bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene
Authors: Thomas Brandon J , Rubio Eric D , Krumm Niklas , Broin Pilib Ó , Bomsztyk Karol , Welcsh Piri , Greally John M , Golden Aaron A , Krumm Anton 
Published: August 2011

Abstract

Background
Random monoallelic expression contributes to phenotypic variation of cells and organisms. However, the epigenetic mechanisms by which individual alleles are randomly selected for expression are not known. Taking cues from chromatin signatures at imprinted gene loci such as the insulin-like growth factor 2 gene 2 (IGF2), we evaluated the contribution of CTCF, a zinc finger protein required for parent-of-origin-specific expression of the IGF2 gene, as well as a role for allele-specific association with DNA methylation, histone modification and RNA polymerase II.

Results
Using array-based chromatin immunoprecipitation, we identified 293 genomic loci that are associated with both CTCF and histone H3 trimethylated at lysine 9 (H3K9me3). A comparison of their genomic positions with those of previously published monoallelically expressed genes revealed no significant overlap between allele-specifically expressed genes and colocalized CTCF/H3K9me3. To analyze the contributions of CTCF and H3K9me3 to gene regulation in more detail, we focused on the monoallelically expressed IGF2BP1 gene. In vitro binding assays using the CTCF target motif at the IGF2BP1 gene, as well as allele-specific analysis of cytosine methylation and CTCF binding, revealed that CTCF does not regulate mono- or biallelic IGF2BP1 expression. Surprisingly, we found that RNA polymerase II is detected on both the maternal and paternal alleles in B lymphoblasts that express IGF2BP1 primarily from one allele. Thus, allele-specific control of RNA polymerase II elongation regulates the allelic bias of IGF2BP1 gene expression.

Conclusions
Colocalization of CTCF and H3K9me3 does not represent a reliable chromatin signature indicative of monoallelic expression. Moreover, association of individual alleles with both active (H3K4me3) and silent (H3K27me3) chromatin modifications (allelic bivalent chromatin) or with RNA polymerase II also fails to identify monoallelically expressed gene loci. The selection of individual alleles for expression occurs in part during transcription elongation.
Type of Dietary Fat Is Associated with the 25-Hydroxyvitamin D3 Increment in Response to Vitamin D Supplementation
Authors: Niramitmahapanya Sathit , Harris Susan S. , Dawson-Hughes Bess 
Published: August 2011

Abstract

Context:
Mono- and polyunsaturated fats may have opposing effects on vitamin D absorption.

Objective:
The purpose of this study was to determine whether intakes of different dietary fats are associated with the increase in serum 25-hydroxyvitamin D (25OHD) after supplementation with vitamin D3.

Design, Setting, and Participants:
This analysis was conducted in the active treatment arm of a randomized, double-blind, placebo-controlled trial of vitamin D and calcium supplementation to prevent bone loss and fracture. Subjects included 152 healthy men and women age 65 and older who were assigned to 700 IU/d vitamin D3 and 500 mg/d calcium. Intakes of monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), and saturated fatty acids (SFA) were estimated by food frequency questionnaire.

Main Outcome Measure:
The change in plasma 25OHD during 2 yr vitamin D and calcium supplementation was assessed.

Results:
The change in plasma 25OHD (nanograms per milliliter) during vitamin D supplementation was positively associated with MUFA, (β = 0.94; P = 0.016), negatively associated with PUFA, (β = −0.93; P = 0.038), and positively associated with the MUFA/PUFA ratio (β = 6.46; P = 0.014).

Conclusion:
The fat composition of the diet may influence the 25OHD response to supplemental vitamin D3. Diets rich in MUFA may improve and those rich in PUFA may reduce the effectiveness of vitamin D3 supplements in healthy older adults. More studies are needed to confirm these findings.
Comparing the treatment response of great saphenous and small saphenous vein incompetence following surgery and endovenous laser ablation: a retrospective cohort study
Authors: Carradice D , Samuel N , Wallace T , Mazari F A K , Hatfield J , Chetter I 
Published: August 2011

Objective Many venous trials mix patients with great saphenous vein (GSV) and small saphenous vein (SSV) diseases. There is no evidence that both respond similarly to treatment and our aim was to test this assumption. Method This cohort study compares patients with isolated GSV and SSV incompetence following treatment with open surgical ligation or endovenous laser ablation (EVLA). Outcomes included: quality of life (QoL; Aberdeen Varicose Vein Questionnaire [AVVQ]; Short Form 36 [SF36]; Euroqol [EQ5D]; and Venous Clinical Severity Score [VCSS]). Results A total of 370 patients with no differences in baseline QoL, underwent treatment. Despite equivalent morbidity, SSV sufferers had a lower VCSS ( P < 0.001). Following surgery, SSV patients scored higher (worse) on AVVQ ( P = 0.045) than GSV sufferers, but lower (better) following EVLA ( P = 0.042). Conclusion The morbidity associated with SSV incompetence is greater than suggested by its clinical severity and responds differently following treatment to that of the GSV. Trials should consider patients with GSV and SSV reflux separately. EVLA may offer additional benefits to SSV sufferers.
Analyzing Two-Color Babylon
Authors: Goadrich Mark , Schlatter Mark 
Published: August 2011

AbstractWe examine the impartial combinatorial game Babylon. We abstract the game so that it is suitable to combinatorial analysis, and present a full characterization and strategies for the cases with odd number of tokens and only two colors. We also demonstrate partial results on games with even tokens with two colors, an initial extension to three colors, and offer directions for future work.
Low genetic diversity, moderate local adaptation, and phylogeographic insights in Cornus nuttallii (Cornaceae)
Authors: Keir Karolyn R. , Bemmels Jordan B. , Aitken Sally N. 
Published: August 2011

•Premise of the study: Genetic knowledge is completely lacking for Pacific dogwood (Cornus nuttallii), a western North American temperate tree that is pollinated and dispersed by biological vectors. We investigated how history, geography, and climate have affected population genetic structure, local adaptation, and the phylogeography of this species.•Methods: We examined patterns and levels of diversity in nuclear microsatellites (SSRs) and cpDNA haplotypes in populations from across the species range. We compared these results to population differentiation and genetic clines in phenotypic traits in a common garden.•Key results: Genetic diversity was low for both nuclear SSRs and cpDNA. There was a lack of population structure (FST = 0.090) in the coastal portion of the species range, with estimates of population genetic diversity in microsatellite markers decreasing with latitude from California to British Columbia. A disjunct interior population in Idaho 450 km from the coastal range had the lowest diversity but the highest divergence of all populations studied. Only a single nucleotide polymorphism was discovered after sequencing 5547 base pairs in seven noncoding regions of cpDNA. Both cpDNA haplotypes were widely distributed throughout the species range. Quantitative variation among populations was moderate (0.11 ≤ QST ≤ 0.63), and weak but significant adaptive clines were found between quantitative traits and population climatic variables (0.09 ≤ R2 ≤ 0.34).•Conclusions: Cornus nuttallii likely faced a population bottleneck in a single southern refugium during the Last Glacial Maximum. Despite low genetic diversity, it is weakly to moderately locally adapted.
Frequent pseudogenization and loss of the plastid‐encoded sulfate‐transport genecysA throughout the evolution of liverworts
Authors: Wickett Norman J. , Forrest Laura L. , Budke Jessica M. , Shaw Blanka , Goffinet Bernard 
Published: August 2011

•Premise of the study:The presence or absence of a functional copy of a plastid gene may reflect relaxed selection, and may be phylogenetically significant, reflecting shared ancestry. In some liverworts, the plastid genecysA is a pseudogene (inferred to be nonfunctional). We surveyed 63 liverworts from all major clades to determine whether the loss ofcysA is phylogenetically significant, whether intact copies ofcysA are under selective constraints, and whether rates of nucleotide substitution differ in other plastid genes from taxa with and without a functional copy ofcysA.•Methods:Primers annealing to flanking and internal regions were used to amplify and sequencecysA from 61 liverworts. Two additionalcysA sequences were downloaded from NCBI. The ancestral states ofcysA were reconstructed on a phylogenetic hypothesis inferred from seven markers. Rates of nucleotide substitution were estimated for three plastid loci to reflect the intrinsic mutation rate in the plastid genome. The ratio of nonsynonymous to synonymous substitutions was estimated for intact copies ofcysA to infer selective constraints.•Key results:Throughout liverworts,cysA has been lost up to 29 times, yet intact copies ofcysA are evolving under selective constraints. Gene loss is more frequent in groups with an increased substitution rate in the plastid genome.•Conclusions:The number of inferred losses ofcysA in liverworts exceeds any other reported plastid gene. Despite frequent losses,cysA is evolving under purifying selection in liverworts that retain the gene. It appears thatcysA is lost more frequently in lineages characterized by a higher rate of nucleotide substitutions in the plastid.
Amputation of Finger by Horse Bite With Complete Avulsion of Both Flexor Tendons
Authors: Koren Lior , Stahl Shalom , Rovitsky Alexey , Peled Eli 
Published: August 2011

Amputation of fingers with tendon avulsion occurs through a traction injury, and most occur through a ring avulsion mechanism. Usually the flexor digitorum profundus is torn out with the amputated finger. Replantation usually is recommended only when the amputation is distal to the flexor digitorum superficialis insertion. Animal bites are relatively common, with a decreasing order of frequency of dogs, cats, and humans. Horse bites are relatively infrequent but are associated with crush injuries and tissue loss when they occur.
This article describes a 23-year-old man with amputation of his middle finger at the level of the proximal phalanx after being bitten by a horse. The amputated stump was avulsed with the middle finger flexor digitorum profundus and flexor digitorum superficialis torn from the muscle-tendon junction from approximately the middle of the forearm. The patient had no other injuries, and he was able to move his other 4 fingers with only mild pain. As the amputated digit was not suitable for replantation, the wound was irrigated and debrided. The edges of the phalanx were trimmed, and the edges of the wound were sutured. Tetanus toxoid and rabies vaccine were administered, along with intravenous amoxicillin and clavulanic acid. The patient was discharged from the hospital 2 days later, with no sign of infection of the wound or compartment syndrome of the forearm. This case demonstrates the weakest point in the myotendinous junction and emphasizes the importance of a careful physical examination in patients with a traumatic amputation.
TiO2 Nanocrystals Synthesized by Laser Pyrolysis for the Up‐Scaling of Efficient Solid‐State Dye‐Sensitized Solar Cells
Authors: Melhem Hussein , Simon Pardis , Beouch Layla , Goubard Fabrice , Boucharef Mourad , Di Bin Catherine , Leconte Yann , Ratier Bernard , Herlin‐Boime Nathalie , Bouclé Johann 
Published: August 2011

AbstractA crucial issue regarding emerging nanotechnologies remains the up‐scaling of new functional nanostructured materials towards their implementation in high performance applications on a large scale. In this context, we demonstrate high efficiency solid‐state dye‐sensitized solar cells prepared from new porous TiO2 photoanodes based on laser pyrolysis nanocrystals. This strategy exploits a reduced number of processing steps as well as non‐toxic chemical compounds to demonstrate highly porous TiO2 films. The possibility to easily tune the TiO2 nanocrystal physical properties allows us to demonstrate all solid‐state dye‐sensitized devices based on a commercial benchmark materials (organic indoline dye and molecular hole transporter) presenting state‐of‐the‐art performance comparable with reference devices based on a commercial TiO2 paste. In particular, a drastic improvement in pore infiltration, which is found to balance a relatively lower surface area compared to the reference electrode, is evidenced using laser‐synthesized nanocrystals resulting in an improved short‐circuit current density under full sunlight. Transient photovoltage decay measurements suggest that charge recombination kinetics still limit device performance. However, the proposed strategy emphasizes the potentialities of the laser pyrolysis technique for up‐scaling nanoporous TiO2 electrodes for various applications, especially for solar energy conversion.
Impact of gene vector design on the control of recombinant monoclonal antibody production by chinese hamster ovary cells
Authors: Davies Sarah L. , O'Callaghan Peter M. , McLeod Jane , Pybus Leon P. , Sung Yun Hee , Rance James , Wilkinson Stephen J. , Racher Andrew J. , Young Robert J. , James David C. 
Published: August 2011

AbstractIn this study, we systematically compare two vector design strategies for recombinant monoclonal antibody (Mab) synthesis by Chinese hamster ovary (CHO) cells; a dual open reading frame (ORF) expression vector utilizing separate cytomegalovirus (CMV) promoters to drive heavy chain (HC) and light chain (LC) expression independently, and a single ORF vector design employing a single CMV promoter to drive HC and LC polypeptide expression joined by a foot and mouth disease virus F2A polypeptide self‐cleaving linker sequence. Initial analysis of stable transfectants showed that transfectants utilizing the single ORF vector designs exhibited significantly reduced Mab production. We employed an empirical modeling strategy to quantitatively describe the cellular constraints on recombinant Mab synthesis in all stable transfectants. In all transfectants, an intracellular molar excess of LC polypeptide over HC polypeptide was observed. For CHO cells transfected with the single ORF vectors, model‐predicted, and empirical intracellular intermediate levels could only be reconciled by inclusion of nascent HC polypeptide degradation. Whilst a local sensitivity analysis showed that qMab of all transfectants was primarily constrained by recombinant mRNA translation rate, our data indicated that all single ORF transfectants exhibited a reduced level of recombinant gene transcription and that Mab folding and assembly reactions generically exerted greater control over qMab. We infer that the productivity of single ORF transfectants is limited by ER processing/degradation “capacity” which sets a limit on transcriptional input. We conclude that gene vector design for oligomeric recombinant proteins should be based on an understanding of protein‐specific synthetic kinetics rather than polypeptide stoichiometry. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011
Separated and Trafficked Children: The Challenges for Child Protection Professionals
Authors: Rigby Paul 
Published: August 2011

Unaccompanied asylum‐seeking children are one of the most vulnerable groups of children and those who have been trafficked present with additional needs, posing new challenges for child protection professionals. Drawing on a research programme commissioned to inform policy and practice in Glasgow, this paper identifies issues emerging for practitioners working with separated children who have been trafficked. The commitment of frontline staff and increased multiagency working appear to be positive aspects of the work. Initial identification and assessment present a major challenge for reasons including cultural issues, the trauma and fear of children affecting engagement and the potential for ongoing contact with traffickers to compromise safeguarding. Trafficking is a particularly complex area of child protection work, made more problematic by the international dimensions to the trade and the absence of a clear definition and conceptual framework that can fully inform interventions and practice. Copyright © 2011 John Wiley & Sons, Ltd.‘Initial identification and assessment present a major challenge’
Robust exponential l2 − l ∞  control for discrete‐time switched system: A cone complement linearization method
Authors: Hou Linlin , Zong Guangdeng , Wu Yuqiang 
Published: August 2011

SUMMARYThe robust exponential l2 − l ∞  control problem is considered in this paper for discrete‐time switched systems with both time‐varying delay and norm‐bounded parameter uncertainties. An exponential l2 − l ∞  performance index is first introduced for the discrete‐time switched systems. The designed controller is a memory exponential l2 − l ∞  controller. By introducing an average dwell time approach and a Lyapunov–Krasovskii functional technique, some sufficient criteria guaranteeing exponential stability are presented, and the desired memory exponential l2 − l ∞  controller is established by resorting to a cone complement linearization method. Some results on exponential stability using memoryless exponential l2 − l ∞  controller and asymptotical stability with traditional l2 − l ∞  performance index are also established. Finally, a numerical example is provided to demonstrate that the proposed approach can lead to less conservatism compared with the developed result using memoryless exponential l2 − l ∞  controller and asymptotical stability analysis with traditional l2 − l ∞  performance index. Copyright © 2011 John Wiley & Sons, Ltd.
Nanostructure and properties of proton‐conducting sulfonated poly(ether ether ketone) (SPEEK) and zirconia–SPEEK hybrid membranes for direct alcohol fuel cells: effect of the nature of swelling solvent and incorporation of heteropolyacid
Authors: Kawaguti Carla Akimi , Dahmouche Karim , Gomes Ailton de Souza 
Published: August 2011

AbstractThe influence, on membrane nanostructure and properties, of water or ethanol as swelling solvent of sulfonated poly(ether ether ketone) (SPEEK) and zirconia–SPEEK hybrid membranes prepared using the sol–gel process has been investigated. Independent of the solvent, small‐angle X‐ray scattering measurements reveal the existence of a two‐level hierarchical structure in SPEEK of greater sulfonation level, consisting of solvent‐swelled spatially correlated primary SO3H‐rich ionic clusters of around 15 Å in size, forming larger secondary aggregates well dispersed in the PEEK matrix. The size of the primary nanodomains and the connectivity between domains are determining parameters for protonic conductivity, solvent swelling ability and permeability of the membranes. For both SPEEK and zirconia–SPEEK membranes containing ethanol, the pronounced affinity of ethanol molecules with SPEEK leads to an increase in the size of ionic clusters and of the number of connecting channels between clusters compared to membranes containing water. This promotes solvent swelling and proton conductivity. The increase in permeability to water induced by incorporation of ethanol in place of water in both polymeric and hybrid membranes is less in the hybrid membranes. This result suggests that the potential use of zirconia–SPEEK hybrid membranes in direct alcohol fuel cells is more promising than that of pure SPEEK, due not only to the less probable alcohol and water penetration in the membranes associated with their lower permeability, but also to the fact that an eventual penetration of alcohol in hybrid membranes should reduce the risk of cathode flooding compared to zirconia‐free SPEEK membranes. Copyright © 2011 Society of Chemical Industry
Use of legume green manures as nitrogen sources for corn production
Authors: Liebman Matt , Graef Rhonda L. , Nettleton Daniel , Cambardella Cynthia A. 
Published: August 2011

AbstractRecent volatility in supplies and prices of natural gas and synthetic nitrogen (N) fertilizer suggests a need to develop and refine alternative strategies for supplying N to corn. In this study, conducted in north-eastern Iowa, we examined the use of red clover and alfalfa green manures as means of supplying N to a succeeding corn crop. Red clover intercropped with oat produced significantly more biomass and contained more N than alfalfa intercropped with oat. Tilling green manures in the fall or delaying tillage until the following spring did not have a consistent effect on green manure N content. Without N fertilizer, corn grain yield following oat–red clover and oat–alfalfa was 25–63% greater than following oat grown alone, but at the highest fertilizer rate (202 kg N ha−1), there was no difference in corn yield between oat–legume and oat-alone treatments. These patterns support the premise that legume green manure effects on corn yield were N-related. Red clover green manure had an N fertilizer replacement value for corn of 87–184 kg N ha−1; alfalfa supplied corn with the equivalent of 70–121 kg N ha−1. At a fossil energy cost for N fertilizer of 57 MJ kg−1N, reducing synthetic N fertilizer applications to corn by 70–184 kg N ha−1would represent a fossil fuel savings of 3990–10,488 MJ ha−1, equivalent to the energy content of 104–274 m3of natural gas. These types of savings are likely to become increasingly important as fossil energy supplies become scarcer and fertilizer prices rise.
Immunogenic and tolerogenic signatures in human immunodeficiency virus (HIV)-infected controllers compared with progressors and a conversion strategy of virus control
Authors: Whittall T , Peters B , Rahman D , Kingsley C I , Vaughan R , Lehner T 
Published: August 2011

Summary
Epidemiological studies have identified a small cohort of controllers of human immunodeficiency virus (HIV)-1 infection, who without treatment have no detectable virus, and others who progress at a variable rate. The objective of this study was to distinguish immune signatures in HIV controllers and progressors, by evaluating tolerogenic and immunogenic factors in untreated HIV-1 infected individuals. The recruited population was divided into putative elite controllers (PEC), long-term non-progressors (LTNP), normal progressors (NP) and fast progressors (FP). The proportion of regulatory T cells [Tregs, CD4+CD25+forkhead box P3 (FoxP3+)], programmed death (PD)-1 and cytotoxic T lymphocyte antigen (CTLA)-inhibitory molecules and CD40L, CD69 and Ki67 activation markers were evaluated in peripheral blood mononuclear cells (PBMC) by flow cytometry. Significant differences were found between HIV controllers and HIV progressors, with up-regulation of Tregs, PD-1 and CTLA-4 and decrease of CD40L expression in progressors compared with controllers. Expression of CD40L and concentrations of interleukin (IL)-6, CCL-3, and CCL-4 were significantly higher in PEC and LTNP than in NP and FP. In an attempt to convert immune signatures of progressors to those of controllers, seven agents were used to stimulate PBMC from the four cohorts. Treatment with CD40L and IL-4 or PD-1 antibodies in vitro were most effective in converting the immune signatures of progressors to those observed in controllers by down-regulating Tregs and up-regulating CD40L expression in CD4+ T cells. The conversion concept merits translation to in vivo immune control of HIV infection.