bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel approach in leather finishing: Surface modification with flock fibers
Authors: Basaran Bahri , Yorgancioglu Ali , Onem Ersin 
Published: June 2012

In recent years, finishing has begun introducing an extraordinary touch and appearance to the surface of leathers by surface modification. Because some superficial anomalies cannot be recovered by conventional finishing procedures, those can only be drawn on by coating techniques. Coating aims at obtaining an alluring product, which must both recover the surface anomalies and be compatible with the leather characteristics. This study is for valorization of leathers with inferior quality, which contain surface defects, thereby being aimed at improvement of the surface characteristics. The product should have ease of use, as well as giving a fashionable look and touch to flocked fibrous surfaces, whether applied to synthetic leather types or Alcantara. For covered and patterned fibrous surfaces, the experimentations of different flock formulations with different binder types were executed, superficial characteristics were imaged with optoanalytical techniques and the fiber adhesion onto the surface was examined by abrasion tests. The research results showed that polyurethane binder had acceptable qualities for bags, footwear, garments and accessories and yielded superior binding characteristics compared to acrylic binder.
Older Adults’ Driving Reduction and Cessation
Authors: Connell Cathleen M , Harmon Annie , Janevic Mary R. , Kostyniuk Lidia P. 
Published: June 2012

Purpose of the Study. Adult children are often directly affected by aging parents’ decision to limit or stop driving. This qualitative study examined the process of driving reduction and cessation (DRC) from the perspective of adult children, with a focus on family communication. Design and Methods. Four focus group interviews were conducted with 37 adult children (29/37 female; mean age = 45.5) of older parents using a structured protocol. Transcripts were analyzed by two independent coders to identify major themes. Results. Themes represented three aspects of the DRC process: family communication and dynamics (i.e., discussion, negotiation, and planning; avoidance and side stepping; resignation and refusal), taking action to end a parent’s driving career (i.e., engaging a third party; taking away the car), and post-cessation reflection (i.e., relief; social benefits; resentment and guilt). Implications. Despite the potential benefits of planning for DRC, families are unsure about how best to approach this topic. Adult children worry about assuming responsibility for their parents’ transportation needs and their parents’ reactions to restricted mobility. Despite a reluctance to communicate openly about DRC, adult children and their parents share similar and significant concerns that merit increased attention.
Clinical Evidence of Early Acute Lung Injury Often Precedes the Diagnosis of ALI
Authors: Rackley Craig R. , Levitt Joseph E. , Zhuo Hanjing , Matthay Michael A. , Calfee Carolyn S. 
Published: June 2012

Background: Acute lung injury (ALI) has been primarily defined in patients who require positive pressure ventilation. As a result, the clinical characteristics of patients with early ALI (EALI) prior to the need for mechanical ventilation have not been well characterized. Early identification of patients with ALI and the impending need for positive pressure ventilation could define a study population for trials of novel therapies. Methods: We analyzed clinical data from 93 patients at 12, 24, and 48 hours prior to the standard diagnosis of ALI. The time of ALI diagnosis was defined when patients were mechanically ventilated and met the 1994 American–European Consensus Conference diagnostic criteria for ALI. Results: The majority of patients with ALI presented to the hospital more than 24 hours prior to developing ALI. Specifically, 73% presented more than 12 hours prior to diagnosis, and 57% presented more than 24 hours prior to diagnosis. Of patients hospitalized for at least 12 hours prior to ALI diagnosis, 94% had either bilateral infiltrates on chest radiograph, tachypnea, or an oxygen requirement greater than 2 L/min; 79% and 48% had 2 and 3 of these abnormalities, respectively. Conclusion: The majority of hospitalized patients who are destined to develop ALI demonstrate tachypnea, increased oxygen requirements, and/or bilateral infiltrates on chest radiograph more than 12 hours prior to meeting criteria for diagnosis. Some patients with EALI may be identified prior to meeting diagnostic criteria during a potential therapeutic window.
How I treat immune thrombocytopenia: the choice between splenectomy or a medical therapy as a second-line treatment
Authors: Ghanima Waleed , Godeau Bertrand , Cines Douglas B. , Bussel James B. 
Published: June 2012

Abstract
The paradigm for managing primary immune thrombocytopenia (ITP) in adults has changed with the advent of rituximab and thrombopoietin receptor agonists (TPO-RAs) as options for second-line therapy. Splenectomy continues to provide the highest cure rate (60%-70% at 5+ years). Nonetheless, splenectomy is invasive, irreversible, associated with postoperative complications, and its outcome is currently unpredictable, leading some physicians and patients toward postponement and use of alternative approaches. An important predicament is the lack of studies comparing second-line options to splenectomy and to each other. Furthermore, some adults will improve spontaneously within 1-2 years. Rituximab has been given to more than 1 million patients worldwide, is generally well tolerated, and its short-term toxicity is acceptable. In adults with ITP, 40% of patients are complete responders at one year and 20% remain responders at 3-5 years. Newer approaches to using rituximab are under study. TPO-RAs induce platelet counts > 50 000/μL in 60%-90% of adults with ITP, are well-tolerated, and show relatively little short-term toxicity. The fraction of TPO-RA–treated patients who will be treatment-free after 12-24 months of therapy is unknown but likely to be low. As each approach has advantages and disadvantages, treatment needs to be individualized, and patient participation in decision-making is paramount.
Stress hematopoiesis reveals abnormal control of self-renewal, lineage bias, and myeloid differentiation in Mll partial tandem duplication (Mll-PTD) hematopoietic stem/progenitor cells
Authors: Zhang Yue , Yan Xiaomei , Sashida Goro , Zhao Xinghui , Rao Yalan , Goyama Susumu , Whitman Susan P. , Zorko Nicholas , Bernot Kelsie , Conway Rajeana M. , Witte David , Wang Qian-fei , Tenen Daniel G. , Xiao Zhijian , Marcucci Guido , Mulloy James C. , Grimes H. Leighton , Caligiuri Michael A. , Huang Gang 
Published: June 2012

Abstract
One mechanism for disrupting the MLL gene in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) is through partial tandem duplication (MLL-PTD); however, the mechanism by which MLL-PTD contributes to MDS and AML development and maintenance is currently unknown. Herein, we investigated hematopoietic stem/progenitor cell (HSPC) phenotypes of Mll-PTD knock-in mice. Although HSPCs (Lin−Sca1+Kit+ (LSK)/SLAM+ and LSK) in MllPTD/WT mice are reduced in absolute number in steady state because of increased apoptosis, they have a proliferative advantage in colony replating assays, CFU-spleen assays, and competitive transplantation assays over wild-type HSPCs. The MllPTD/WT-derived phenotypic short-term (ST)–HSCs/multipotent progenitors and granulocyte/macrophage progenitors have self-renewal capability, rescuing hematopoiesis by giving rise to long-term repopulating cells in recipient mice with an unexpected myeloid differentiation blockade and lymphoid-lineage bias. However, MllPTD/WT HSPCs never develop leukemia in primary or recipient mice, suggesting that additional genetic and/or epigenetic defects are necessary for full leukemogenic transformation. Thus, the Mll-PTD aberrantly alters HSPCs, enhances self-renewal, causes lineage bias, and blocks myeloid differentiation. These findings provide a framework by which we can ascertain the underlying pathogenic role of MLL-PTD in the clonal evolution of human leukemia, which should facilitate improved therapies and patient outcomes.
Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales
Authors: Andam Cheryl P , Harlow Timothy J , Papke R Thane , Gogarten J Peter 
Published: June 2012

AbstractBackgroundHorizontal gene transfer (HGT) has greatly impacted the genealogical history of many lineages, particularly for prokaryotes, with genes frequently moving in and out of a line of descent. Many genes that were acquired by a lineage in the past likely originated from ancestral relatives that have since gone extinct. During the course of evolution, HGT has played an essential role in the origin and dissemination of genetic and metabolic novelty.ResultsThree divergent forms of leucyl-tRNA synthetase (LeuRS) exist in the archaeal order Halobacteriales, commonly known as haloarchaea. Few haloarchaeal genomes have the typical archaeal form of this enzyme and phylogenetic analysis indicates it clusters within the Euryarchaeota as expected. The majority of sequenced halobacterial genomes possess a bacterial form of LeuRS. Phylogenetic reconstruction puts this larger group of haloarchaea at the base of the bacterial domain. The most parsimonious explanation is that an ancient transfer of LeuRS took place from an organism related to the ancestor of the bacterial domain to the haloarchaea. The bacterial form of LeuRS further underwent gene duplications and/or gene transfers within the haloarchaea, with some genomes possessing two distinct types of bacterial LeuRS. The cognate tRNALeualso reveals two distinct clusters for the haloarchaea; however, these tRNALeuclusters do not coincide with the groupings found in the LeuRS tree, revealing that LeuRS evolved independently of its cognate tRNA.ConclusionsThe study of leucyl-tRNA synthetase in haloarchaea illustrates the importance of gene transfer originating in lineages that went extinct since the transfer occurred. The haloarchaeal LeuRS and tRNALeudid not co-evolve.
Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort
Authors: Valsesia Armand , Stevenson Brian J , Waterworth Dawn , Mooser Vincent , Vollenweider Peter , Waeber Gérard , Jongeneel C Victor , Beckmann Jacques S , Kutalik Zoltán , Bergmann Sven 
Published: June 2012

Abstract

Background
Genotypes obtained with commercial SNP arrays have been extensively used in many large case-control or population-based cohorts for SNP-based genome-wide association studies for a multitude of traits. Yet, these genotypes capture only a small fraction of the variance of the studied traits. Genomic structural variants (GSV) such as Copy Number Variation (CNV) may account for part of the missing heritability, but their comprehensive detection requires either next-generation arrays or sequencing. Sophisticated algorithms that infer CNVs by combining the intensities from SNP-probes for the two alleles can already be used to extract a partial view of such GSV from existing data sets.

Results
Here we present several advances to facilitate the latter approach. First, we introduce a novel CNV detection method based on a Gaussian Mixture Model. Second, we propose a new algorithm, PCA merge, for combining copy-number profiles from many individuals into consensus regions. We applied both our new methods as well as existing ones to data from 5612 individuals from the CoLaus study who were genotyped on Affymetrix 500K arrays. We developed a number of procedures in order to evaluate the performance of the different methods. This includes comparison with previously published CNVs as well as using a replication sample of 239 individuals, genotyped with Illumina 550K arrays. We also established a new evaluation procedure that employs the fact that related individuals are expected to share their CNVs more frequently than randomly selected individuals. The ability to detect both rare and common CNVs provides a valuable resource that will facilitate association studies exploring potential phenotypic associations with CNVs.

Conclusion
Our new methodologies for CNV detection and their evaluation will help in extracting additional information from the large amount of SNP-genotyping data on various cohorts and use this to explore structural variants and their impact on complex traits.
An elm EST database for identifying leaf beetle egg-induced defense genes
Authors: Büchel Kerstin , McDowell Eric , Nelson Will , Descour Anne , Gershenzon Jonathan , Hilker Monika , Soderlund Carol , Gang David R , Fenning Trevor , Meiners Torsten 
Published: June 2012

AbstractBackgroundPlants can defend themselves against herbivorous insects prior to the onset of larval feeding by responding to the eggs laid on their leaves. In the European field elm (Ulmus minor), egg laying by the elm leaf beetle (Xanthogaleruca luteola) activates the emission of volatiles that attract specialised egg parasitoids, which in turn kill the eggs. Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes.ResultsHere we present the first large scale study of egg-induced changes in the transcriptional profile of a tree. Five cDNA libraries were generated from leaves of (i) untreated control elms, and elms treated with (ii) egg laying and feeding by elm leaf beetles, (iii) feeding, (iv) artificial transfer of egg clutches, and (v) methyl jasmonate. A total of 361,196 ESTs expressed sequence tags (ESTs) were identified which clustered into 52,823 unique transcripts (Unitrans) and were stored in a database with a public web interface. Among the analyzed Unitrans, 73% could be annotated by homology to known genes in the UniProt (Plant) database, particularly to those fromVitis,Ricinus,PopulusandArabidopsis. Comparativein silicoanalysis among the different treatments revealed differences in Gene Ontology term abundances. Defense- and stress-related gene transcripts were present in high abundance in leaves after herbivore egg laying, but transcripts involved in photosynthesis showed decreased abundance. Many pathogen-related genes and genes involved in phytohormone signaling were expressed, indicative of jasmonic acid biosynthesis and activation of jasmonic acid responsive genes. Cross-comparisons between different libraries based on expression profiles allowed the identification of genes with a potential relevance in egg-induced defenses, as well as other biological processes, including signal transduction, transport and primary metabolism.ConclusionHere we present a dataset for a large-scale study of the mechanisms of plant defense against insect eggs in a co-evolved, natural ecological plant–insect system. The EST database analysis provided here is a first step in elucidating the transcriptional responses of elm to elm leaf beetle infestation, and adds further to our knowledge on insect egg-induced transcriptomic changes in plants. The sequences identified in our comparative analysis give many hints about novel defense mechanisms directed towards eggs.
Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus
Authors: Higgins Janet , Magusin Andreas , Trick Martin , Fraser Fiona , Bancroft Ian 
Published: June 2012

AbstractBackgroundPolyploidy often results in considerable changes in gene expression, both immediately and over evolutionary time. New phenotypes often arise with polyploid formation and may contribute to the fitness of polyploids in nature or their selection for use in agriculture. Oilseed rape (Brassica napus) is widely used to study the process of polyploidy both in artificially resynthesised and natural forms. mRNA-Seq, a recently developed approach to transcriptome profiling using deep-sequencing technologies is an alternative to microarrays for the study of gene expression in a polyploid.ResultsIllumina mRNA-Seq is comparable to microarray analysis for transcript quantification but has increased sensitivity and, very importantly, the potential to distinguish between homoeologous genes in polyploids. Using a novel curing process, we adapted a reference sequence that was a consensus derived from ESTs from bothBrassicaA and C genomes to one containing separate A and C genome versions for each of the 94,558 original unigenes. We aligned reads fromB. napusto this cured reference, finding 38% more reads mapping from resynthesised lines and 28% more reads mapping from natural lines. Where the A and C versions differed at single nucleotide positions, termed inter-homoeologue polymorphisms (IHPs), we were able to apportion expression in the polyploid between the A and C genome homoeologues. 43,761 unigenes contained at least one IHP, with a mean frequency of 10.5 per kb unigene sequence. 6,350 of the unigenes with IHPs were differentially expressed between homoeologous gene pairs in resynthesisedB. napus. 3,212 unigenes showed a similar pattern of differential expression across a range of naturalB. napuscrop varieties and, of these, 995 were in common with resynthesisedB. napus.Functional classification showed over-representation in gene ontology categories not associated with dosage-sensitivity.ConclusionmRNA-Seq is the method of choice for measuring transcript abundance in polyploids due to its ability to measure the contributions of homoeologues to gene expression. The identification of large numbers of differentially expressed genes in both a newly resynthesised polyploid and naturalB. napusconfirms that there are both immediate and long-term alterations in the expression of homoeologous gene pairs following polyploidy.
Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology
Authors: O’Loughlin Aran , Lynn David J , McGee Mark , Doyle Sean , McCabe Matthew , Earley Bernadette 
Published: June 2012

AbstractBackgroundWeaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq.ResultsThe leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling.ConclusionsThis study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress.
Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes
Authors: Sreesankar Easwaran , Senthilkumar Ramamoorthy , Bharathi Vellaichamy , Mishra Rakesh K , Mishra Krishnaveni 
Published: June 2012

Abstract

Background
Telomeres are nucleoprotein complexes at the end of linear eukaryotic chromosomes which maintain the genome integrity by regulating telomere length, preventing recombination and end to end fusion events. Multiple proteins associate with telomeres and function in concert to carry out these functions. Rap1 interacting factor 1 (Rif1), was identified as a protein involved in telomere length regulation in yeast. Rif1 is conserved upto mammals but its function has diversified from telomere length regulation to maintenance of genome integrity.

Results
We have carried out detailed bioinformatic analyses and identified Rif1 homologues in 92 organisms from yeast to human. We identified Rif1 homologues in Drosophila melanogaster, even though fly telomeres are maintained by a telomerase independent pathway. Our analysis shows that Drosophila Rif1 (dRif1) sequence is phylogenetically closer to the one of vertebrates than yeast and has identified a few Rif1 specific motifs conserved through evolution. This includes a Rif1 family specific conserved region within the HEAT repeat domain and a motif involved in protein phosphatase1 docking. We show that dRif1 is nuclear localized with a prominent heterochromatin association and unlike human Rif1, it does not respond to DNA damage by localizing to damaged sites. To test the evolutionary conservation of dRif1 function, we expressed the dRif1 protein in yeast and HeLa cells. In yeast, dRif1 did not perturb yeast Rif1 (yRif1) functions; and in HeLa cells it did not colocalize with DNA damage foci.

Conclusions
Telomeres are maintained by retrotransposons in all Drosophila species and consequently, telomerase and many of the telomere associated protein homologues are absent, including Rap1, which is the binding partner of Rif1. We found that a homologue of yRif1 protein is present in fly and dRif1 has evolutionarily conserved motifs. Functional studies show that dRif1 responds differently to DNA damage, implying that dRif1 may have a different function and this may be conserved in other organisms as well.