bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porcine dentin sialoprotein glycosylation and glycosaminoglycan attachments
Authors: Yamakoshi Yasuo , Nagano Takatoshi , Hu Jan CC , Yamakoshi Fumiko , Simmer James P 
Published: February 2011

Abstract

Background
Dentin sialophosphoprotein (Dspp) is a multidomain, secreted protein that is critical for the formation of tooth dentin. Mutations in DSPP cause inherited dentin defects categorized as dentin dysplasia type II and dentinogenesis imperfecta type II and type III. Dentin sialoprotein (Dsp), the N-terminal domain of dentin sialophosphoprotein (Dspp), is a highly glycosylated proteoglycan, but little is known about the number, character, and attachment sites of its carbohydrate moieties.

Results
To identify its carbohydrate attachment sites we isolated Dsp from developing porcine molars and digested it with endoproteinase Glu-C or pronase, fractionated the digestion products, identified fractions containing glycosylated peptides using a phenol sulfuric acid assay, and characterized the glycopeptides by N-terminal sequencing, amino acid analyses, or LC/MSMS. To determine the average number of sialic acid attachments per N-glycosylation, we digested Dsp with glycopeptidase A, labeled the released N-glycosylations with 2-aminobenzoic acid, and quantified the moles of released glycosylations by comparison to labeled standards of known concentration. Sialic acid was released by sialidase digestion and quantified by measuring β-NADH reduction of pyruvic acid, which was generated stoichiometrically from sialic acid by aldolase. To determine its forms, sialic acid released by sialidase digestion was labeled with 1,2-diamino-4,5-methyleneoxybenzene (DMB) and compared to a DMB-labeled sialic acid reference panel by RP-HPLC. To determine the composition of Dsp glycosaminoglycan (GAG) attachments, we digested Dsp with chondroitinase ABC and compared the chromotagraphic profiles of the released disaccharides to commercial standards. N-glycosylations were identified at Asn37, Asn77, Asn136, Asn155, Asn161, and Asn176. Dsp averages one sialic acid per N-glycosylation, which is always in the form of N-acetylneuraminic acid. O-glycosylations were tentatively assigned at Thr200, Thr216 and Thr316. Porcine Dsp GAG attachments were found at Ser238 and Ser250 and were comprised of chondroitin 6-sulfate and chondroitin 4-sulfate in a ratio of 7 to 3, respectively.

Conclusions
The distribution of porcine Dsp posttranslational modifications indicate that porcine Dsp has an N-terminal domain with at least six N-glycosylations and a C-terminal domain with two GAG attachments and at least two O-glycosylations.
Hierarchical graphs for rule-based modeling of biochemical systems
Authors: Lemons Nathan W , Hu Bin , Hlavacek William S 
Published: February 2011

AbstractBackgroundIn rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system.ResultsFor purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm.ConclusionsHierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language (BNGL). Thus, the proposed use of hierarchical graphs should promote clarity and better understanding of rule-based models.
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach
Authors: Zhang Wangshu , Sun Fengzhu , Jiang Rui 
Published: February 2011

Abstract

Background
The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated great success in prioritizing candidate genes for human diseases. However, most of these methods rely on a single protein-protein interaction (PPI) network to calculate similarities between genes, and thus greatly restrict the scope of application of such methods. Meanwhile, independently constructed and maintained PPI networks are usually quite diverse in coverage and quality, making the selection of a suitable PPI network inevitable but difficult.

Methods
We adopt a linear model to explain similarities between disease phenotypes using gene proximities that are quantified by diffusion kernels of one or more PPI networks. We solve this model via a Bayesian approach, and we derive an analytic form for Bayes factor that naturally measures the strength of association between a query disease and a candidate gene and thus can be used as a score to prioritize candidate genes. This method is intrinsically capable of integrating multiple PPI networks.

Results
We show that gene proximities calculated from PPI networks imply phenotype similarities. We demonstrate the effectiveness of the Bayesian regression approach on five PPI networks via large scale leave-one-out cross-validation experiments and summarize the results in terms of the mean rank ratio of known disease genes and the area under the receiver operating characteristic curve (AUC). We further show the capability of our approach in integrating multiple PPI networks.

Conclusions
The Bayesian regression approach can achieve much higher performance than the existing CIPHER approach and the ordinary linear regression method. The integration of multiple PPI networks can greatly improve the scope of application of the proposed method in the inference of disease genes.
Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties
Authors: Huang Hui-Lin , Lin I-Che , Liou Yi-Fan , Tsai Chia-Ta , Hsu Kai-Ti , Huang Wen-Lin , Ho Shinn-Jang , Ho Shinn-Ying 
Published: February 2011

Abstract

Background
Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors.

Results
This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing an efficient genetic algorithm based optimization method IBCGA to select an informative feature set of size m to represent sequences, and 3) analyzing the selected features to identify related physicochemical properties which may affect the binding mechanism of DNA-binding domains/proteins. The proposed Auto-IDPCPs identified m=22 features of properties belonging to five clusters for predicting DNA-binding domains with a five-fold cross-validation accuracy of 87.12%, which is promising compared with the accuracy of 86.62% of the existing method PSSM-400. For predicting DNA-binding sequences, the accuracy of 75.50% was obtained using m=28 features, where PSSM-400 has an accuracy of 74.22%. Auto-IDPCPs and PSSM-400 have accuracies of 80.73% and 82.81%, respectively, applied to an independent test data set of DNA-binding domains. Some typical physicochemical properties discovered are hydrophobicity, secondary structure, charge, solvent accessibility, polarity, flexibility, normalized Van Der Waals volume, pK (pK-C, pK-N, pK-COOH and pK-a(RCOOH)), etc.

Conclusions
The proposed approach Auto-IDPCPs would help designers to investigate informative physicochemical and biochemical properties by considering both prediction accuracy and analysis of binding mechanism simultaneously. The approach Auto-IDPCPs can be also applicable to predict and analyze other protein functions from sequences.
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads
Authors: Duitama Jorge , Kennedy Justin , Dinakar Sanjiv , Hernández Yözen , Wu Yufeng , Măndoiu Ion I 
Published: February 2011

Abstract

Background
Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-genome SNP genotyping.

Results
In this paper we introduce a new multi-locus statistical model and computationally efficient genotype calling algorithms that integrate shotgun sequencing data with linkage disequilibrium (LD) information extracted from reference population panels such as Hapmap or the 1000 genomes project. Experiments on publicly available 454, Illumina, and ABI SOLiD sequencing datasets suggest that integration of LD information results in genotype calling accuracy comparable to that of microarray platforms from sequencing data of low-coverage. A software package implementing our algorithm, released under the GNU General Public License, is available at http://dna.engr.uconn.edu/software/GeneSeq/.

Conclusions
Integration of LD information leads to significant improvements in genotype calling accuracy compared to prior LD-oblivious methods, rendering low-coverage sequencing as a viable alternative to microarrays for conducting large-scale genome-wide association studies.
Incorporating Ab Initio energy into threading approaches for protein structure prediction
Authors: Shao Mingfu , Wang Sheng , Wang Chao , Yuan Xiongying , Li Shuai Cheng , Zheng Weimou , Bu Dongbo 
Published: February 2011

Abstract

Background
Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates.

Results
In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an Ab Initio energy function to evaluate the “partial” decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function.
Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison.

Conclusions
Incorporating Ab Initio energy functions into threading can greatly improve alignment accuracy.
Musculoskeletal comorbidities in cardiovascular disease, diabetes and respiratory disease: the impact on activity limitations; a representative population-based study
Authors: Slater Morgan , Perruccio Anthony V , Badley Elizabeth M 
Published: February 2011

Abstract

Background
The purpose of this study was to quantify the contribution of comorbidity to activity limitations in populations with chronic cardiovascular disease, diabetes or respiratory disease (index conditions), with emphasis on musculoskeletal comorbidity (arthritis or back problems).

Methods
Analysis of the 2005 Canadian Community Health Survey 3.1 (age 20+ years, n = 115,915). Prevalence ratios for activity limitations in people with the index conditions and co-occurring musculoskeletal disease, adjusted for age, gender, and socioeconomic factors, were used to estimate population associated fractions (PAF).

Results
Comorbid arthritis and back problems significantly increased the risk of activity limitations across all index conditions with prevalence ratios of 1.60 and 1.46 for cardiovascular disease, 1.51 and 1.36 for diabetes, and 1.38 and 1.44 for respiratory disease for arthritis and back problems respectively. Arthritis and back problems accounted for at least 13% and 9% of activity limitations in the index populations.

Conclusions
While chronic musculoskeletal conditions are not always considered priorities in chronic disease prevention, they account for a substantial proportion of activity restrictions seen in people with cardiovascular disease, diabetes and respiratory disease, with implications for prevention and control strategies.
Factors affecting commencement and cessation of betel quid chewing behaviour in Malaysian adults
Authors: Ghani Wan MN , Razak Ishak A , Yang Yi-Hsin , Talib Norain A , Ikeda Noriaki , Axell Tony , Gupta Prakash C , Handa Yujiro , Abdullah Norlida , Zain Rosnah B 
Published: February 2011

Abstract

Background
Betel quid chewing is a common habit widely practiced in Southern Asian populations. However, variations are seen in the content of a betel quid across the different countries. Factors associated with commencement and cessation of this habit has been numerously studied. Unfortunately, data on Malaysian population is non-existent. This study aims to determine the factors associated with the inception and also cessation of betel quid chewing behaviour among Malaysian adults.

Method
This study is part of a nationwide survey on oral mucosal lesions carried out among 11,697 adults in all fourteen states in Malaysia. The questionnaire included sociodemographic information and details on betel quid chewing habit such as duration, type and frequency. The Kaplan-Meier estimates were calculated and plotted to compare the rates for the commencement and cessation of betel quid chewing behaviour. Cox proportional hazard regression models were used to calculate the hazard rate ratios for factors related to commencement or cessation of this habit.

Results
Of the total subjects, 8.2% were found to be betel quid chewers. This habit was more prevalent among females and, in terms of ethnicity, among the Indians and the Indigenous people of Sabah and Sarawak. Cessation of this habit was more commonly seen among males and the Chinese. Females were found to be significantly more likely to start (p < 0.0001) and less likely to stop the quid chewing habit. Females, those over 40 years old, Indians and a history of smoking was found to significantly increase the likelihood of developing a quid chewing habit (p < 0.0001). However, those who had stopped smoking were found to be significantly more likely to promote stopping the habit (p = 0.0064). Cessation was also more likely to be seen among those who chewed less than 5 quids per day (p < 0.05) and less likely to be seen among those who included areca nut and tobacco in their quid (p < 0.0001).

Conclusion
Factors that influence the development and cessation of this behaviour are gender, age, ethnicity, and also history of smoking habit while frequency and type of quid chewed are important factors for cessation of this habit.
Ion beam-induced shaping of Ni nanoparticles embedded in a silica matrix: from spherical to prolate shape
Authors: Kumar Hardeep , Ghosh Santanu , Avasthi Devesh Kumar , Kabiraj Debdulal , Mücklich Arndt , Zhou Shengqiang , Schmidt Heidemarie , Stoquert Jean-Paul 
Published: February 2011

AbstractPresent work reports the elongation of spherical Ni nanoparticles (NPs) parallel to each other, due to bombardment with 120 MeV Au+9 ions at a fluence of 5 × 1013 ions/cm2. The Ni NPs embedded in silica matrix have been prepared by atom beam sputtering technique and subsequent annealing. The elongation of Ni NPs due to interaction with Au+9 ions as investigated by cross-sectional transmission electron microscopy (TEM) shows a strong dependence on initial Ni particle size and is explained on the basis of thermal spike model. Irradiation induces a change from single crystalline nature of spherical particles to polycrystalline nature of elongated particles. Magnetization measurements indicate that changes in coercivity (Hc) and remanence ratio (Mr/Ms) are stronger in the ion beam direction due to the preferential easy axis of elongated particles in the beam direction.
New Si-based multilayers for solar cell applications
Authors: Nalini R Pratibha , Dufour Christian , Cardin Julien , Gourbilleau Fabrice 
Published: February 2011

AbstractIn this article, we have fabricated and studied a new multilayer structure Si-SiO2/SiN
x
by reactive magnetron sputtering. The comparison between SiO2 and SiN
x
host matrices in the optical properties of the multilayers is detailed. Structural analysis was made on the multilayer structures using Fourier transform infrared spectroscopy. The effect of specific annealing treatments on the optical properties is studied and we report a higher visible luminescence with a control over the thermal budget when SiO2 is replaced by the SiN
x
matrix. The latter seems to be a potential candidate to replace the most sought SiO2 host matrix.
Interactions between Sex Hormones and a 1,2-Di-O-myristoyl-sn-glycero-3-phosphocholine Molecular Layer: Characteristics of the Liposome, Surface Area versus Surface Pressure of the Monolayer, and Microscopic Observation
Authors: Nakata Satoshi , Ikeguchi Ayaka , Shiota Takaya , Komori Ryouhei , Kumazawa Noriyuki , Tsutsumi Moe , Denda Mitsuhiro 
Published: February 2011

Abstract
The interactions between sex hormones (estradiol and testosterone) and a 1,2-di-O-myristoyl-sn-glycero-3-phosphocholine (DMPC) molecular layer were investigated by observing the liposome and the surface area (A) vs. surface pressure (π) of the DMPC monolayer at an air–water interface. The shape and size of the liposome changed with the addition of estradiol and testosterone. The π–A isotherm, the time variation of the surface pressure, and the microscopic observation of monolayer were examined to clarify the different effects of the steroid hormones. These experimental results are discussed in relation to the formation of a rigid membrane due to hydrogen bonding between estradiol and DMPC.
A Molecular Dynamic Simulation of Crosslinking of Bisphenol and Triazine by United Atom Model: A Polycyanurate Model
Authors: Ikeno Taketo , Tsubuku Makoto , Katagiri Masayuki , Tsujimoto Tomoo 
Published: February 2011

Abstract
Polycyanurate networks were densely built by crosslinking of bisphenols and triazine. A molecular dynamics study of the networks from bisphenol A, bisphenol E, and fluorene bisphenol qualitatively reproduced the glass-transition temperatures in correct orders.
Szemlélet- és gyakorlatváltozás a rectalis digitális vizsgálat indikációjában és kivitelezésben appendicitis acuta gyanúja esetén gyermekkorban
Authors: Kutasy Balázs , Mohay Gabriella , Pintér András 
Published: February 2011

Absztrakt
A laboratóriumi és képalkotó diagnosztika fejlődésével a nem kielégítő hatékonyságú, kellemetlen és fájdalmas rectalis digitális vizsgálat heveny vakbélgyulladás esetén nem szükségszerűen a fizikális vizsgálat része. Ugyanakkor egyes kérdéses esetekben hasznos. Ilyenkor azonban a megváltozott jogi és társadalmi környezet miatt a vizsgálat altatásban történő végzése mérlegelendő.
Posztkondicionálás kísérletes vizsgálata vékonybél ischaemiás-reperfusiós modelljében
Authors: Rosero Olivér , Ónody Péter , Stangl Rita , Hegedűs Viktor , Lotz Gábor , Blázovics Anna , Kupcsulik Péter , Szijártó Attila 
Published: February 2011

AbsztraktBevezetés:A vékonybél ischaemiás-reperfusiós károsodása – mely az arteria mesenterica superior occlusiója vagy keringési redistributio során jelentkezik leggyakrabban – jelentős mortalitású kórkép. Kísérletünk során a posztkondicionálás felmerülő protektív hatását vizsgáltuk patkányvékonybél ischaemiás-reperfusiós modelljében.Módszer:Hím Wistar-patkányokon az arteria mesenterica superior 60 perces kirekesztését végeztük. Az állatokat négy – áloperált, kontroll- és két posztkondicionált csoportra osztottuk. A posztkondicionált csoportokban a kirekesztést követően háromszor 1 perces, illetve 10 másodperces reperfusiós-reocclusiós ciklusok ismétlése után került sor 60 perc reperfusióra. A vékonybél microcirculatióját laser Doppler-flowmeterrel detektáltuk. A reperfusio első órájának végén vér- és szöveti mintavétel történt. Szérum-necroenzim- és IL-6-szinteket, fénymikroszkópos szöveti képet, mesenterialis vénás vérgázértékeket és nyálkahártya-antioxidáns-statust vizsgáltunk.Eredmények:A microcirculatiót jellemző paraméterek mindkét posztkondicionált csoportban szignifikánsan javultak. A gyulladásos válaszjelenségek és a szövetkárosodás mértéke szignifikáns módon csökkent, mely a necroenzimszint-csökkenéssel is korrelált. Megfigyelhető volt továbbá az antioxidáns-statusra gyakorolt kedvező hatás és a pH késleltetett normalizálódása is.Következtetés:A posztkondicionálás alkalmas sebésztechnikai módszer lehet a vékonybél túlélési esélyének javítására arteria mesenterica superior occlusiója során kialakuló ischaemiás-reperfusiós károsodás esetén.