bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards
Authors: Tsai Tsung-Heng , Tadesse Mahlet G. , Di Poto Cristina , Pannell Lewis K. , Mechref Yehia , Wang Yue , Ressom Habtom W. 
Published: September 2013

Abstract
Motivation: Liquid chromatography-mass spectrometry (LC-MS) has been widely used for profiling expression levels of biomolecules in various ‘-omic’ studies including proteomics, metabolomics and glycomics. Appropriate LC-MS data preprocessing steps are needed to detect true differences between biological groups. Retention time (RT) alignment, which is required to ensure that ion intensity measurements among multiple LC-MS runs are comparable, is one of the most important yet challenging preprocessing steps. Current alignment approaches estimate RT variability using either single chromatograms or detected peaks, but do not simultaneously take into account the complementary information embedded in the entire LC-MS data.
Results: We propose a Bayesian alignment model for LC-MS data analysis. The alignment model provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of information including internal standards and clustered chromatograms in a mathematically rigorous framework. We apply the model to LC-MS metabolomic, proteomic and glycomic data. The performance of the model is evaluated based on ground-truth data, by measuring correlation of variation, RT difference across runs and peak-matching performance. We demonstrate that Bayesian alignment model improves significantly the RT alignment performance through appropriate integration of relevant information.
Availability and implementation: MATLAB code, raw and preprocessed LC-MS data are available at http://omics.georgetown.edu/alignLCMS.html
Contact: hwr@georgetown.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire
Authors: Park Hae-Min , Park Ju-Hyeong , Kim Yoon-Woo , Kim Kyoung-Jin , Jeong Hee-Jin , Jang Kyoung-Soon , Kim Byung-Gee , Kim Yun-Gon 
Published: September 2013

Abstract
Summary: In recent years, the improvement of mass spectrometry-based glycomics techniques (i.e. highly sensitive, quantitative and high-throughput analytical tools) has enabled us to obtain a large dataset of glycans. Here we present a database named Xeno-glycomics database (XDB) that contains cell- or tissue-specific pig glycomes analyzed with mass spectrometry-based techniques, including a comprehensive pig glycan information on chemical structures, mass values, types and relative quantities. It was designed as a user-friendly web-based interface that allows users to query the database according to pig tissue/cell types or glycan masses. This database will contribute in providing qualitative and quantitative information on glycomes characterized from various pig cells/organs in xenotransplantation and might eventually provide new targets in the α1,3-galactosyltransferase gene-knock out pigs era.
Availability: The database can be accessed on the web at http://bioinformatics.snu.ac.kr/xdb.
Contact: byungkim@snu.ac.kr or ygkim@ssu.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Mechanical properties of DNA-like polymers
Authors: Peters Justin P. , Yelgaonkar Shweta P. , Srivatsan Seergazhi G. , Tor Yitzhak , James Maher L. 
Published: September 2013

Abstract
The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of the relative roles of attractive base stacking forces and repulsive electrostatic forces creating this stiffness. To gain insight, we have created a family of double-helical DNA-like polymers where one of the four normal bases is replaced with various cationic, anionic or neutral analogs. We apply DNA ligase-catalyzed cyclization kinetics experiments to measure the bending and twisting flexibilities of these polymers under low salt conditions. Interestingly, we show that these modifications alter DNA bending stiffness by only 20%, but have much stronger (5-fold) effects on twist flexibility. We suggest that rather than modifying DNA stiffness through a mechanism easily interpretable as electrostatic, the more dominant effect of neutral and charged base modifications is their ability to drive transitions to helical conformations different from canonical B-form DNA.
Exome Sequencing Reveals Novel Rare Variants in the Ryanodine Receptor and Calcium Channel Genes in Malignant Hyperthermia Families
Authors: Kim Jerry H. , Jarvik Gail P. , Browning Brian L. , Rajagopalan Ramakrishnan , Gordon Adam S. , Rieder Mark J. , Robertson Peggy D. , Nickerson Deborah A. , Fisher Nickla A. , Hopkins Philip M. 
Published: September 2013

Abstract

Background:
About half of malignant hyperthermia (MH) cases are associated with skeletal muscle ryanodine receptor 1 (RYR1) and calcium channel, voltage-dependent, L type, α1S subunit (CACNA1S) gene mutations, leaving many with an unknown cause. The authors chose to apply a sequencing approach to uncover causal variants in unknown cases. Sequencing the exome, the protein-coding region of the genome, has power at low sample sizes and identified the cause of over a dozen Mendelian disorders.

Methods:
The authors considered four families with multiple MH cases lacking mutations in RYR1 and CACNA1S by Sanger sequencing of complementary DNA. Exome sequencing in two affecteds per family, chosen for maximum genetic distance, were compared. Variants were ranked by allele frequency, protein change, and measures of conservation among mammals to assess likelihood of causation. Finally, putative pathogenic mutations were genotyped in other family members to verify cosegregation with MH.

Results:
Exome sequencing revealed one rare RYR1 nonsynonymous variant in each of three families (Asp1056His, Val2627Met, Val4234Leu), and one CACNA1S variant (Thr1009Lys) in the fourth family. These were not seen in variant databases or in our control population sample of 5,379 exomes. Follow-up sequencing in other family members verified cosegregation of alleles with MH.

Conclusions:
The authors found that using both exome sequencing and allele frequency data from large sequencing efforts may aid genetic diagnosis of MH. In a sample selected by the authors, this technique was more sensitive for variant detection in known genes than Sanger sequencing of complementary DNA, and allows for the possibility of novel gene discovery.
Associations between measures of central adiposity and periodontitis among older adults
Authors: Muñoz‐Torres Francisco J. , Jiménez Monik C. , Rivas‐Tumanyan Sona , Joshipura Kaumudi J. 
Published: September 2013

AbstractObjectiveTo evaluate the association between measures of adiposity and periodontitis among older Puerto Rican adults.MethodsA cross‐sectional study was conducted among 147 representative adults ≥70 years living in the San Juan metropolitan area. Height, weight, waist circumference (WC), and hip circumference were measured by trained personnel. Periodontal probing depth and attachment loss (AL) were measured by calibrated examiners. Periodontitis was classified according to the Center for Disease Control/American Academy of Periodontology (CDC‐AAP) definitions and using tertiles of mean AL and percent of sites with AL ≥3 mm. Multivariable polytomous logistic regression models adjusted for age, gender, smoking, education, diabetes status, physical activity, and total fruit and vegetable intake were used to model associations between WC, waist‐to‐hip ratio (WHR), and periodontitis.ResultsHigh WC (men: ≥102 cm versus <102 cm, women: ≥88 cm versus <88 cm) compared with normal showed nonsignificant associations with severe (OR = 2.56, 95% CI: 0.76–8.67), moderate periodontitis (OR = 1.53, 95% CI: 0.65–3.60), and upper tertile of mean AL (OR = 2.28, 95% CI: 0.83–6.23). Elevated WHR versus normal (men: ≥0.95 versus <0.95, women: ≥0.88 versus <0.88) was associated with moderate periodontitis (OR = 2.36, 95% CI: 1.01–5.52) and showed a borderline significant association with the upper tertile of mean AL (OR = 2.52, 95% CI: 0.96–6.63, P = 0.06).ConclusionsCentral adiposity was associated with a greater risk of periodontitis in this population of older adults, although analyses were underpowered. These results hold important public health implications given the high prevalence of adiposity and periodontitis among older adults.
Telomere length and Parkinson's disease in men: a nested case−control study
Authors: Schürks M. , Buring J. , Dushkes R. , Gaziano J. M. , Zee R. Y. L. , Kurth T. 
Published: September 2013

Background and purposeTelomere shortening has been implicated in neurodegenerative disorders. However, available data on the association between telomere length and Parkinson's disease (PD) are inconclusive.MethodsA nested case−control design was used amongst men participating in the prospective Physicians’ Health Study. A large proportion of participants provided blood samples in 1997 and they were followed through 2010. Men with self‐reported PD were age‐matched to controls in a 1:2 ratio. Quantitative PCR was used to determine the telomere repeat copy number to single gene copy number ratio (TSR) in genomic DNA extracted from peripheral blood leukocytes. TSR was used as a measure for relative telomere length (RTL) in our analyses. Conditional logistic regression was used to determine the risk of PD associated with RTL.ResultsData on RTL were available from 408 cases and 809 controls. Median TSR was shorter in controls than in cases (47.7 vs. 50.2; P = 0.02). The age‐adjusted odds ratio (OR) for PD was 0.66 [95% confidence interval (CI) 0.46–0.95; Ptrend over quartiles 0.02] comparing the lowest to the highest quartile. The pattern of association was unchanged when comparing RTL below versus above the median (age‐adjusted OR 0.75; 95% CI 0.59–0.96). Associations were similar after additional adjustment for many covariates.ConclusionContrary to what was expected, in this large nested case−control study amongst men shorter telomeres were associated with reduced PD risk. Future research on the nature of this counterintuitive association is warranted.
Simple variables predict miserable outcome after intravenous thrombolysis
Authors: Seiffge D. J. , Karagiannis A. , Strbian D. , Gensicke H. , Peters N. , Bonati L. H. , Kotisaari K. , Leppä M. , Kejda‐Scharler J. , Tränka C. , Ginsbach P. , Tatlisumak T. , Lyrer P. A. , Engelter S. T. 
Published: September 2013

Background and purposeTo test the predictability of miserable outcome amongst ischaemic stroke patients receiving intravenous thrombolysis (IVT) based on a simple variables model (SVM) and to compare the model's predictive performance with that of an existing score which includes imaging and laboratory parameters (DRAGON).MethodsThe SVM consists of the parameters age, independence before stroke, normal Glasgow coma verbal score, able to lift arms and able to walk. In a derivation cohort (n = 1346) and a validation cohort (n = 638) of consecutive IVT‐treated stroke patients, the probability estimated by SVM and the observed occurrence of miserable 3‐month outcome (modified Rankin score 5–6) were compared. The performances of SVM and the DRAGON score were compared. The area under the receiver operating curve (AUC) (95% confidence interval, CI) and the bootstrapping approach were used to compare the predictive performance.ResultsThe AUCs to predict miserable outcome in the derivation cohort were 0.807 (95% CI 0.774–0.838) using the SVM and 0.822 (0.790–0.850) using the DRAGON score (P = 0.3). For the validation cohort, AUCs were 0.786 (0.742–0.829) for the SVM and 0.809 (0.774–0.845) for the DRAGON score (P = 0.23). Only one patient with an SVM probability of >70% for miserable outcome in either cohort had a good outcome whilst 83% had a miserable outcome. An online SVM calculator to estimate the probability of miserable outcome for individual patients is available under http://www.unispital-basel.ch/SVM‐Tool.ConclusionThe SVM was similar in accuracy to the DRAGON score for predicting miserable outcome after IVT. As these simple variables are available already at the pre‐hospital stage, the SVM may facilitate and accelerate pre‐hospital triage of patients at high risk for miserable outcome after IVT towards endovascular treatment.
Squaring the circle: reconciling fishing and conservation of aquatic ecosystems
Authors: Law Richard , Kolding Jeppe , Plank Michael J 
Published: September 2013

AbstractSize‐at‐entry regulations in fisheries cause major disruption to aquatic ecosystems, including truncation of age‐ and size‐structures, destabilization of fish stocks, directional selection on phenotypic traits and a by‐catch of unwanted species and sizes. Here, we use simple dynamic models of size‐spectra to examine an alternative, so‐called balanced harvesting. Balanced harvesting helps in retaining the approximate power‐law size‐structure of natural ecosystems, whereas size‐at‐entry regulations do not. Balanced harvesting is less likely to destabilize steady states than size‐at‐entry regulations set close to the size at maturation. Surprisingly, our numerical results suggest that steady‐state biomass yield can be substantially increased by switching from size‐at‐entry to balanced harvesting. On the basis of these results, we argue that the goals of conservation and of greater yields seem less difficult to reconcile than have previously been thought. However, to work towards these goals require a change in our approach to fishing.
Mechanistic insights into 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase, a key enzyme of the MEP terpenoid biosynthetic pathway
Authors: Li Heng , Tian Jie , Sun Wei , Qin Wei , Gao Wen‐Yun 
Published: September 2013

The binding mode of 1‐deoxy‐d‐xylulose 5‐phosphate (DXP) to 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase (DXR) (EC 1.1.1.267) from Escherichia coli was investigated via 18O isotope exchange experiments and determination of the kinetic parameters of the reaction. The results support a C3–C4 substrate binding mode in which DXP chelates a DXR‐bound divalent cation via its hydroxyl groups at C3 and C4. Based on this binding mode and the early results, a catalytic cycle for the conversion of DXP to 2‐methyl‐d‐erythritol 4‐phosphate mediated by DXR including a pseudo‐single molecule transition state of the retro‐aldol intermediates is proposed. Taking into account the binding mode of DXP and the catalytic cycle of DXR, the mechanistic insights of DXR are disclosed and the current discrepancies concerning the catalysis of this enzyme are interpreted within the accepted retro‐aldol/aldol sequence.
The effect of modified atmosphere packaging on the microbiological, physical, chemical and sensory characteristics of broadtail squid (Illex coindetii)
Authors: Bouletis Achilleas D. , Arvanitoyannis Ioannis S. , Hadjichristodoulou Christos , Neofitou Christos , Sakkomitrou Maria , Kolokythopoulou Foteini 
Published: September 2013

SummaryThe aim of this work was to evaluate the effect of various atmosphere compositions (20% CO2/80% N2 for modified atmosphere packaging (MAP) 1, 50% CO2/50% N2 for MAP 2, 70% CO2/30% N2 for MAP 3 and vacuum packaging) on the microbial (mesophiles, psychrophiles, Pseudomonas spp., Brochothrix thermosphacta and Enterobacteriaceae), physical, chemical [trimethylamine (TMA) and total volatile basic nitrogen (TVBN)] and sensorial characteristics of broadtail squid (Illex coindetii) stored for 10 days at 2 ± 1 °C. All microbial populations were severely restrained by MAP 3 with the exception of Enterobacteriaceae, which seemed to take advantage of the lack of competitive microflora and had enhanced microbial counts on MAP samples (P < 0.05). Colour attributes were better maintained on MAP‐stored samples. Drip loss was less on vacuum‐packaged squids. MAP 2 was the best atmosphere for the preservation of tissue consistency. TMA and TVBN formation was limited by high CO2 atmospheres, even though both elevated in all studied conditions. Shelf life based on sensory characteristics was determined to be 10, 8, 6, 6 and 4 days for MAP 3, MAP 2, MAP 1, vacuum and control samples, respectively.
Variations in lipid and fatty acid contents in different body parts of Black Sea whiting, Merlangius merlangus euxinus (Nordmann, 1840)
Authors: Tufan Bekir , Köse Sevim 
Published: September 2013

SummaryWhiting is a commercially important fish species of the world. This study demonstrates monthly variations in lipid and fatty acid (FA) contents of muscle, liver and roes of Black Sea whiting, Merlangius merlangus euxinus. Significant changes occurred in lipid contents between months (P < 0.05) with the highest values representing in liver 33.8–64.5%. Total polyunsaturated fatty acids (PUFA) in all groups were higher than total saturated and monounsaturated FAs with significant variations between months (P < 0.05). The highest PUFA of muscles, livers and roes were 60.0, 45.9 and 50.9%, respectively. The main FA was docosahexaenoic acid (DHA) of muscle tissue and roes, while oleic acid was the major FA in livers. Although about 164–357 g in muscle tissue or 224–392 g of whiting roe are necessary to consume to cover 1 g day−1 of eicosapentaenoic acid (EPA)+DHA for a healthy diet, only as low as 5.5–10.0 g of liver would be enough to cover the same amount of daily EPA+DHA requirement. The results indicated that whiting livers constitute a rich and underexploited source of polyunsatured FAs. Furthermore, the results may aid further research on the nutritional studies, the physiology and stock management of whiting species.
Isolation, purification and characterisation of polygalacturonase from ripened banana (Musa acuminata cv. Kadali)
Authors: Gayathri Thulasy , Nair Ashalatha S. 
Published: September 2013

SummaryBananas are the most important fruit crop in the world. Short shelf life of the fruit is the major limiting factor in international trade, and this is due to the softening of the pulp during ripening. Fruit softening is an important aspect of ripening process in fleshy fruits and is caused by the cumulative action of a group of cell wall‐modifying enzymes. Polygalacturonase (PG) is the key enzyme involved in the fruit softening process in banana, and this study reports the isolation, purification and characterisation of polygalacturonase enzyme from ripened fruits of a delayed ripened banana cultivar found specifically in Kerala (Musa acuminata cv. Kadali). PG was purified by ammonium sulphate fractionation followed by DEAE cellulose ion exchange chromatography and gel filtration using Sephadex G 100. The purified protein showed two subunits on SDS‐PAGE and a single band on native PAGE. Enzyme showed maximum activity at pH 3.5 and 40 °C. Fe3+ enhanced the activity more, while Mg2+ and Ca2+ slightly stimulated the activity of purified enzyme. Km value for substrate polygalacturonic acid was 0.06%.
Effect of blanching and drying treatments on quality of bamboo shoot slices
Authors: Zheng Jiong , Zhang Fusheng , Song Jiaxin , Lin Mao , Kan Jianquan 
Published: September 2013

SummaryThe enzymes activity, texture, pectin, microstructure and colour change in bamboo shoots (Dendrocalamus latiflorus) were examined to evaluate the effect of blanching and drying treatments on quality of bamboo shoot slices (BSS). Peroxidase (POD), phenylalanine ammonia‐lyase and polyphenol oxidase in BSS will become completely inactive at 95 °C for 6‐, 9‐ and 12‐min blanching treatments, respectively. The hardness and protopectin (PP) content decreased after the blanching treatment. Meanwhile, the content of water‐soluble pectin increased initially and then decreased gradually during the blanching. After the blanching treatment, the L* and a* of BSS decreased, while b* increased, ΔE > 2. The hardness of rehydrated BSS decreased by 43.57% after freeze drying (FD), which, however, decreased more after hot air drying (HAD). The pectin of rehydrated BSS was also determined to explain the hardness change in BSS. The BSS acquired similar microstructure of fresh samples after FD, while microstructure of BSS was severely damaged after HAD. The colour of BSS changes significantly after drying treatment. However, FD can maintain better colour of BSS than HAD. The results may provide a reference for industrial production of BSS.
Structural, functional, thermal and rheological properties of nixtamalised and extruded blue maize (Zea maysL.) flour with different calcium sources
Authors: Sánchez‐Madrigal Miguel Ángel , Meléndez‐Pizarro Carmen O. , Martínez‐Bustos Fernando , Ruiz‐Gutiérrez Martha G. , Quintero‐Ramos Armando , Márquez‐Meléndez Rubén , Lardizábal‐Gutiérrez Daniel , Campos‐Venegas Karla 
Published: September 2013

SummaryThe effects of different concentrations of calcium hydroxide [Ca(OH)2] and calcium lactate [C6H10O6Ca] on the functional and physical properties of extruded (EF) and nixtamalised (NF) blue maize flours were evaluated. Calcium source and concentration showed no significant effects on theEFexpansion index. The water absorption index (WAI) ofEFdecreased as the concentrations of both calcium sources increased, andNFwith C6H10O6Ca had the lowestWAI. The thermal and pasting properties ofNFs were higher than those ofEF.NFwith C6H10O6Ca showed the highest final viscosity (FinV), indicating less damage to the starch granules, and this was correlated with microscopic analysis. In contrast, the FinV ofEFs was significantly affected by calcium source and concentration. Extrusion with 0.3% and nixtamalisation at 2.95% of C6H10O6Ca yielded highWAIvalue and the best rheological properties in maize flour, respectively. These results suggest the use of C6H10O6Ca in extrusion or nixtamalisation to produce blue maize flours for tortilla or snacks with antioxidants.
Plasma levels of high‐sensitive C‐reactive protein do not correlate with inflammatory activity in carotid atherosclerotic plaques
Authors: Grufman H. , Gonçalves I. , Edsfeldt A. , Nitulescu M. , Persson A. , Nilsson M. , Nilsson J. 
Published: September 2013

AbstractBackgroundIt is well established that subjects with moderately elevated plasma levels of C‐reactive protein (CRP) have an increased risk of development of cardiovascular events. As atherosclerosis is a disease characterized by chronic arterial inflammation, it is possible that moderate increases in CRP level reflect the presence of plaque inflammation. To investigate this possibility, we compared plasma levels of hsCRP the day before carotid endarterectomy with the degree of inflammation in the excised plaque tissue.MethodsLuminex immunoassays were used to determine the levels of IL‐6, IL‐10, monocyte chemoattractant protein‐1 and tumour necrosis factor‐α (TNF‐α) in plasma and in homogenized plaque tissue from 160 endarterectomy specimens. Plaque sections were stained with antibodies against CD68 to determine the plaque macrophage content.ResultsPlasma high‐sensitivity (hs)CRP levels were significantly correlated with plasma IL‐6 and TNF‐α. However, there were no significant associations between plasma hsCRP concentration and plaque cytokine levels or macrophage contents.ConclusionsThe present findings strongly argue against hsCRP as a marker of plaque inflammation. Hence, it is more likely that elevated hsCRP is a sign of a subclinical systemic inflammation and this in turn may contribute to progression of cardiovascular disease.