bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Adaptive Approach to Mitigate Background Covariance Limitations in the Ensemble Kalman Filter
Authors: Song Hajoon , Hoteit Ibrahim , Cornuelle Bruce D. , Subramanian Aneesh C. 
Published: February 2010

Abstract
A new approach is proposed to address the background covariance limitations arising from undersampled ensembles and unaccounted model errors in the ensemble Kalman filter (EnKF). The method enhances the representativeness of the EnKF ensemble by augmenting it with new members chosen adaptively to add missing information that prevents the EnKF from fully fitting the data to the ensemble. The vectors to be added are obtained by back projecting the residuals of the observation misfits from the EnKF analysis step onto the state space. The back projection is done using an optimal interpolation (OI) scheme based on an estimated covariance of the subspace missing from the ensemble. In the experiments reported here, the OI uses a preselected stationary background covariance matrix, as in the hybrid EnKF–three-dimensional variational data assimilation (3DVAR) approach, but the resulting correction is included as a new ensemble member instead of being added to all existing ensemble members.
The adaptive approach is tested with the Lorenz-96 model. The hybrid EnKF–3DVAR is used as a benchmark to evaluate the performance of the adaptive approach. Assimilation experiments suggest that the new adaptive scheme significantly improves the EnKF behavior when it suffers from small size ensembles and neglected model errors. It was further found to be competitive with the hybrid EnKF–3DVAR approach, depending on ensemble size and data coverage.
Analysis of chick (Gallus gallus) middle ear columella formation
Authors: Wood Jamie L , Hughes Ami J , Mercer Kathryn J , Chapman Susan C 
Published: February 2010

Abstract

Background
The chick middle ear bone, the columella, provides an accessible model in which to study the tissue and molecular interactions necessary for induction and patterning of the columella, as well as associated multiple aspects of endochondral ossification. These include mesenchymal condensation, chondrogenesis, ossification of the medial footplate and shaft, and joint formation between the persistent cartilage of the extracolumella and ossified columella. Middle and external ear defects are responsible for approximately 10% of congenital hearing defects. Thus, understanding the morphogenesis and the molecular mechanisms of the formation of the middle ear is important to understanding normal and abnormal development of this essential component of the hearing apparatus.

Results
The columella, which arises from proximal ectomesenchyme of the second pharyngeal arch, is induced and patterned in a dynamic multi-step process. From the footplate, which inserts into the inner ear oval window, the shaft spans the pneumatic middle ear cavity, and the extracolumella inserts into the tympanic membrane. Through marker gene and immunolabeling analysis, we have determined the onset of each stage in the columella's development, from condensation to ossification. Significantly, a single condensation with the putative shaft and extracolumella arms already distinguishable is observed shortly before initiation of five separate chondrogenic centers within these structures. Ossification begins later, with periosteum formation in the shaft and, unexpectedly, a separate periosteum in the footplate.

Conclusions
The data presented in this study document the spatiotemporal events leading to morphogenesis of the columella and middle ear structures and provide the first gene expression data for this region. These data identify candidate genes and facilitate future functional studies and elucidation of the molecular mechanisms of columella formation.
An enhancer peptide for membrane-disrupting antimicrobial peptides
Authors: Ueno Satoshi , Kusaka Kohtaro , Tamada Yasushi , Zhang Hong , Minaba Masaomi , Kato Yusuke 
Published: February 2010

Abstract

Background
NP4P is a synthetic peptide derived from a natural, non-antimicrobial peptide fragment (pro-region of nematode cecropin P4) by substitution of all acidic amino acid residues with amides (i.e., Glu → Gln, and Asp → Asn).

Results
In the presence of NP4P, some membrane-disrupting antimicrobial peptides (ASABF-α, polymyxin B, and nisin) killed microbes at lower concentration (e.g., 10 times lower minimum bactericidal concentration for ASABF-α against Staphylococcus aureus), whereas NP4P itself was not bactericidal and did not interfere with bacterial growth at ≤ 300 μg/mL. In contrast, the activities of antimicrobial agents with a distinct mode of action (indolicidin, ampicillin, kanamycin, and enrofloxacin) were unaffected. Although the membrane-disrupting activity of NP4P was slight or undetectable, ASABF-α permeabilized S. aureus membranes with enhanced efficacy in the presence of NP4P.

Conclusions
NP4P selectively enhanced the bactericidal activities of membrane-disrupting antimicrobial peptides by increasing the efficacy of membrane disruption against the cytoplasmic membrane.
Effect of anti-glycosphingolipid monoclonal antibodies in pathogenic fungal growth and differentiation. Characterization of monoclonal antibody MEST-3 directed to Manp α1→3Manp α1→2IPC
Authors: Toledo Marcos S , Tagliari Loriane , Suzuki Erika , Silva Claudinei M , Straus Anita H , Takahashi Helio K 
Published: February 2010

Abstract

Background
Studies carried out during the 1990's demonstrated the presence of fungal glycoinositol phosphorylceramides (GIPCs) with unique structures, some of them showed reactivity with sera of patients with histoplasmosis, paracoccidioidomycosis or aspergillosis. It was also observed that fungal GIPCs were able to inhibit T lymphocyte proliferation "in vitro", and studies regarding the importance of these molecules to fungal survival showed that many species of fungi are vulnerable to inhibitors of sphingolipid biosynthesis.

Results
In this paper, we describe a detailed characterization of an IgG2a monoclonal antibody (mAb), termed MEST-3, directed to the Paracoccidioides brasiliensis glycolipid antigen Pb-2 (Manp α1→3Manp α1→2IPC). mAb MEST-3 also recognizes GIPCs bearing the same structure in other fungi. Studies performed on fungal cultures clearly showed the strong inhibitory activity of MEST-3 on differentiation and colony formation of Paracoccidioides brasiliensis, Histoplasma capsulatum and Sporothrix schenckii. Similar inhibitory results were observed when these fungi where incubated with a different mAb, which recognizes GIPCs bearing terminal residues of β-D-galactofuranose linked to mannose (mAb MEST-1). On the other hand, mAb MEST-2 specifically directed to fungal glucosylceramide (GlcCer) was able to promote only a weak inhibition on fungal differentiation and colony formation.

Conclusions
These results strongly suggest that mAbs directed to specific glycosphingolipids are able to interfere on fungal growth and differentiation. Thus, studies on surface distribution of GIPCs in yeast and mycelium forms of fungi may yield valuable information regarding the relevance of glycosphingolipids in processes of fungal growth, morphological transition and infectivity.
Endothelial dysfunction in obese non-hypertensive children without evidence of sleep disordered breathing
Authors: Bhattacharjee Rakesh , Alotaibi Wadha H , Kheirandish-Gozal Leila , Capdevila Oscar Sans , Gozal David 
Published: February 2010

Abstract

Background
Endothelial dysfunction is a complication of both obesity and obstructive sleep apnea syndrome (OSAS), the latter being highly prevalent among obese children. It is unknown whether obesity causes endothelial dysfunction in children in the absence of OSAS. This study examines endothelial function in obese and non-obese children without OSAS.

Methods
Pre-pubertal non-hypertensive children were recruited. Endothelial function was assessed in a morning fasted state, using a modified hyperemic test involving cuff-induced occlusion of the radial and ulnar arteries. The absence of OSAS was confirmed by overnight polysomnography. Anthropometry was also performed.

Results
55 obese children (mean age 8.6 ± 1.4 years, mean BMI z-score: 2.3 ± 0.3) were compared to 50 non-obese children (mean age 8.0 ± 1.6 years, mean BMI z-score 0.3 ± 0.9). Significant delays to peak capillary reperfusion after occlusion release occurred in obese compared to non-obese children (45.3 ± 21.9 sec vs. 31.5 ± 14.1 sec, p < 0.01), but no differences in the magnitude of hyperemia emerged. Time to peak reperfusion and percentage of body fat were positively correlated (r = 0.365, p < 0.01).

Conclusions
Our findings confirm that endothelial dysfunction occurs early in life in obese children, even in the absence of OSAS. Thus, mechanisms underlying endothelial dysfunction in pediatric obesity are operational in the absence of sleep-disordered breathing.
Characterization of two diesel fuel degrading microbial consortia enriched from a non acclimated, complex source of microorganisms
Authors: Zanaroli Giulio , Di Toro Sara , Todaro Daniela , Varese Giovanna C , Bertolotto Antonio , Fava Fabio 
Published: February 2010

Abstract

Background
The bioremediation of soils impacted by diesel fuels is very often limited by the lack of indigenous microflora with the required broad substrate specificity. In such cases, the soil inoculation with cultures with the desired catabolic capabilities (bioaugmentation) is an essential option. The use of consortia of microorganisms obtained from rich sources of microbes (e.g., sludges, composts, manure) via enrichment (i.e., serial growth transfers) on the polluting hydrocarbons would provide bioremediation enhancements more robust and reproducible than those achieved with specialized pure cultures or tailored combinations (co-cultures) of them, together with none or minor risks of soil loading with unrelated or pathogenic allocthonous microorganisms.

Results
In this work, two microbial consortia, i.e., ENZ-G1 and ENZ-G2, were enriched from ENZYVEBA (a complex commercial source of microorganisms) on Diesel (G1) and HiQ Diesel (G2), respectively, and characterized in terms of microbial composition and hydrocarbon biodegradation capability and specificity.
ENZ-G1 and ENZ-G2 exhibited a comparable and remarkable biodegradation capability and specificity towards n-C10 to n-C24 linear paraffins by removing about 90% of 1 g l-1 of diesel fuel applied after 10 days of aerobic shaken flask batch culture incubation at 30°C. Cultivation dependent and independent approaches evidenced that both consortia consist of bacteria belonging to the genera Chryseobacterium, Acinetobacter, Psudomonas, Stenotrophomonas, Alcaligenes and Gordonia along with the fungus Trametes gibbosa. However, only the fungus was found to grow and remarkably biodegrade G1 and G2 hydrocarbons under the same conditions. The biodegradation activity and specificity and the microbial composition of ENZ-G1 and ENZ-G2 did not significantly change after cryopreservation and storage at -20°C for several months.

Conclusions
ENZ-G1 and ENZ-G2 are very similar highly enriched consortia of bacteria and a fungus capable of extensively degrading a broad range of the hydrocarbons mainly composing diesel fuels. Given their remarkable biodegradation potential, stability and resistance to cryopreservation, both consortia appear very interesting candidates for bioaugmentation operations on Diesel fuel impacted soils and sites.
COU254, a specific 3-carboxamide-coumarin inhibitor of coagulation factor XII, does not protect mice from acute ischemic stroke
Authors: Kraft Peter , Schwarz Tobias , Pochet Lionel , Stoll Guido , Kleinschnitz Christoph 
Published: February 2010

Abstract

Background
Anticoagulation is an important means to prevent from acute ischemic stroke but is associated with a significant risk of severe hemorrhages. Previous studies have shown that blood coagulation factor XII (FXII)-deficient mice are protected from pathological thrombus formation during cerebral ischemia without bearing an increased bleeding tendency. Hence, pharmacological blockade of FXII might be a promising and safe approach to prevent acute ischemic stroke and possibly other thromboembolic disorders but pharmacological inhibitors selective over FXII are still lacking. In the present study we investigated the efficacy of COU254, a novel nonpeptidic 3-carboxamide-coumarin that selectively blocks FXII activity, on stroke development and post stroke functional outcome in mice.

Methods
C57Bl/6 mice were treated with COU254 (40 mg/kg i.p.) or vehicle and subjected to 60 min transient middle cerebral artery occlusion (tMCAO) using the intraluminal filament method. After 24 h infarct volumes were determined from 2,3,5-Triphenyltetrazoliumchloride(TTC)-stained brain sections and functional scores were assessed. Hematoxylin and eosin (H&E) staining was used to estimate the extent of neuronal cell damage. Thrombus formation within the infarcted brain areas was analyzed by immunoblot.

Results
Infarct volumes and functional outcomes on day 1 after tMCAO did not significantly differ between COU254 pre-treated mice or untreated controls (p > 0.05). Histology revealed extensive ischemic neuronal damage regularly including the cortex and the basal ganglia in both groups. COU254 treatment did not prevent intracerebral fibrin(ogen) formation.

Conclusions
COU254 at the given concentration of 40 mg/kg failed to demonstrate efficacy in acute ischemic stroke in this preliminary study. Further preclinical evaluation of 3-carboxamide-coumarins is needed before the antithrombotic potential of this novel class of FXII inhibitors can be finally judged.
Enhanced late-outgrowth circulating endothelial progenitor cell levels in rheumatoid arthritis and correlation with disease activity
Authors: Jodon de Villeroché Vanina , Avouac Jérome , Ponceau Aurélie , Ruiz Barbara , Kahan André , Boileau Catherine , Uzan Georges , Allanore Yannick 
Published: February 2010

AbstractIntroductionAngiogenesis and vasculogenesis are critical in rheumatoid arthritis (RA) as they could be a key issue for chronic synovitis. Contradictory results have been published regarding circulating endothelial progenitor cells (EPCs) in RA. We herein investigated late outgrowth EPC sub-population using recent recommendations in patients with RA and healthy controls.MethodsEPCs, defined as Lin-/7AAD-/CD34+/CD133+/VEGFR-2+ cells, were quantified by flow cytometry in peripheral blood mononuclear cells (PBMCs) from 59 RA patients (mean age: 54 ± 15 years, disease duration: 16 ± 11 years) and 36 controls (mean age: 53 ± 19 years) free of cardiovascular events and of cardiovascular risk factors. Concomitantly, late outgrowth endothelial cell colonies derived from culture of PBMCs were analyzed by colony-forming units (CFUs).ResultsRA patients displayed higher circulating EPC counts than controls (median 112 [27 to 588] vs. 60 [5 to 275]) per million Lin- mononuclear cells;P= 0.0007). The number of circulating EPCs positively correlated with disease activity reflected by DAS-28 score (r = 0.43;P= 0.0028) and lower counts were found in RA patients fulfilling remission criteria (P= 0.0069). Furthermore, late outgrowth CFU number was increased in RA patients compared to controls. In RA, there was no association between the number of EPCs and serum markers of inflammation or endothelial injury or synovitis.ConclusionsOur data, based on a well characterized definition of late outgrowth EPCs, demonstrate enhanced levels in RA and relationship with disease activity. This supports the contribution of vasculogenesis in the inflammatory articular process that occurs in RA by mobilization of EPCs.
Preparation of Charge-transfer Host Complex Composed of [9,9′-Biphenanthryl]-10,10′-diol Having a Large and Widely π-Conjugated Phenanthrene Ring
Authors: Ukegawa Tatsuya , Kinuta Takafumi , Sato Tomohiro , Tajima Nobuo , Kuroda Reiko , Matsubara Yoshio , Imai Yoshitane 
Published: February 2010

Abstract
A colored supramolecular charge-transfer (CT) host complex composed of racemic rac-[9,9′-biphenanthryl]-10,10′-diol, having a large and widely π-conjugated phenanthrene ring, as an electron donor and 2,5-dimethyl-1,4-benzoquinone as an electron acceptor has been developed. The molecular recognition properties (guest inclusion behavior and color) of the CT complex can be tuned by using electron donor molecules with different steric bulkiness and electron-donating properties.
Photoabsorption Study of Pigments in Mosses: Scopelophila ligulata Has an Abnormally High Formation Rate of Pheophytin
Authors: Nakajima Hiromitsu , Itoh Kiminori , Otake Hideaki , Fujimoto Kenjiro 
Published: February 2010

Abstract
To understand the characteristics of a Fe-accumulating moss Scopelophila ligulata, we compared the photoabsorption spectra of pigments from this and several other mosses and found that some of the absorption bands observed only for S. ligulata can be assigned to pheophytin a. The conversion rate from chlorophyll to pheophytin in S. ligulata was calculated to be 25%. This striking characteristic of S. ligulata could be explained by considering its habitat conditions.
Effect of Coating by Perfluorosulfonated Ionomer Film on Electrochemical Behaviors of Pt(111) Electrode in Acidic Solutions
Authors: Sonsudin Faridah , Masuda Takuya , Ikeda Katsuyoshi , Naohara Hideo , Uosaki Kohei 
Published: February 2010

Abstract
Electrochemical behaviors of bare and perfluorosulfonated ionomer (PFSI) film-coated Pt(111) electrodes in perchloric and sulfuric acid solutions were investigated. While current peaks corresponding to specific adsorption and desorption of anions were clearly observed at the bare electrode, no such peaks were observed at the PFSI-coated electrode, showing that anions do not reach the electrode surface because of the cation-selective nature and/or adsorption of PFSI film. Although no structural change was observed by repetitive potential cycling as far as positive potential limit was more negative than that of oxide formation, significant structural change was noticed during potential cycling if the anodic potential limit was made more positive than oxide formation potential.
Associations Between ADH Gene Variants and Alcohol Phenotypes in Dutch Adults
Authors: van Beek Jenny H. D. A. , Willemsen Gonneke , de Moor Marleen H. M. , Hottenga Jouke Jan , Boomsma Dorret I. 
Published: February 2010

AbstractRecently, Macgregor et al. (2009) demonstrated significant associations of ADH polymorphisms with reactions to alcohol and alcohol consumption measures in an Australian sample. The aim of the present study was to replicate these findings in a Dutch sample. Survey data on alcohol phenotypes came from 1,754 unrelated individuals registered with the Netherlands Twin Register. SNPs in the ADH gene cluster located on chromosome 4q (n= 491) were subdivided in seven gene sets: ADH5, ADH4, ADH6, ADH1A, ADH1B, ADH1C and ADH7. Within these sets associations of SNPs with alcohol consumption measures, age at onset variables, reactions to alcohol and problem drinking liability were examined. Of the original 38 SNPs studied by Macgregor et al. (2009), six SNPs were not available in our dataset, because one of them had a minor allele frequency < .01 (rs1229984) and five could not be imputed. The remaining SNP associations with alcohol phenotypes as identified by Macgregor et al. (2009) were not replicated in the Dutch sample, after correcting for multiple genotype and phenotype testing. Significant associations were found however, for reactions to alcohol with a SNP in ADH5 (rs6827292,p= .001) and a SNP just upstream of ADH5 (rs6819724,p= .0007) that is in strong LD with rs6827292. Furthermore, an association between age at onset of regular alcohol use and a SNP just upstream of ADH7 (rs2654849,p= .003) was observed. No significant associations were found for alcohol consumption and problem drinking liability. Although these findings do not replicate the earlier findings at the SNP level, the results confirm the role of the ADH gene cluster in alcohol phenotypes.
Gemini: A UK Twin Birth Cohort With a Focus on Early Childhood Weight Trajectories, Appetite and the Family Environment
Authors: van Jaarsveld Cornelia H. M. , Johnson Laura , Llewellyn Clare , Wardle Jane 
Published: February 2010

AbstractGemini is a cohort study of young twins in the United Kingdom designed to assess genetic and environmental influences on early childhood weight trajectories with a focus on infant appetite and the family environment. A total of 2402 families with twins born in England and Wales between March and December 2007 agreed to participate and returned completed baseline questionnaires. The sample includes 1586 same-sex and 816 opposite-sex twins. The study is currently funded for 5 years of follow-up, but is planned to continue into early adolescence and beyond, pending funding. With current funding of the study, families will be followed up when twins are: 8 months old (baseline), and then at 15, 20, 24, 36 and 48 months of age. Gemini is in its early stages, with baseline and first follow-up data collection completed. This is the first twin cohort to focus on childhood weight gain with detailed and repeated measures of children's appetite, food preferences, activity behavior and parental feeding styles, alongside detailed and repeated collection of anthropometrics. This article reviews the rationale for the Gemini study, its representativeness and the main measures.
Physical Features Observation: Is it Repeatable in Zygosity Determination of Chinese Adult Twins?
Authors: Gao Wenjing , Li Liming , Cao Weihua , Zhan Siyan , Zhao Yunlong , Wang Hui , Hu Yonghua 
Published: February 2010

AbstractThis study reports on the inter- and intrarater reliability of physical features observation. Study subjects were 176 Chinese adult persons, consisting of 89 males and 87 females. Three trained research assistants responded simultaneously and respectively to 12 items regarding the subject's physical features including ‘hair’, ‘Mongoloid folds’, left and right ‘ear lobes’, ‘earwax’, ‘nostril shape’, ‘tongue rolling’, left and right ‘hitchhiker's thumb’, ‘mid-digital hair’ and left and right ‘simian crease’ at the moment of interview. And 14 days later, these subjects received the same observation once again. The results showed that the inter- and intra-observer agreements of ‘hair’, ‘earwax’, ‘tongue rolling’, ‘mid-digital hair’ and ‘simian crease’ were almost perfect with most kappa (κ) coefficients ≥ .80, while ‘Mongoloid fold’ and ‘nostril shape’ showed poor inter-observer agreement and ‘nostril shape’ showed poor intra-observer agreement (κ < .40). Two other physical features, ‘hitchhiker's thumb’ and ‘ear lobes’ showed moderate inter-observer agreement and three features, ‘hitchhiker's thumb’, ‘ear lobes’ and ‘Mongoloid fold’, showed moderate intra-observer agreement (.40≤ κ <.80). In conclusion, this study suggests that as far as reliability is concerned, the five features which were ‘hair’, ‘earwax’, ‘tongue rolling’, ‘mid-digital hair’ and ‘simian crease’ could be considered in zygosity determination of Chinese adult twins, while the two features, ‘Mongoloid fold’ and ‘nostril shape’, should be abandoned.