bluuebunny/crossref_metadata_2025_split huggingface dataset:
The mucosal response of hamsters to a low-intensity superimposed secondary infection with the hookworm Ancylostoma ceylanicum
Authors: Alkazmi L.M.M. , Behnke J.M. 
Published: April 2010

AbstractAn experiment was conducted to assess the mucosal response to low-dose superimposed challenge with Ancylostoma ceylanicum. Hamsters were assigned to five treatment groups (1–5 respectively): naïve controls; primary immunizing infection controls; challenge controls; immunized, anthelmintic–treated, challenged group; immunized, superimposed challenge group. Group 4 hamsters were resistant to challenge, whereas most of the challenge inoculum larvae established in Group 5. Villus height and crypt depth measurements were initially markedly divergent between these two groups but over time post-challenge (pc) values for both parameters drew nearer and by day 31 pc they were indistinguishable. The greatest change was experienced by Group 4 which showed increasing inflammation and gut pathology during the challenge infection. Mitotic activity in crypts and mast cell counts in the mucosa were highest in Group 5 on day 10 pc, but there was little to distinguish between Groups 4 and 5 by day 31 pc. Goblet cell, eosinophil and Paneth cell counts were very similar throughout in both groups but, in the case of Paneth cells, they were consistent with a possible role in protective immunity to challenge. Some adult worms survived throughout the period of intense inflammation, emphasizing their tremendous resilience and resistance to mucosal host protective responses.
Stroke medicine for the geriatrician 2010
Authors: Keir SL , Strachan K 
Published: April 2010

SummaryThis review explores the recent advances in investigation and treatment of acute stroke, as well as its secondary prevention, with emphasis on the relevance of the evidence for the older population. Hyperacute reperfusion treatment is becoming increasingly embedded into the day-to-day management of stroke and trials are ongoing that will help determine its safety in the older patient. Managing all stroke patients in a stroke unit is known to improve outcome and recent work has helped to inform care decisions. Application of the robust data available on secondary prevention treatments may have to be weighed alongside the degree of frailty of the patient for whom treatment is being considered.
Research on ageing and longevity in Estonia
Authors: Tamm Riin , Saks Kai , Pääsuke Mati 
Published: April 2010

SummaryDue to demographic changes, the population ageing process in Estonia accelerated rapidly at the end of the 20th century. In Estonia, research in gerontology and geriatrics has no long-standing tradition. In the beginning, social aspects like the pension system, coping strategies and well-being of aged people, were the research focus. More recently, epidemiological studies of diseases seen in the older population have been extensively conducted. In clinical medicine, the main research topics have been osteoporosis, Parkinson's disease, dementia and stroke.In this review, changes in neuromuscular function and hormonal regulation during ageing, and the genetic aspects of the Estonian Longevity Study will be described. The aim of the current paper is to introduce the main fields of gerontological research in Estonia to allow better integration with other research groups.
GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
Authors: He Zhili , Deng Ye , Van Nostrand Joy D , Tu Qichao , Xu Meiying , Hemme Christopher L , Li Xingyuan , Wu Liyou , Gentry Terry J , Yin Yifeng , Liebich Jost , Hazen Terry C , Zhou Jizhong 
Published: April 2010

Abstract
A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with ∼28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036–0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.
Effectiveness of Alcohol-Based Hand Rubs for Removal ofClostridium difficileSpores from Hands
Authors: Jabbar Umair , Leischner Julie , Kasper Douglas , Gerber Robert , Sambol Susan P. , Parada Jorge P. , Johnson Stuart , Gerding Dale N. 
Published: April 2010

Background.Alcohol-based hand rubs (ABHRs) are an effective means of decreasing the transmission of bacterial pathogens. Alcohol is not effective againstClostridium difficilespores. We examined the retention ofC. difficilespores on the hands of volunteers after ABHR use and the subsequent transfer of these spores through physical contact.Methods.NontoxigenicC. difficilespores were spread on the bare palms of 10 volunteers. Use of 3 ABHRs and chlorhexidine soap-and-water washing were compared with plain water rubbing alone for removal ofC. difficilespores. Palmar cultures were performed before and after hand decontamination by means of a plate stamping method. Transferability ofC. difficileafter application of ABHR was tested by having each volunteer shake hands with an uninoculated volunteer.Results.Plain water rubbing reduced palmar culture counts by a mean (± standard deviation [SD]) of 1.57 ± 0.11 log10colony-forming units (CFU) per cm2, and this value was set as the zero point for the other products. Compared with water washing, chlorhexidine soap washing reduced spore counts by a mean ( ± SD) of 0.89 ± 0.34 log10CFU per cm2; among the ABHRs, Isagel accounted for a reduction of 0.11 ± 0.20 log10CFU per cm2(P= .005), Endure for a reduction of 0.37 ± 0.42 log10CFU per cm2(P= .010), and Purell for a reduction of 0.14 ± 0.33 log10CFU per cm2(P= .005). There were no statistically significant differences between the reductions achieved by the ABHRs; only Endure had a reduction statistically different from that for water control rubbing (P= .040). After ABHR use, handshaking transferred a mean of 30% of the residualC. difficilespores to the hands of recipients.Conclusions.Hand washing with soap and water is significantly more effective at removingC. difficilespores from the hands of volunteers than are ABHRs. Residual spores are readily transferred by a handshake after use of ABHR.
Parallelization of the MAFFT multiple sequence alignment program
Authors: Katoh Kazutaka , Toh Hiroyuki 
Published: April 2010

Abstract
Summary: Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key technique for reducing the time required for large-scale sequence analyses. The three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the MAFFT MSA program were parallelized using the POSIX Threads library. Two natural parallelization strategies (best-first and simple hill-climbing) were implemented for the iterative refinement stage. Based on comparisons of the objective scores and benchmark scores between the two approaches, we selected a simple hill-climbing approach as the default.
Availability: The parallelized version of MAFFT is available at http://mafft.cbrc.jp/alignment/software/. This version currently supports the Linux operating system only.
Contact: kazutaka.katoh@aist.go.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Semantic integration of data on transcriptional regulation
Authors: Baitaluk Michael , Ponomarenko Julia 
Published: April 2010

Abstract
Motivation: Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources. However, there are no resources to integrate these data automatically or to provide a ‘one-stop shop’ experience for users seeking information essential for deciphering and modeling gene regulatory networks.
Results: IntegromeDB, a semantic graph-based ‘deep-web’ data integration system that automatically captures, integrates and manages publicly available data concerning transcriptional regulation, as well as other relevant biological information, is proposed in this article. The problems associated with data integration are addressed by ontology-driven data mapping, multiple data annotation and heterogeneous data querying, also enabling integration of the user's data. IntegromeDB integrates over 100 experimental and computational data sources relating to genomics, transcriptomics, genetics, and functional and interaction data concerning gene transcriptional regulation in eukaryotes and prokaryotes.
Availability: IntegromeDB is accessible through the integrated research environment BiologicalNetworks at http://www.BiologicalNetworks.org
Contact: baitaluk@sdsc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Modeling RNA loops using sequence homology and geometric constraints
Authors: Schudoma Christian , May Patrick , Walther Dirk 
Published: April 2010

Abstract
Summary: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface.
Availability and Implementation: The application was implemented in Python, MySQL and Apache. A web interface to the database and loop modeling application is freely available at http://rloom.mpimp-golm.mpg.de
Contact: schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de
Bone marrow dysfunction in chronic heart failure patients
Authors: Westenbrink B. Daan , Voors Adriaan A. , de Boer Rudolf A. , Schuringa Jan J. , Klinkenberg Theo , van der Harst Pim , Vellenga Edo , van Veldhuisen Dirk J. , van Gilst Wiek H. 
Published: April 2010

AimsTo investigate whether chronic heart failure (CHF) is associated with a general dysfunction of the haematopoietic compartment.Methods and resultsBone marrow was obtained during coronary artery bypass graft surgery from 20 patients with CHF (age 67 ± 6 years, 75% NYHA class ≥ III, LVEF 32 ± 6%), and 20 age‐ and gender‐matched control patients with normal cardiac function. CD34+ haematopoietic progenitor cells were isolated and cultured with increasing doses of erythropoietin (0.02–10 IU/mL, EPO), myeloid growth factors or a mix of both. After 14 days, burst forming units erythroid (BFU‐E), and granulocyte or monocyte colony forming units (CFU‐G, CFU‐M, respectively) were counted. Apoptosis and erythropoietin‐receptor (EPO‐R) density were quantified by flow cytometry. Throughout the EPO dose range, the CD34+ cells from CHF patients produced a two‐fold lower number of BFU‐E colonies compared with controls (P = 0.02). The resistance to EPO was associated with markedly increased apoptosis during erythroid differentiation in CHF patients compared with controls [5.3% (2.9–8.1%) vs. 1.5% (0.8–3.4%), P = 0.01]. Erythropoietin‐receptor expression was, however, comparable between CHF patients and controls and the anti‐apoptotic cytokine interleukin‐3 did not rescue erythropoiesis. In the myeloid cultures, the number of CFU‐G and CFU‐M colonies was also two‐fold lower in CHF patients compared with controls (both P < 0.01). In the mixed‐culture assay, myelopoiesis and erythropoiesis were reduced to a similar magnitude in CHF patients. The impaired clonogenic potential was independently associated with clinical and biochemical severity of CHF, but not with the presence of anaemia.ConclusionChronic heart failure is associated with profound and general bone marrow dysfunction, simultaneously affecting multiple haematopoietic lineages.
Differences between karyotypically normal and abnormal human embryonic stem cells
Authors: Yang S. , Lin G. , Tan Y.‐Q. , Deng L.‐Y. , Yuan D. , Lu G.‐X. 
Published: April 2010

AbstractObjectives:  To compare different biological characteristics of human embryonic stem cells (HESCs) between those with normal and those with abnormal karyotype.Materials and methods:  Culture‐adapted HESCs (chHES‐3) with abnormal karyotype were compared with karyotypically normal cells, with regard to pluripotency and differentiation capacity, ultrastructure, growth characteristics, gene expression profiles and signalling pathways.Results:  We found a new abnormal karyotype of HESCs. We observed that chHES‐3 cells with normal and abnormal karyotypes shared similarities in expression markers of pluripotency; however, karyotypically abnormal chHES‐3 cells had a tendency for differentiation towards ectoderm lineages and were easily maintained in suboptimal culturing conditions. Abnormal chHES‐3 cells displayed relatively mature cell organelles compared to normal cells, and karyotypically abnormal chHES‐3 cells had increased survival and population growth. Genes related to cell proliferation and apoptosis were up‐regulated, but genes associated with genetic instability (p53, Rb, BRCA1) were down‐regulated in the karyotypically abnormal cells.Conclusion:  Karyotypically abnormal chHES‐3 cells had a more developed capacity for proliferation, resistance to apoptosis and less genetic stability compared to normal chHES‐3 cells and may be an excellent model for studying and characterizing initial stages that determine transition of embryonic stem cells into cancer stem cells.
Global gene expression reveals a set of new genes involved in the modification of cells during erythroid differentiation
Authors: Da Cunha A. F. , Brugnerotto A. F. , Duarte A. S. , Lanaro C. , Costa G. G. L. , Saad S. T. O. , Costa F. F. 
Published: April 2010

AbstractObjectives:  Erythroid differentiation is a dynamic process in which a pluripotent stem cell undergoes a series of developmental changes that commit it to a specific lineage. These alterations involve changes in gene expression profiles. In this study, gene expression profiles during differentiation of human erythroid cells of a normal blood donor were evaluated using SAGE.Materials and methods:  Global gene expression was evaluated in cells collected immediately before addition of erythropoietin (0 h) and 192 and 336 h after addition of this hormone. Real‐time PCR was used to evaluate activation of differentially expressed genes.Results:  The data indicate that global aspects of the transcriptome were similar during differentiation of the majority of the genes and that a relatively small set of genes is probably involved in modification of erythroid cells during differentiation. We have identified 93 differentially expressed genes during erythroid development, and expression of some of these was confirmed by qPCR. Various genes including EYA3, ERH, HES6, TIMELESS and TRIB3 were found to be homologous to those of Drosophila melanogaster and here are described for the first time during erythroid development. An important and unique carboxypeptidase inhibitor described in mammalians, LXN, was also identified.Conclusions:  The results of this study amplify previously published data and may contribute to comprehension of erythroid differentiation and identification of new target genes involved in some erythroid concerning diseases.
Multiple benefits of cooperative breeding in purple‐crowned fairy‐wrens: a consequence of fidelity?
Authors: Kingma Sjouke A. , Hall Michelle L. , Arriero Elena , Peters Anne 
Published: April 2010

Summary1.Kin selection is one of the mechanisms that can explain apparent altruism by subordinate individuals in cooperatively breeding species, if subordinates boost the production of kin. We compared productivity and breeder survival in pairs with and without subordinates in a genetically monogamous cooperatively breeding bird, the purple‐crowned fairy‐wrenMalurus coronatus.2.Additive effects of subordinate help increased productivity. Total feeding rates to the nest were increased by two or more subordinates, and fledgling production was greater in larger groups. Not all subordinates contributed to nestling feeding, and the effect of group size was greater when non‐contributors were excluded from analyses, suggesting that increased fledgling production was a direct result of help.3.Compensatory effects of subordinate help improved breeder survival. Assisted breeders reduced their workload by 20–30%, irrespective of the number of helpers. Although re‐nesting intervals were not affected by group size, reduced breeder feeding rates resulted in improved survival and breeders in larger groups survived better.4.Subordinates and nestlings are usually progeny of the breeding pair in this species, and benefits of cooperative breeding are very different from three congeners with extremely high levels of extra‐group paternity (EGP). In theseMalurus, fledgling production and survival of male breeders are not enhanced in larger groups. This is consistent with the expectation that kin‐selected benefits vary with relatedness, and thus levels of EGP.5.We tested whether benefits of cooperative breeding in 37 avian species varied with levels of extra‐group mating. Both direct and phylogenetically controlled comparisons showed that improvement of (male) breeder survival and enhanced productivity are more likely when fidelity is higher, as predicted when investment of subordinates correlates with relatedness to offspring. This pattern highlights the importance of considering the genetic mating system for understanding the evolution of cooperative breeding.
Vitamin D deficiency and frailty in older Americans
Authors: Wilhelm‐Leen E. R. , Hall Y. N. , DeBoer I. H. , Chertow G. M. 
Published: April 2010

Abstract.  Wilhelm‐Leen ER, Hall YN, deBoer IH, Chertow GM. (Stanford University School of Medicine; University of Washington; Stanford University School of Medicine, Palo Alto, CA, USA). Vitamin D deficiency and frailty in older Americans. J Intern Med 2010; 268: 171–180.Objective.  To explore the relation between 25‐hydroxyvitamin D deficiency and frailty. Frailty is a multidimensional phenotype that describes declining physical function and a vulnerability to adverse outcomes in the setting of physical stress such as illness or hospitalization. Low serum concentrations of 25‐hydroxyvitamin D are known to be associated with multiple chronic diseases such as cardiovascular disease and diabetes, in addition to all cause mortality.Design.  Using data from the Third National Health and Nutrition Survey (NHANES III), we evaluated the association between low serum 25‐hydroxyvitamin D concentration and frailty, defined according to a set of criteria derived from a definition previously described and validated.Subjects.  Nationally representative survey of noninstitutionalized US residents collected between 1988 and 1994.Results.  25‐Hydroxyvitamin D deficiency, defined as a serum concentration <15 ng mL−1, was associated with a 3.7‐fold increase in the odds of frailty amongst whites and a fourfold increase in the odds of frailty amongst non‐whites. This association persisted after sensitivity analyses adjusting for season of the year and latitude of residence, intended to reduce misclassification of persons as 25‐hydroxyvitamin D deficient or insufficient.Conclusion.  Low serum 25‐hydroxyvitamin D concentrations are associated with frailty amongst older adults.
Biotic stress globally downregulates photosynthesis genes
Authors: BILGIN DAMLA D. , ZAVALA JORGE A. , ZHU JIN , CLOUGH STEVEN J. , ORT DONALD R. , DeLUCIA EVAN H. 
Published: April 2010

ABSTRACTTo determine if damage to foliage by biotic agents, including arthropods, fungi, bacteria and viral pathogens, universally downregulates the expression of genes involved in photosynthesis, we compared transcriptome data from microarray experiments after twenty two different forms of biotic damage on eight different plant species. Transcript levels of photosynthesis light reaction, carbon reduction cycle and pigment synthesis genes decreased regardless of the type of biotic attack. The corresponding upregulation of genes coding for the synthesis of jasmonic acid and those involved in the responses to salicylic acid and ethylene suggest that the downregulation of photosynthesis‐related genes was part of a defence response. Analysis of the sub‐cellular targeting of co‐expressed gene clusters revealed that the transcript levels of 84% of the genes that carry a chloroplast targeting peptide sequence decreased. The majority of these downregulated genes shared common regulatory elements, such as G‐box (CACGTG), T‐box (ACTTTG) and SORLIP (GCCAC) motifs. Strong convergence in the response of transcription suggests that the universal downregulation of photosynthesis‐related gene expression is an adaptive response to biotic attack. We hypothesize that slow turnover of many photosynthetic proteins allows plants to invest resources in immediate defence needs without debilitating near term losses in photosynthetic capacity.
Passive Acquisition of Protective Antibodies Reactive with Bordetella pertussis in Newborns via Placental Transfer and Breast‐feeding
Authors: Quinello C. , Quintilio W. , Carneiro‐Sampaio M. , Palmeira P. 
Published: April 2010

AbstractAlthough acquisition of anti‐pertussis antibodies by the newborn via placental transfer has been demonstrated, a subsequent recrudescence of pertussis infection is often observed, particularly in infants. The present study investigated the passive transfer of anti‐pertussis IgG and IgA antibodies to term newborns and their ability to neutralize bacterial pathogenicity in an in vivo experimental model using mice intracerebrally challenged with viable Bordetella pertussis. Forty paired samples of maternal/umbilical cord sera and colostrum were obtained. Anti‐pertussis antibodies were analysed by immunoenzymatic assay and by Immunoblotting. Antibody neutralizing ability was assessed through intracerebral B. pertussis challenges in mice. Anti‐pertussis IgG titres were equivalent in both maternal and newborn sera (medians = 1:225 and 1:265), with a transfer rate of 118%. The colostrum samples had variable specific IgA titres (median = 1:74). The immunoblotting assays demonstrated identical recognition profiles of paired maternal and newborn serum pools but different bacterial recognition intensities by colostrum pools. In the animal model, significant differences were always observed when the serum and colostrum samples and pools were compared with the positive control (P < 0.05). Unlike samples with lower anti‐pertussis titres, samples with high titres showed protective capacities above 50%. Pertussis‐absorbed serum and colostrum pools protected 30% of mice and purified IgG antibodies protected 65%. Both pooled and single‐sample protective abilities were correlated with antibody titres (P < 0.01). Our data demonstrated the effectiveness of anti‐pertussis antibodies in bacterial pathogenesis neutralization, emphasizing the importance of placental transfer and breast‐feeding in protecting infants against respiratory infections caused by Bordetella pertussis.