bluuebunny/crossref_metadata_2025_split huggingface dataset:
VarDetect: a nucleotide sequence variation exploratory tool
Authors: Ngamphiw Chumpol , Kulawonganunchai Supasak , Assawamakin Anunchai , Jenwitheesuk Ekachai , Tongsima Sissades 
Published: December 2008

Abstract

Background
Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs associated with predisposing genes in complex diseases. Accurate detection of SNPs requires software that can correctly interpret chromatogram signals to nucleotides.

Results
We present VarDetect, a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces. Accurate SNP base-calling is achieved using pre-calculated peak content ratios, and is enhanced by rules which account for common sequence reading artifacts. The proposed software tool is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) using fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 two-pooled DNA samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency.

Availability
VarDetect is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at http://www.biotec.or.th/GI/tools/vardetect.
Imputation of missing genotypes: an empirical evaluation of IMPUTE
Authors: Zhao Zhenming , Timofeev Nadia , Hartley Stephen W , Chui David HK , Fucharoen Supan , Perls Thomas T , Steinberg Martin H , Baldwin Clinton T , Sebastiani Paola 
Published: December 2008

Abstract

Background
Imputation of missing genotypes is becoming a very popular solution for synchronizing genotype data collected with different microarray platforms but the effect of ethnic background, subject ascertainment, and amount of missing data on the accuracy of imputation are not well understood.

Results
We evaluated the accuracy of the program IMPUTE to generate the genotype data of partially or fully untyped single nucleotide polymorphisms (SNPs). The program uses a model-based approach to imputation that reconstructs the genotype distribution given a set of referent haplotypes and the observed data, and uses this distribution to compute the marginal probability of each missing genotype for each individual subject that is used to impute the missing data. We assembled genome-wide data from five different studies and three different ethnic groups comprising Caucasians, African Americans and Asians. We randomly removed genotype data and then compared the observed genotypes with those generated by IMPUTE. Our analysis shows 97% median accuracy in Caucasian subjects when less than 10% of the SNPs are untyped and missing genotypes are accepted regardless of their posterior probability. The median accuracy increases to 99% when we require 0.95 minimum posterior probability for an imputed genotype to be acceptable. The accuracy decreases to 86% or 94% when subjects are African Americans or Asians. We propose a strategy to improve the accuracy by leveraging the level of admixture in African Americans.

Conclusion
Our analysis suggests that IMPUTE is very accurate in samples of Caucasians origin, it is slightly less accurate in samples of Asians background, but substantially less accurate in samples of admixed background such as African Americans. Sample size and ascertainment do not seem to affect the accuracy of imputation.
Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms
Authors: Watkins WS , Thara R , Mowry BJ , Zhang Y , Witherspoon DJ , Tolpinrud W , Bamshad MJ , Tirupati S , Padmavati R , Smith H , Nancarrow D , Filippich C , Jorde LB 
Published: December 2008

AbstractBackgroundMajor population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.ResultsWe report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST= 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST= 0.96%, Andhra Pradesh RST= 0.77%) exceeds the estimate of variation between these geographically separated groups (RST= 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.ConclusionGenetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.
Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism
Authors: Hernández Martín A , Mohn William W , Martínez Eliana , Rost Enrique , Alvarez Adrián F , Alvarez Héctor M 
Published: December 2008

Abstract

Background
Members of the genus Rhodococcus are frequently found in soil and other natural environments and are highly resistant to stresses common in those environments. The accumulation of storage compounds permits cells to survive and metabolically adapt during fluctuating environmental conditions. The purpose of this study was to perform a genome-wide bioinformatic analysis of key genes encoding metabolism of diverse storage compounds by Rhodococcus jostii RHA1 and to examine its ability to synthesize and accumulate triacylglycerols (TAG), wax esters, polyhydroxyalkanoates (PHA), glycogen and polyphosphate (PolyP).

Results
We identified in the RHA1 genome: 14 genes encoding putative wax ester synthase/acyl-CoA:diacylglycerol acyltransferase enzymes (WS/DGATs) likely involved in TAG and wax esters biosynthesis; a total of 54 genes coding for putative lipase/esterase enzymes possibly involved in TAG and wax ester degradation; 3 sets of genes encoding PHA synthases and PHA depolymerases; 6 genes encoding key enzymes for glycogen metabolism, one gene coding for a putative polyphosphate kinase and 3 putative exopolyphosphatase genes. Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification. RHA1 cells grown under N-limiting conditions, accumulated TAG as the main storage compounds plus wax esters, PHA (with 3-hydroxybutyrate and 3-hydroxyvalerate monomers), glycogen and PolyP. Rhodococcus members were previously known to accumulate TAG, wax esters, PHAs and polyP, but this is the first report of glycogen accumulation in this genus.

Conclusion
RHA1 possess key genes to accumulate diverse storage compounds. Under nitrogen-limiting conditions lipids are the principal storage compounds. An extensive capacity to synthesize and metabolize storage compounds appears to contribute versatility to RHA1 in its responses to environmental stresses.
The PPARGC1AGly482Ser polymorphism is associated with left ventricular diastolic dysfunction in men
Authors: Ingelsson Erik , Bennet Louise , Ridderstråle Martin , Söderström Marianne , Råstam Lennart , Lindblad Ulf 
Published: December 2008

Abstract

Background
The Gly482Ser polymorphism in peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PPARGC1A) has been demonstrated to be associated with diabetes, obesity and hypertension, all of which are important risk factors for left ventricular diastolic dysfunction.

Methods
The PPARGC1A Gly482Ser polymorphism was genotyped in a community-based cohort of 499 men and 533 women, who also underwent an echocardiographic examination to determine their left ventricular diastolic function. The association between the polymorphism and the presence of diastolic dysfunction was evaluated using logistic regression models.

Results
The Ser allele of the PPARGC1A Gly482Ser polymorphism was significantly associated with a lower risk of diastolic dysfunction in men, but not in women. In a model adjusting for potential confounders (age, body mass index, leisure time physical activity, hypertension and diabetes) the results were still significant and substantial (odds ratio 0.13, 95% confidence interval 0.03–0.54, p for trend = 0.004). The results were consistent in a series of models, and they imply a multiplicative, protective effect of the Ser allele, with lower risk of diastolic dysfunction for each copy of the allele.

Conclusion
The Ser allele of the PPARGC1A Gly482Ser polymorphism was associated with decreased risk of diastolic left ventricular dysfunction in men, but not in women, in our large community-based sample. It was associated with a substantially decreased risk, even after adjustment for potential confounders. The clinical importance of the findings has to be established in further studies.
Knottin cyclization: impact on structure and dynamics
Authors: Heitz Annie , Avrutina Olga , Le-Nguyen Dung , Diederichsen Ulf , Hernandez Jean-François , Gracy Jérôme , Kolmar Harald , Chiche Laurent 
Published: December 2008

Abstract

Background
Present in various species, the knottins (also referred to as inhibitor cystine knots) constitute a group of extremely stable miniproteins with a plethora of biological activities. Owing to their small size and their high stability, knottins are considered as excellent leads or scaffolds in drug design. Two knottin families contain macrocyclic compounds, namely the cyclotides and the squash inhibitors. The cyclotide family nearly exclusively contains head-to-tail cyclized members. On the other hand, the squash family predominantly contains linear members. Head-to-tail cyclization is intuitively expected to improve bioactivities by increasing stability and lowering flexibility as well as sensitivity to proteolytic attack.

Results
In this paper, we report data on solution structure, thermal stability, and flexibility as inferred from NMR experiments and molecular dynamics simulations of a linear squash inhibitor EETI-II, a circular squash inhibitor MCoTI-II, and a linear analog lin-MCoTI. Strikingly, the head-to-tail linker in cyclic MCoTI-II is by far the most flexible region of all three compounds. Moreover, we show that cyclic and linear squash inhibitors do not display large differences in structure or flexibility in standard conditions, raising the question as to why few squash inhibitors have evolved into cyclic compounds. The simulations revealed however that the cyclization increases resistance to high temperatures by limiting structure unfolding.

Conclusion
In this work, we show that, in contrast to what could have been intuitively expected, cyclization of squash inhibitors does not provide clear stability or flexibility modification. Overall, our results suggest that, for squash inhibitors in standard conditions, the circularization impact might come from incorporation of an additional loop sequence, that can contribute to the miniprotein specificity and affinity, rather than from an increase in conformational rigidity or protein stability. Unfolding simulations showed however that cyclization is a stabilizing factor in strongly denaturing conditions. This information should be useful if one wants to use the squash inhibitor scaffold in drug design.
Lipocalin 2 promotes lung metastasis of murine breast cancer cells
Authors: Shi Han , Gu Yuchao , Yang Jing , Xu Liang , Mi Wenyi , Yu Wengong 
Published: December 2008

AbstractBackgroundLipocalin 2, an iron binding protein, is abnormally expressed in some malignant human cancers and may play an important role in tumor metastasis. However, the roles of lipocalin 2 in breast cancer formation and metastasis have not been clearly shown. This study aimed to investigate the roles of lipocalin 2 in breast tumor metastasis.MethodsLipocalin 2 was overexpressed in the metastatic 4T1 murine mammary cancer cells. The effects of lipocalin 2 overexpression on the malignancy of breast cancer cells were examined using cell proliferation assay, migration assay, invasion assay, and soft agar assayin vitro. Tumor formation and metastasis abilities were examined using a well established mouse mammary tumor modelin vivo.ResultsLipocalin 2 overexpression significantly enhanced the migration and invasion abilities of 4T1 cellsin vitro, and lung metastasisin vivo. But overexpression of lipocalin 2 in 4T1 cells didn't affect cell proliferation and anchorage-independent growthin vitro, and primary tumor weightin vivo. Further studies demonstrated that the inhibition of the PI3K/Akt pathway could be a causative mechanism for the promotion of breast cancer migration/invasion induced by lipocalin 2 overexpression.ConclusionThese results clarified that lipocalin 2 could promote lung metastasis of 4T1 cells through the inhibition of the PI3K/Akt pathway, suggesting that lipocalin 2 was a potential target for therapy of breast cancer.
Preparation and Characterization of Spherical and Balloon-Like Calcium Phosphate Particles
Authors: Kandori Kazuhiko , Tada Kiri , Fukusumi Masao , Morisada Yoshiaki 
Published: December 2008

Abstract
Calcium phosphate particles were prepared by aging a solution of CaCl2 and sodium triphosphate (sodium tripolyphosphate, Natpp: Na5P3O10) at 100–150 °C for 16 h in a Teflon-lined screw-capped Pyrex test tube. The rod-like and spherical particles were precipitated at an extremely fast rate of reaction under 100 °C. The spherical particles were only produced in a very narrow region at 100 °C by aggregation of primary small particles. The rod-like particles were CaNa2P2O7·4H2O but the uniform spherical ones were amorphous and the latter ones were crystallized to β-Ca2P2O7 after being calcined above 600 °C. The aging temperature drastically varied the particle shape under conditions for producing uniform spherical particles; solid spherical particles were produced up to the aging temperature of 115 °C but balloon-like hollow spheres were precipitated at 120 °C. However, large and irregular agglomerates made up of extremely small rod-like particles were precipitated after aging the solution above 125 °C. TEM observation and ICP-AES measurements revealed that the balloon-like hollow spheres were produced by dissolving the interior of solid spherical particles after reinforced their shell by the adsorption of unhydrolyzed tpp. The spherical and balloon-like calcium phosphate particles with amorphous crystal form showed high selective adsorption of H2O by rehydration of Ca2+ ions by penetrated H2O molecules into the particles. In particular, the balloon-like hollow spheres of calcium phosphate may hold potential as drug delivery vehicles and have biocompatibility advantages.
Matrix Isolation Infrared Spectroscopic and Density Functional Theory Studies on the Reactions of Dysprosium Hydride with Carbon Monoxide
Authors: Teng Yun-Lei , Xu Qiang 
Published: December 2008

Abstract
Laser-ablated dysprosium hydride has been co-deposited at 4 K with carbon monoxide in excess argon. Product HDyCO has been formed in the present experiments and characterized using infrared spectroscopy on the basis of the results of the isotopic shifts, mixed isotopic splitting patterns, stepwise annealing, and the comparison with theoretical predictions. Density functional theory calculations have been performed. The agreement between the experimental and calculated vibrational frequencies, and isotopic shifts supports the identification of the molecule from the matrix infrared spectra. A plausible reaction mechanism has been proposed to account for the formation of this molecule.
Structural Effect of Amphiphilic Crown Ether Azoprobes on Alkali Metal Ion Recognition and Aggregation Behavior in Water
Authors: Sato Fuyuki , Tsukano Miki , Sakamoto Koki , Umemoto Wakako , Hashimoto Takeshi , Hayashita Takashi 
Published: December 2008

Abstract
Amphiphilic azoprobes having a crown ether moiety (15C5–Azo–Cn; n=4, 6, 8, and 12 and 18C6–Azo–Cn; n=4, 6, and 8) were synthesized. We examined the effect of alkyl spacer length of the amphiphilic azoprobes on the spectral response to alkali metal ions in water by UV–vis spectral and 1H NMR measurements. 15C5–Azo–Cn exhibited self-assembly in response to K+ selectively and the most selective response to K+ was observed for an azoprobe possessing a hexyl spacer unit (15C5–Azo–C6). 15C5–Azo–C12 formed nano-size aggregates. 18C6–Azo–Cn (n=6 and 8) showed Cs+ selectivity and its molecular aggregation behavior was similar to that of 15C5–Azo–Cn.
Remarkable Substituent Effects on the Oxidizing Ability of Tetraarylbismuthonium Tetrafluoroborates in Alcohol Oxidation
Authors: Matano Yoshihiro , Suzuki Takeshi , Iwata Takaharu , Shinokura Tomonori , Imahori Hiroshi 
Published: December 2008

Abstract
Substituent effects on the oxidizing ability of tetraarylbismuthonium tetrafluoroborates in alcohol oxidation are reported. Intermolecular and intramolecular competition experiments on geraniol oxidation by the combined use of tetraarylbismuthonium tetrafluoroborates and N,N,N′,N′-tetramethylguanidine (TMG) have revealed that the oxidizing ability of the bismuthonium salt increases by the introduction of methyl groups at the ortho position and an electron-withdrawing group at the para position of the aryl ligands. The intermolecular and intramolecular H/D kinetic isotope effects observed for the competitive oxidation of p-bromobenzyl alcohols have shown that the present oxidation reaction consists of fast pre-equilibrium leading to alkoxytetraarylbismuth(V) intermediates (first step) and α-hydrogen abstraction by the aryl ligand attached to the bismuth (second step). The experimental results demonstrate that the electron-deficient aryl ligands enhance the electrophilicity at the bismuth center to put forward the first step and that the bulky ligands destabilize the alkoxybismuth(V) intermediates to accelerate the second step. The newly explored mesityl- and 2,6-xylyltriarylbismuthonium salts have proven to convert primary and secondary alcohols to the corresponding carbonyl compounds with high efficiency under mild conditions. A remarkable steric effect of these oxidants has also been exhibited in the chemoselective oxidation between primary and secondary benzylic alcohols.
Improvement of Co3O4 Nanoparticle Synthesis in Apoferritin Cavity by Outer Surface PEGylation
Authors: Tsukamoto Rikako , Muraoka Masahiro , Fukushige Yoshitsugi , Nakagawa Hiromichi , Kawaguchi Tomohiro , Nakatsuji Yohji , Yamashita Ichiro 
Published: December 2008

Abstract
The outer surface of horse spleen apoferritin (HsAFr) was chemically modified by poly(ethylene glycol) (PEG) to prevent bulk precipitation during artificial biomineralization of the cobalt-oxide core (Co3O4) in its cavity. Two kinds of PEGs, with average molecular weights of 2000 and 5000 were covalently attached (PEGylation) on the outer surface of HsAFr and suppressed the bulk precipitation drastically, whereas neither free PEGs nor short PEG (N-{2-[2-(2-methoxyethoxy)ethoxy]ethanoyloxy}succinimide) performed such suppression. The PEGylated HsAFr accommodated fully developed Co3O4 cores and achieved a high yield of homogeneous Co3O4 nanoparticles. Investigation of the early biomineralization stage suggested that [CoIIIO] complex ions were accumulated around the negatively charged outer surface of HsAFr.
Electrocatalytic Reduction of Nitrate Using Cu–Pd and Cu–Pt Cathodes/H+-Conducting Solid Polymer Electrolyte Membrane Assemblies
Authors: Hasnat Mohammad Abul , Ishibashi Isao , Sato Kiwako , Agui Ryoko , Yamaguchi Tsuyoshi , Ikeue Keita , Machida Masato 
Published: December 2008

Abstract
Electrocatalytic reduction of nitrate ions (NO3−) was carried out over Cu–Pd and Cu–Pt bimetallic cathodes, which were deposited on a Nafion-117 H+-conducting polymer membrane. By applying DC current to the membrane–electrode assembly (MEA), H2 evolved on the cathode caused monotonic degradation of NO3− in the cathode compartment. The NO3− reduction proceeded in a consecutive manner and copper increased significantly the catalytic activity for the first step from NO3− to NO2−. The Cu–Pd and Cu–Pt cathodes, with 38 and 20 mol % Cu, respectively, exhibited the highest reduction rate. The product selectivity was also dependent on the content of Cu. The Cu–Pd cathode showed a lower selectivity to NO2− and a higher selectivity to NH4+, because the catalytic activity for NO2− reduction is high. The rate of nitrate reduction was increased by supplying CO2, which plays a role of a buffer to keep pH lower than 7 and promotes the reaction, 2NO3−+5H2→N2+2OH−+4H2O.
Psychophysiological effects of biofeedback treatment in tinnitus sufferers
Authors: Heinecke Kristin , Weise Cornelia , Rief Winfried 
Published: December 2008

Objectives. Psychophysiological factors in maintaining tinnitus‐related distress have been emphasized in current tinnitus models. Hyperreactivity in the autonomous nervous system is supposed to hinder habituation processes and might contribute to maladjustment to tinnitus symptoms in the long run. Accordingly, biofeedback treatment targeting physiological activity ought to reduce tinnitus annoyance and facilitate habituation.Subjects. One hundred and thirty patients completed a manual‐based psychological treatment especially developed for chronic tinnitus sufferers. A subsample consisting of 67 participants were randomly assigned to a waiting list (3 months) and served as a control group. The programme consisted of 15 sessions of cognitive‐behavioural therapy combined with a psychophysiological treatment using a biofeedback approach.Method. Different muscle regions of the head and neck and skin conductance level were assessed with biofeedback equipment. Physiological treatment effects were analysed using the pre‐post effect sizes in comparison to the waitlist group. Correlations for physiological changes and psychological treatment effects were computed.Results. Moderate to large effect sizes for physiological changes were demonstrated. Physiological and psychological treatment effects were found to be unrelated.Discussion. Our treatment approach, which combined biofeedback therapy with CBT elements, was found to be highly effective in reducing psychophysiological activation. Psychological and physiological variables seem to represent independent response systems.