bluuebunny/crossref_metadata_2025_split huggingface dataset:
The older brain, inflammation, vaccination and the prevention of dementia
Authors: Neal JW 
Published: July 2010

SummaryAn important protective function of the brain's innate immune system is to detect the presence of proteins such as amyloid and to remove them before they become neurotoxic, as is thought to occur in Alzheimer's disease (AD). Ageing affects the immune system response to infection and can influence the systemic response to vaccination and other potential immunotherapeutic agents. The generation of systemic antibodies is a vital component of the immune response, facilitating the identification and clearance of pathogens from the central nervous system (CNS). Experimental evidence using transgenic animal models of AD has shown successful clearance of amyloid from the CNS following vaccination with an amyloid peptide, and consequently a trial of amyloid beta peptide (Aβ) vaccination was undertaken in older people with AD. This produced some unexpected results, as not only was there evidence for amyloid plaque removal, but also a small number of cases developed encephalitis. A detailed review of the response to vaccination and the neuropathology findings are discussed, showing that the findings are understandable given the effects of ageing upon the innate immune system in the brain. Finally, the therapeutic potential of manipulating the regulatory components of the ageing innate immune system in order to inhibit brain inflammation and reduce cognitive decline is outlined.
Review: Role of tubal environment in preimplantation embryogenesis: application to co-culture assays
Authors: Guérin Pierre , Ménézo Yves 
Published: July 2010

SummaryThe culture of early preimplantation stage embryo is still delicate and the metabolic pathways of embryos are not completely understood. Embryo needs are evolutionary during the preimplantation development, consequently it is difficult to meet embryo needsin vitro.Culture conditions have to respect several physical and chemical equilibria: such as redox potential, pH, osmotic pressure, metabolic flux of energetic compounds, endogenous pools of amino acids and transcripts, etc. Embryo culture media are generally supplemented with amino acids, glucose, other energetic metabolites and antioxidant compounds, vitamin, and growth factors etc. Furthermore autocrine and paracrine regulation of embryo development probably exist. In fact embryo culture conditions have to be as non-toxic as possible. Various types of co-culture systems have been devised to overcome these problems. Complex interrelations exist between embryos and co-cultured cells. The beneficial effects of co-cultured cells may be due to continuous modifications of the culture medium, i.e. the elimination of toxic compounds and/or the supply of embryotrophic factors.
Nutrients and foods consumed by New Zealand children on schooldays and non-schooldays
Authors: Rockell Jennifer E , Parnell Winsome R , Wilson Noela C , Skidmore Paula ML , Regan Asher 
Published: July 2010

AbstractObjectiveTo describe and compare food and nutrient intakes in New Zealand (NZ) children on schooldays and non-schooldays.DesignSecondary analysis of cross-sectional data from the NZ 2002 Children’s Nutrition Survey. Dietary intake was assessed using computer-assisted multi-pass 24 h dietary recalls in the home. Data were adjusted for survey weightings to be representative of the NZ population. The effect of day category on nutrient intake, and likelihood of consumption of food categories were determined using linear and logistic regression.SettingNZ homes and schools.SubjectsA total of 2572 children (538 non-schooldays and 2034 schooldays) at the age of 5–14 years.ResultsThere were differences in the proportion consuming some food groups between schooldays and non-schooldays, although the majority of nutrient intakes including energy did not differ by day category. Mean cholesterol intake was higher on non-schooldays; dietary fibre and available carbohydrate, in particular sucrose and fructose, were higher on schooldays. Hot chips were twice as likely to be consumed on a non-schoolday. Soft drink consumption was higher on non-schooldays for Māori/New Zealand European and others and powdered drinks/cordial consumption did not vary by day category. More children consumed snack bars (normal weight, obese), fruit, sandwiches, biscuits/crackers and snack foods on schooldays. There was no difference in consumption of pies/sausage rolls by day category.ConclusionsThe proportion of consumers of a variety of foods differed significantly between non-schooldays and schooldays; few nutrient intakes differed. The present study indicates that family food, wherever it is consumed, is the mainstay of nutrition for NZ schoolchildren.
SKY BRIGHTNESS AND TRANSPARENCY IN THE i-BAND AT DOME A, ANTARCTICA
Authors: Zou Hu , Zhou Xu , Jiang Zhaoji , Ashley M. C. B. , Cui Xiangqun , Feng Longlong , Gong Xuefei , Hu Jingyao , Kulesa C. A. , Lawrence J. S. , Liu Genrong , Luong-Van D. M. , Ma Jun , Moore A. M. , Pennypacker C. R. , Qin Weijia , Shang Zhaohui , Storey J. W. V. , Sun Bo , Travouillon T. , Walker C. K. , Wang Jiali , Wang Lifan , Wu Jianghua , Wu Zhenyu , Xia Lirong , Yan Jun , Yang Ji , Yang Huigen , Yao Yongqiang , Yuan Xiangyan , York D. G. , Zhang Zhanhai , Zhu Zhenxi 
Published: July 2010

ABSTRACT
The i-band observing conditions at Dome A on the Antarctic plateau have been investigated using data acquired during 2008 with the Chinese Small Telescope Array. The sky brightness, variations in atmospheric transparency, cloud cover, and the presence of aurorae are obtained from these images. The median sky brightness of moonless clear nights is 20.5 mag arcsec−2 in the SDSS i band at the south celestial pole (which includes a contribution of about 0.06 mag from diffuse Galactic light). The median over all Moon phases in the Antarctic winter is about 19.8 mag arcsec−2. There were no thick clouds in 2008. We model contributions of the Sun and the Moon to the sky background to obtain the relationship between the sky brightness and transparency. Aurorae are identified by comparing the observed sky brightness to the sky brightness expected from this model. About 2% of the images are affected by relatively strong aurorae.
DEPENDENCE OF THE TURBULENT VELOCITY FIELD ON GAS DENSITY IN L1551
Authors: Yoshida Atsushi , Kitamura Yoshimi , Shimajiri Yoshito , Kawabe Ryohei 
Published: July 2010

ABSTRACT
We have carried out mapping observations of the entire L1551 molecular cloud with about 2 pc × 2 pc size in the 12CO(1–0) line with the Nobeyama 45 m radio telescope at the high effective resolution of 22″ (corresponding to 0.017 pc at the distance of 160 pc), and analyzed the 12CO data together with the 13CO(1–0) and C18O(1–0) data from the Nobeyama Radio Observatory database. We derived the new non-thermal line width–size relations, σNT ∝ L
γ, for the three molecular lines, corrected for the effect of optical depth and the line-of-sight integration. To investigate the characteristic of the intrinsic turbulence, the effects of the outflows were removed. The derived relations are (σNT/km s−1) = (0.18 ± 0.010)(L/pc)0.45 ± 0.095, (0.20 ± 0.020)(L/pc)0.48 ± 0.091, and (0.22 ± 0.050) (L/pc)0.54 ± 0.21 for the 12CO, 13CO, and C18O lines, respectively, suggesting that the line width–size relation of the turbulence very weakly depends on our observed molecular lines, i.e., the relation does not change between the density ranges of 102–103 and 103–104 cm−3. In addition, the relations indicate that incompressible turbulence is dominant at the scales smaller than 0.6 pc in L1551. The power spectrum indices converted from the relations, however, seem to be larger than that of the Kolmogorov spectrum for incompressible flow. The disagreement could be explained by the anisotropy in the turbulent velocity field in L1551, as expected in MHD turbulence. Actually, the autocorrelation functions of the centroid velocity fluctuations show larger correlation along the direction of the magnetic field measured for the whole Taurus cloud, which is consistent with the results of numerical simulations for incompressible MHD flow.
Analyzing taxonomic classification using extensible Markov models
Authors: Kotamarti Rao M. , Hahsler Michael , Raiford Douglas , McGee Monnie , Dunham Margaret H. 
Published: July 2010

Abstract
Motivation: As next generation sequencing is rapidly adding new genomes, their correct placement in the taxonomy needs verification. However, the current methods for confirming classification of a taxon or suggesting revision for a potential misplacement relies on computationally intense multi-sequence alignment followed by an iterative adjustment of the distance matrix. Due to intra-heterogeneity issues with the 16S rRNA marker, no classifier is available for sub-genus level, which could readily suggest a classification for a novel 16S rRNA sequence. Metagenomics further complicates the issue by generating fragmented 16S rRNA sequences. This article proposes a novel alignment-free method for representing the microbial profiles using extensible Markov models (EMMs) with an extended Karlin–Altschul statistical framework similar to the classic alignment paradigm. We propose a log odds (LODs) score classifier based on Gumbel difference distribution that confirms correct classifications with statistical significance qualifications and suggests revisions where necessary.
Results: We tested our method by generating a sub-genus level classifier with which we re-evaluated classifications of 676 microbial organisms using the NCBI FTP database for the 16S rRNA. The results confirm current classification for all genera while ascertaining significance at 95%. Furthermore, this novel classifier isolates heterogeneity issues to a mere 12 strains while confirming classifications with significance qualification for the remaining 98%. The models require less memory than that needed by multi-sequence alignments and have better time complexity than the current methods. The classifier operates at sub-genus level, and thus outperforms the naive Bayes classifier of the RNA Database Project where much of the taxonomic analysis is available online. Finally, using information redundancy in model building, we show that the method applies to metagenomic fragment classification of 19 Escherichia coli strains.
Availability and implementation: Source code and binaries freely available for download at http://lyle.smu.edu/IDA/EMMSA/, implemented in JAVA and supported on MS Windows.
Contact: mallik@kotamarti.com; mhd@lyle.smu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Dealing with sparse data in predicting outcomes of HIV combination therapies
Authors: Bogojeska Jasmina , Bickel Steffen , Altmann André , Lengauer Thomas 
Published: July 2010

Abstract
Motivation: As there exists no cure or vaccine for the infection with human immunodeficiency virus (HIV), the standard approach to treating HIV patients is to repeatedly administer different combinations of several antiretroviral drugs. Because of the large number of possible drug combinations, manually finding a successful regimen becomes practically impossible. This presents a major challenge for HIV treatment. The application of machine learning methods for predicting virological responses to potential therapies is a possible approach to solving this problem. However, due to evolving trends in treating HIV patients the available clinical datasets have a highly unbalanced representation, which might negatively affect the usefulness of derived statistical models.
Results: This article presents an approach that tackles the problem of predicting virological response to combination therapies by learning a separate logistic regression model for each therapy. The models are fitted by using not only the data from the target therapy but also the information from similar therapies. For this purpose, we introduce and evaluate two different measures of therapy similarity. The models are also able to incorporate phenotypic knowledge on the therapy outcomes through a Gaussian prior. With our approach we balance the uneven therapy representation in the datasets and produce higher quality models for therapies with very few training samples. According to the results from the computational experiments our therapy similarity model performs significantly better than training separate models for each therapy by using solely their examples. Furthermore, the model's performance is as good as an approach that encodes therapy information in the input feature space with the advantage of delivering better results for therapies with very few training samples.
Availability: Code of the efficient logistic regression is available from http://www.mpi-inf.mpg.de/%7Ejasmina/fastLogistic.zip
Contact: jasmina@mpi-inf.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
iAlign: a method for the structural comparison of protein–protein interfaces
Authors: Gao Mu , Skolnick Jeffrey 
Published: July 2010

Abstract
Motivation: Protein–protein interactions play an essential role in many cellular processes. The rapid accumulation of protein–protein complex structures provides an unprecedented opportunity for comparative studies of protein–protein interactions. To facilitate such studies, it is necessary to develop an accurate and efficient computational algorithm for the comparison of protein–protein interaction modes. While there are many structural comparison approaches developed for individual proteins, very few methods are available for protein–protein complexes.
Results: We present a novel interface alignment method, iAlign, for the structural alignment of protein–protein interfaces. New scoring schemes for measuring interface similarity are introduced, and an iterative dynamic programming algorithm is implemented. We find that the similarity scores follow extreme value distributions. Using statistical models, we empirically estimate their statistical significance, which is in good agreement with manual classifications by human experts. Large-scale tests of iAlign were conducted on both artificial docking models and experimental structures. In a benchmark test on 1517 dimers, iAlign successfully detects biologically related, structurally similar protein–protein interfaces at a coverage percentage of 90% and an error per query of 0.05. When compared against previously published methods, iAlign is substantially more accurate and efficient.
Availability: The iAlign software package is freely available at http://cssb.biology.gatech.edu/iAlign
Contact: skolnick@gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem
Authors: Geraci Filippo 
Published: July 2010

Abstract
Motivation: Single nucleotide polymorphisms are the most common form of variation in human DNA, and are involved in many research fields, from molecular biology to medical therapy. The technological opportunity to deal with long DNA sequences using shotgun sequencing has raised the problem of fragment recombination. In this regard, Single Individual Haplotyping (SIH) problem has received considerable attention over the past few years.
Results: In this article, we survey seven recent approaches to the SIH problem and evaluate them extensively using real human haplotype data from the HapMap project. We also implemented a data generator tailored to the current shotgun sequencing technology that uses haplotypes from the HapMap project.
Availability: The data we used to compare the algorithms are available on demand, since we think they represent an important benchmark that can be used to easily compare novel algorithmic ideas with the state of the art. Moreover, we had to re-implement six of the algorithms surveyed because the original code was not available to us. Five of these algorithms and the data generator used in this article endowed with a Web interface are available at http://bioalgo.iit.cnr.it/rehap
Contact: filippo.geraci@iit.cnr.it
genoPlotR: comparative gene and genome visualization in R
Authors: Guy Lionel , Roat Kultima Jens , Andersson Siv G. E. 
Published: July 2010

Abstract
Summary: The amount of gene and genome data obtained by next-generation sequencing technologies generates a need for comparative visualization tools. Complementing existing software for comparison and exploration of genomics data, genoPlotR automatically creates publication-grade linear maps of gene and genomes, in a highly automatic, flexible and reproducible way.
Availability: genoPlotR is a platform-independent R package, available with full source code under a GPL2 license at R-Forge: http://genoplotr.r-forge.r-project.org/
Contact: lionel.guy@ebc.uu.se
Interactive and fuzzy search: a dynamic way to explore MEDLINE
Authors: Wang Jiannan , Cetindil Inci , Ji Shengyue , Li Chen , Xie Xiaohui , Li Guoliang , Feng Jianhua 
Published: July 2010

Abstract
Motivation: The MEDLINE database, consisting of over 19 million publication records, is the primary source of information for biomedicine and health questions. Although the database itself has been growing rapidly, the search paradigm of MEDLINE has remained largely unchanged.
Results: Here, we propose a new system for exploring the entire MEDLINE collection, represented by two unique features: (i) interactive: providing instant feedback to users' query letter by letter, and (ii) fuzzy: allowing approximate search. We develop novel index structures and search algorithms to make such a search model possible. We also develop incremental-update techniques to keep the data up to date.
Availability: Interactive and fuzzy searching algorithms for exploring MEDLINE are implemented in a system called iPubMed, freely accessible over the web at http://ipubmed.ics.uci.edu/ and http://tastier.cs.tsinghua.edu.cn/ipubmed/
Contact: chenli@ics.uci.edu; xhx@ics.uci.edu
Successful Reproduction Requires the Function of Arabidopsis YELLOW STRIPE-LIKE1 and YELLOW STRIPE-LIKE3 Metal-Nicotianamine Transporters in Both Vegetative and Reproductive Structures
Authors: Chu Heng-Hsuan , Chiecko Jeff , Punshon Tracy , Lanzirotti Antonio , Lahner Brett , Salt David E. , Walker Elsbeth L. 
Published: July 2010

Abstract
Several members of the Yellow Stripe-Like (YSL) family of proteins are transporters of metals that are bound to the metal chelator nicotianamine or the related set of mugineic acid family chelators known as phytosiderophores. Here, we examine the physiological functions of three closely related Arabidopsis (Arabidopsis thaliana) YSL family members, AtYSL1, AtYSL2, and AtYSL3, to elucidate their role(s) in the allocation of metals into various organs of Arabidopsis. We show that AtYSL3 and AtYSL1 are localized to the plasma membrane and function as iron transporters in yeast functional complementation assays. By using inflorescence grafting, we show that AtYSL1 and AtYSL3 have dual roles in reproduction: their activity in the leaves is required for normal fertility and normal seed development, while activity in the inflorescences themselves is required for proper loading of metals into the seeds. We further demonstrate that the AtYSL1 and AtYSL2 proteins, when expressed from the AtYSL3 promoter, can only partially rescue the phenotypes of a ysl1ysl3 double mutant, suggesting that although these three YSL transporters are closely related and have similar patterns of expression, they have distinct activities in planta. In particular, neither AtYSL1 nor AtYSL2 is able to functionally complement the reproductive defects exhibited by ysl1ysl3 double mutant plants.
Plant Immunity Directly or Indirectly Restricts the Injection of Type III Effectors by the Pseudomonas syringae Type III Secretion System
Authors: Crabill Emerson , Joe Anna , Block Anna , van Rooyen Jennifer M. , Alfano James R. 
Published: July 2010

Abstract
Plants perceive microorganisms by recognizing microbial molecules known as pathogen-associated molecular patterns (PAMPs) inducing PAMP-triggered immunity (PTI) or by recognizing pathogen effectors inducing effector-triggered immunity (ETI). The hypersensitive response (HR), a programmed cell death response associated with ETI, is known to be inhibited by PTI. Here, we show that PTI-induced HR inhibition is due to direct or indirect restriction of the type III protein secretion system's (T3SS) ability to inject type III effectors (T3Es). We found that the Pseudomonas syringae T3SS was restricted in its ability to inject a T3E-adenylate cyclase (CyaA) injection reporter into PTI-induced tobacco (Nicotiana tabacum) cells. We confirmed this restriction with a direct injection assay that monitored the in planta processing of the AvrRpt2 T3E. Virulent P. syringae strains were able to overcome a PAMP pretreatment in tobacco or Arabidopsis (Arabidopsis thaliana) and continue to inject a T3E-CyaA reporter into host cells. In contrast, ETI-inducing P. syringae strains were unable to overcome PTI-induced injection restriction. A P. syringae pv tomato DC3000 mutant lacking about one-third of its T3E inventory was less capable of injecting into PTI-induced Arabidopsis plant cells, grew poorly in planta, and did not cause disease symptoms. PTI-induced transgenic Arabidopsis expressing the T3E HopAO1 or HopF2 allowed higher amounts of the T3E-CyaA reporter to be injected into plant cells compared to wild-type plants. Our results show that PTI-induced HR inhibition is due to direct or indirect restriction of T3E injection and that T3Es can relieve this restriction by suppressing PTI.
Homomeric Interaction of AtVSR1 Is Essential for Its Function as a Vacuolar Sorting Receptor
Authors: Kim Hyeran , Kang Hyangju , Jang Mihue , Chang Jeong Ho , Miao Yansong , Jiang Liwen , Hwang Inhwan 
Published: July 2010

Abstract
Vacuolar sorting receptors, BP80/VSRs, play a critical role in vacuolar trafficking of soluble proteins in plant cells. However, the mechanism of action of BP80 is not well understood. Here, we investigate the action mechanism of AtVSR1, a member of BP80 proteins in Arabidopsis (Arabidopsis thaliana), in vacuolar trafficking. AtVSR1 exists as multiple forms, including a high molecular mass homomeric complex in vivo. Both the transmembrane and carboxyl-terminal cytoplasmic domains of AtVSR1 are necessary for the homomeric interaction. The carboxyl-terminal cytoplasmic domain contains specific sequence information, whereas the transmembrane domain has a structural role in the homomeric interaction. In protoplasts, an AtVSR1 mutant, C2A, that contained alanine substitution of the region involved in the homomeric interaction, was defective in trafficking to the prevacuolar compartment and localized primarily to the trans-Golgi network. In addition, overexpression of C2A, but not wild-type AtVSR1, inhibited trafficking of soluble proteins to the vacuole and caused their secretion into the medium. Furthermore, C2A:hemagglutinin in transgenic plants interfered with the homomeric interaction of endogenous AtVSR1 and inhibited vacuolar trafficking of sporamin:green fluorescent protein. These data suggest that homomeric interaction of AtVSR1 is critical for its function as a vacuolar sorting receptor.