bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of two heparan sulphate-binding sites in the mycobacterial adhesin Hlp
Authors: Portugal Michelle I , Todeschini Adriane R , de Lima Cristiana S , Silva Carlos AM , Mohana-Borges Ronaldo , Ottenhoff Tom HM , Mendonça-Previato Lucia , Previato Jose O , Pessolani Maria CV 
Published: May 2008

Abstract

Background
The histone-like Hlp protein is emerging as a key component in mycobacterial pathogenesis, being involved in the initial events of host colonization by interacting with laminin and glycosaminoglycans (GAGs). In the present study, nuclear magnetic resonance (NMR) was used to map the binding site(s) of Hlp to heparan sulfate and identify the nature of the amino acid residues directly involved in this interaction.

Results
The capacity of a panel of 30 mer synthetic peptides covering the full length of Hlp to bind to heparin/heparan sulfate was analyzed by solid phase assays, NMR, and affinity chromatography. An additional active region between the residues Gly46 and Ala60 was defined at the N-terminal domain of Hlp, expanding the previously defined heparin-binding site between Thr31 and Phe50. Additionally, the C-terminus, rich in Lys residues, was confirmed as another heparan sulfate binding region. The amino acids in Hlp identified as mediators in the interaction with heparan sulfate were Arg, Val, Ile, Lys, Phe, and Thr.

Conclusion
Our data indicate that Hlp interacts with heparan sulfate through two distinct regions of the protein. Both heparan sulfate-binding regions here defined are preserved in all mycobacterial Hlp homologues that have been sequenced, suggesting important but possibly divergent roles for this surface-exposed protein in both pathogenic and saprophic species.
Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)
Authors: Cuc Luu M , Mace Emma S , Crouch Jonathan H , Quang Vu D , Long Tran D , Varshney Rajeev K 
Published: May 2008

AbstractBackgroundCultivated peanut or groundnut (Arachis hypogaeaL.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut.ResultsA microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecieshypogaeawere grouped together in one cluster, while the genotypes belonging to subspeciesfastigiatawere grouped mainly under two clusters.ConclusionNewly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships in cultivated groundnut as well as relatedArachisspecies.
Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade
Authors: Nie Wenhui , Fu Beiyuan , O'Brien Patricia CM , Wang Jinhuan , Su Weiting , Tanomtong Alongkoad , Volobouev Vitaly , Ferguson-Smith Malcolm A , Yang Fengtang 
Published: May 2008

Abstract

Background

Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous.

Results

To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome.

Conclusion

Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.
U12 intron positions are more strongly conserved between animals and plants than U2 intron positions
Authors: Basu Malay Kumar , Makalowski Wojciech , Rogozin Igor B , Koonin Eugene V 
Published: May 2008

Abstract
We report that the positions of minor, U12 introns are conserved in orthologous genes from human and Arabidopsis to an even greater extent than the positions of the major, U2 introns. The U12 introns, especially, conserved ones are concentrated in 5'-portions of plant and animal genes, where the U12 to U2 conversions occurs preferentially in the 3'-portions of genes. These results are compatible with the hypothesis that the high level of conservation of U12 intron positions and their persistence in genomes despite the unidirectional U12 to U2 conversion are explained by the role of the slowly excised U12 introns in down-regulation of gene expression.

Reviewers

This article was reviewed by John Logsdon and Manyuan Long. For the full reviews, please go to the Reviewers' Reports section.
Loss of genes implicated in gastric function during platypus evolution
Authors: Ordoñez Gonzalo R , Hillier LaDeana W , Warren Wesley C , Grützner Frank , López-Otín Carlos , Puente Xose S 
Published: May 2008

Abstract
Background
The duck-billed platypus (Ornithorhynchus anatinus) belongs to the mammalian subclass Prototheria, which diverged from the Theria line early in mammalian evolution. The platypus genome sequence provides a unique opportunity to illuminate some aspects of the biology and evolution of these animals.

Results
We show that several genes implicated in food digestion in the stomach have been deleted or inactivated in platypus. Comparison with other vertebrate genomes revealed that the main genes implicated in the formation and activity of gastric juice have been lost in platypus. These include the aspartyl proteases pepsinogen A and pepsinogens B/C, the hydrochloric acid secretion stimulatory hormone gastrin, and the α subunit of the gastric H+/K+-ATPase. Other genes implicated in gastric functions, such as the β subunit of the H+/K+-ATPase and the aspartyl protease cathepsin E, have been inactivated because of the acquisition of loss-of-function mutations. All of these genes are highly conserved in vertebrates, reflecting a unique pattern of evolution in the platypus genome not previously seen in other mammalian genomes.

Conclusion
The observed loss of genes involved in gastric functions might be responsible for the anatomical and physiological differences in gastrointestinal tract between monotremes and other vertebrates, including small size, lack of glands, and high pH of the monotreme stomach. This study contributes to a better understanding of the mechanisms that underlie the evolution of the platypus genome, might extend the less-is-more evolutionary model to monotremes, and provides novel insights into the importance of gene loss events during mammalian evolution.
Single-stage nosing of thin-walled tubes into hollow spheres using a die
Authors: Alves L M , Martins P A F 
Published: May 2008

In recent work, the present authors reported a thorough analysis of the mechanics of nosing thin-walled tubes into hollow spheres using a die and proposed enhancement of the formability limits of the process by means of preforming stages and preliminary tube-end preparation schemes. In an effort to improve the surface quality and dimensional accuracy and to extend further the formability of thin-walled hollow spheres, the present authors now report a new single-stage process based on the utilization of an innovative tool design consisting of two sharp-edge dies and a floating ring. The overall performance of the new proposed process is evaluated by means of numerical simulations based on the finite element method and experimentation on industrial aluminium alloy 6060 tubes under laboratory-controlled conditions.
Comparison of Measurements Provided by Several Corrosion Rate Meters with Modulated Confinement of the Current
Authors: Martinez I. , Andrade C. , Marie-Victoire E. , Bouteiller V. , Rebolledo N. 
Published: May 2008

Abstract
The main difficulty for the application of Rp on site is the vanishing of the current with the distance which has been overcome with the use of a modulated confinement of the current only feasible if the guard ring is monitored during the measurement by means of electrodes able to detect the distance reached by the current.
In the present paper after a short review of existing corrosion rate meters to measure on site, results of a comparison made of reinforced concrete slabs with various degradations such as carbonation or chloride among several using a guard ring with modulated confinement of the current is presented in order to have a reproducibility and repeatability for the measurements. Results show a good correlation among all the methods used for the corrosion rate evaluation.
Evaluation of contact exposure as a method for acclimatizing growing pigs to porcine reproductive and respiratory syndrome virus
Authors: Vashisht Kapil , Erlandson Keith R. , Firkins Lawrence D. , Zuckermann Federico A. , Goldberg Tony L. 
Published: May 2008

Abstract
Objective—To determine whether 6.5-week-old gilts that have not previously been exposed to porcine reproductive and respiratory syndrome (PRRS) virus can be acclimatized to an endemic strain of the virus by commingling with age-matched gilts inoculated with the endemic PRRS virus strain and whether 10.5-week-old gilts can be acclimatized by commingling with age-matched inoculated or contact-exposed animals.
Design—Randomized controlled longitudinal study.
Animals—80 gilts seronegative for PRRS on a farm in the Midwestern United States with a history of PRRS.
Procedures—20 gilts were inoculated with the endemic PRRS virus strain at 6.5 weeks of age (group 1) and were commingled with 20 gilts that were not inoculated (group 2). Four weeks later, the remaining 40 gilts (group 3) were commingled with gilts in groups 1 and 2. Presence of viral RNA in the tonsils, seroconversion rate, serum neutralizing antibody titers, interferon-γ-mediated cellular immunity, and reproductive outcomes were analyzed.
Results—Acclimatization of PRRS virus-naïve pigs was achieved by means of contact exposure at both 6.5 and 10.5 weeks of age. No differences were observed among the 3 groups with respect to development of anti-PRRS virus-specific immune responses or reproductive outcomes.
Conclusions and Clinical Relevance—Results suggested that contact exposure of 6.5- to 10.5-week-old pigs that had not previously been exposed to PRRS virus to pigs inoculated with endemic PRRS virus may be an efficient acclimatization strategy for controlling outbreaks on commercial farms on which PRRS is endemic.
Effect of a Prenatal Nutritional Intervention Program On Initiation and Duration of Breastfeeding
Authors: Léger-Leblanc Gisèle , Rioux France M. 
Published: May 2008

Purpose: To evaluate initiation and duration of breastfeeding of infants born to mothers who participated in the Early Childhood Initiative (ECI) program. Factors affecting the initiation and the early cessation of breastfeeding were also explored. Methods: Twenty-five pregnant women participating in the ECI program completed this prospective study. At 36 weeks’ gestation, a questionnaire was administered to assess socioeconomic status, intention to breastfeed and breastfeeding experience. When the infants were three and six months of age, feeding practices were assessed with a questionnaire. Results: The breastfeeding initiation rate was 62.5%. At one and three months postpartum, exclusive breastfeeding rates were 39% and 4%, respectively. At six months, none of the women was exclusively breastfeeding. Primiparity, prenatal classes, having been breastfed and intention to breastfeed at 36 weeks’ gestation were positively associated with breastfeeding initiation. Father’s education, intention to breastfeed at 36 weeks’ gestation, no water or formula given to the infant during hospitalization and higher maternal hemoglobin level at 36 weeks’ gestation were positively associated with the duration of breastfeeding. Conclusions: The rate of initiation and duration of breastfeeding for ECI participants were low. To achieve successful interventions, it is important to target modifiable factors known to influence the initiation and duration of breastfeeding within this population.
The Challenge of Skill Transfer: Dietitian Perspectives
Authors: Lordly Daphne 
Published: May 2008

Purpose: The notion of transferable skills is part of the comprehensive education model for dietetic practice. Dietitians’ perspectives were collected to determine their understanding of the concept and which dietetic skills they considered transferable in long-term and acute care environments.Methods: The study included a purposive sample of 14 dietitians representing long-term and acute care internship training and employment. The dietitians completed a questionnaire and were interviewed.Results: All respondents demonstrated an understanding of the concept of transferability of skills. Results indicated that the majority believed dietetic entry-level competencies could be achieved in both long-term and acute care environments. While the majority believed competencies could be transferred from one environment to another, issues were raised about transfer from long-term care to acute care. These issues included limited client communication, fewer resources, and less opportunity for exposure to skill areas. Interpretation of the term “skill,” one-way transferability, and level of competence required for the particular working environment emerged as challenges to operationalization of the concept.Conclusions: Transferability of skills within dietetic practice requires further investigation if it is to be fully understood and used to its full potential.
Decision-making in the Dairy Aisle: Maximizing Taste, Health, Cost and Family Considerations
Authors: Hammond Gail K. , Chapman Gwen E. 
Published: May 2008

Purpose: To gain insight into the decision-making processes used by women when selecting dairy and dairy alternative foods, including examination of the role of bone health concerns. Methods: Semi-structured, point-of-purchase interviews were conducted with a convenience sample of 30 female grocery shoppers. Constant comparative data analysis was used to generate themes on shoppers’ decision-making processes. Results: Women considered multiple issues in their dairy and dairy alternative food choice strategies: taste was most often associated with the fat and sugar content of foods; health concerns were centred on achieving an acceptable body weight and preventing osteoporosis and cardiovascular disease, and women chose foods to satisfy other family members’ needs and preferences and to obtain “good food value.” Women prioritized their food choices by weighing the value of each issue, which led to a strategic process for “maximizing the value” of their food choices. The availability of a wide range of dairy and dairy alternative foods meant that in most instances, it was unnecessary for women to “trade off” one area of concern for another. Conclusions: Dietitians and nutrition educators can help women make dietary changes by helping them identify foods that they perceive as meeting a variety of needs.
Intermittent thinning of Jakobshavn Isbræ, West Greenland, since the Little Ice Age
Authors: Csatho Bea , Schenk Toni , Van Der Veen C.J. , Krabill William B. 
Published: May 2008

AbstractRapid thinning and velocity increase on major Greenland outlet glaciers during the last two decades may indicate that these glaciers became unstable as a consequence of the Jakobshavn effect (Hughes, 1986), with terminus retreat leading to increased discharge from the interior and consequent further thinning and retreat. To assess whether recent trends deviate from longer-term behavior, we measured glacier surface elevations and terminus positions for Jakobshavn Isbræ, West Greenland, using historical photographs acquired in 1944, 1953, 1959, 1964 and 1985. These results were combined with data from historical records, aerial photographs, ground surveys, airborne laser altimetry and field mapping of lateral moraines and trimlines, to reconstruct the history of changes since the Little Ice Age (LIA). We identified three periods of rapid thinning since the LIA: 1902–13, 1930–59 and 1999–present. During the first half of the 20th century, the calving front appears to have been grounded and it started to float during the late 1940s. The south and north tributaries exhibit different behavior. For example, the north tributary was thinning between 1959 and 1985 during a period when the calving front was stationary and the south tributary was in balance. The record of intermittent thinning, combined with changes in ice-marginal extent and position of the calving front, together with changes in velocity, imply that the behavior of the lower parts of this glacier represents a complex ice-dynamical response to local climate forcings and interactions with drainage from the interior.
Combined oceanic and atmospheric influences on net accumulation on Devon Ice Cap, Nunavut, Canada
Authors: Colgan William , Sharp Martin 
Published: May 2008

AbstractAn annual net accumulation history of the high-elevation region of Devon Ice Cap, Nunavut, Canada, was reconstructed for the period 1963–2003 using five shallow firn cores. Annual net accumulation decreased significantly after 1989. To explain variability in the reconstructed annual net accumulation record, monthly and seasonal moisture-source probabilities were calculated for gridcells throughout the Arctic during 1979–2003. Seasonally, moisture-source probabilities reach a maximum in northern Baffin Bay in late summer/early fall and approach zero throughout the Arctic in winter. Late-summer/early-fall moisture-source probabilities were significantly higher around the North Open Water (NOW) Polynya during the 4 year period of highest annual net accumulation during the 1979–2003 period (1984–87), than during the 4 year period with the lowest annual net accumulation (1994–97). This is due to both a significant decrease in the sea-ice fraction and a significant increase in low-elevation atmospheric transport over the NOW area during the high net accumulation period. Anomalously low net accumulation and anomalously high firnification rates during the 1989–2003 period suggest that a change in ice dynamics, rather than a change in surface mass balance, may explain recent ice-cap thickening observed by laser altimetry.
Preparation, Characterization, and Application of L‐Cysteine Functionalized Multiwalled Carbon Nanotubes as a Selective Sorbent for Separation and Preconcentration of Heavy Metals
Authors: Liu Yue , Li Yan , Yan Xiu‐Ping 
Published: May 2008

AbstractL‐cysteine functionalized multi‐walled carbon nanotubes (MWCNTs‐cysteine) are synthesized and characterized by XPS, FT‐IR, XRD, and TEM. The capability of MWCNTs‐cysteine for selective separation and preconcentration of heavy metal ions are statically and dynamically evaluated with Cd2+ as a model heavy metal ion. Unlike MWCNTs, the sorption of Cd2+ onto MWCNTs‐cysteine is not influenced by ionic strength in a wide range. The MWCNTs‐cysteine is demonstrated to be good column packings for on‐line microcolumn separation and preconcentration of Cd2+. Effective preconcentration of Cd2+ on the MWCNTs‐cysteine packed microcolumn is achieved in a pH range of 5.5 to 8.0. The retained Cd2+ is efficiently eluted with 0.5 mol L−1 HCl for on‐line flame atomic absorption spectrometric determination. The MWCNTs‐cysteine exhibit fairly fast kinetics for the adsorption of Cd2+, and offer up to 1600‐fold improvement of the tolerable concentrations of co‐existing metal ions over the MWCNTs for on‐line solid‐phase extraction of Cd2+. With a preconcentration time of 60 s at a sample loading flow rate of 5.0 mL min−1, an enhancement factor of 33 and a sample throughput of 36 h−1 along with a detection limit (3s) of 0.28 µg L−1 are obtained. The precision (RSD) for 11 replicate measurements is 1.6% at the 10 µg L−1 level. The developed method using the MWCNTs‐cysteine as sorbent is successfully applied to determination of trace cadmium in a variety of biological and environmental materials.