patients without psoriatic arthritis. The diagnosis of psoriatic arthritis was made by rheumatologists and participants completed a self‐administered standardized questionnaire. The maximum BSA involved was determined from the case notes. Psoriatic arthritis was not significantly associated with sex, race, age of onset of psoriasis, a family history of psoriasis, smoking and alcohol consumption but was significantly associated with a family history of psoriatic arthritis (P < 0.001) and the maximum body surface involved (P = 0.05). Using multivariate analysis to control for variables, the presence of psoriatic arthritis was significantly associated with a family history of psoriatic arthritis (odds ratio [OR] = 20.5; 95% confidence interval [CI] = 2.49–169.10) and the maximum BSA involved (OR = 2.52; 95% CI = 1.33–4.75). Indian psoriatic patients were more likely to have psoriatic arthritis compared to the other races. A family history of psoriatic arthritis and a greater maximum body surface involved may be associated with having psoriatic arthritis in this study population of psoriasis patients.