bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Method for Adaptive Habit Prediction in Bulk Microphysical Models. Part I: Theoretical Development
Authors: Harrington Jerry Y. , Sulia Kara , Morrison Hugh 
Published: September 2012

AbstractBulk microphysical schemes use the capacitance model for ice vapor growth in combination with mass–size relationships to determine the evolution of ice water content (IWC) and ice particle maximum dimension in time. These approaches are limited since a single axis length is used, the aspect ratio is usually held constant and mass–size relations have many available coefficients for similar ice types. Fixing the crystal aspect ratio severs the nonlinear link between aspect ratio changes and increased growth rates that occur during crystal growth. A method is presented here for predicting two crystal axes and the crystal aspect ratio in bulk models. Evolution of the ice mass mixing ratio is tied to the evolution of two axis length mixing ratios through the use of a historical axis ratio parameter containing memory of crystal shape. This parameter links the distributions of the two axes, allowing characterization of particle lengths using a single distribution. The method uses four prognostic variables: the mass and number mixing ratios, and two axis length mixing ratios. Development of the method is presented, with testing described in Part II.
Meis1 regulates the metabolic phenotype and oxidant defense of hematopoietic stem cells
Authors: Kocabas Fatih , Zheng Junke , Thet Suwannee , Copeland Neal G. , Jenkins Nancy A. , DeBerardinis Ralph J. , Zhang Chengcheng , Sadek Hesham A. 
Published: September 2012

Abstract
The role of Meis1 in leukemia is well established, but its role in hematopoietic stem cells (HSCs) remains poorly understood. Previously, we showed that HSCs use glycolytic metabolism to meet their energy demands. However, the mechanism of regulation of HSC metabolism, and the importance of maintaining this distinct metabolic phenotype on HSC function has not been determined. More importantly, the primary function of Meis1 in HSCs remains unknown. Here, we examined the effect of loss of Meis1 on HSC function and metabolism. Inducible Meis1 deletion in adult mouse HSCs resulted in loss of HSC quiescence, and failure of bone marrow repopulation after transplantation. While we previously showed that Meis1 regulates Hif-1α transcription in vitro, we demonstrate here that loss of Meis1 results in down-regulation of both Hif-1α and Hif-2α in HSCs. This resulted in a shift to mitochondrial metabolism, increased reactive oxygen species production, and apoptosis of HSCs. Finally, we demonstrate that the effect of Meis1 knockout on HSCs is entirely mediated through reactive oxygen species where treatment of the Meis1 knockout mice with the scavenger N-acetylcystein restored HSC quiescence and rescued HSC function. These results uncover an important transcriptional network that regulates metabolism, oxidant defense, and maintenance of HSCs.
Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)
Authors: Aspeborg Henrik , Coutinho Pedro M , Wang Yang , Brumer Harry , Henrissat Bernard 
Published: September 2012

Abstract

Background
The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on β-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5.

Results
About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions.

Conclusion
Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at http://www.cazy.org/GH5.html.
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints
Authors: Xu Fuyu , Park Myoung-Ryoul , Kitazumi Ai , Herath Venura , Mohanty Bijayalaxmi , Yun Song Joong , de los Reyes Benildo G 
Published: September 2012

AbstractBackgroundThe potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns.ResultsThe most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis.ConclusionsPatterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics.
Phase I study of miriplatin combined with transarterial chemotherapy using CDDP powder in patients with hepatocellular carcinoma
Authors: Kamimura Kenya , Suda Takeshi , Tamura Yasushi , Takamura Masaaki , Yokoo Takeshi , Igarashi Masato , Kawai Hirokazu , Yamagiwa Satoshi , Nomoto Minoru , Aoyagi Yutaka 
Published: September 2012

Abstract

Background
There is no standard therapeutic procedure for the hepatocellular carcinoma (HCC) in patients with poor hepatic reserve function. With the approval of newly developed chemotherapeutic agent of miriplatin, we have firstly conducted the phase I study of CDDP powder (DDP-H) and miriplatin combination therapy and reported its safety and efficacy for treating unresectable HCC in such cases. To determine the maximum tolerated dose (MTD) and dose-limiting toxicity (DLT) for the combination of transarterial oily chemoembolization (TOCE) and transarterial chemotherapy (TAC) using miriplatin and DDP-H for treating unresectable hepatocellular carcinoma (HCC).

Methods
Transarterial chemotherapy using DDP-H was performed through the proper hepatic artery targeting the HCC nodules by increasing the dose of DDP-H (35–65 mg/m2) followed by targeting the HCC nodules by transarterial oily chemoembolization with miriplatin.

Results
A total of nine patients were enrolled in this study and no DLT was observed with any dose of DDP-H in all cases in whom 80 mg (median, 18–120) miriplatin was administered. An anti-tumour efficacy rating for partial response was obtained in one patient, while a total of four patients (among eight evaluated) showed stable disease response, leading to 62.5% of disease control rate. The pharmacokinetic results showed no further increase in plasma platinum concentration following miriplatin administration.

Conclusion
Our results suggest that a combination of DDP-H and miriplatin can be safely administered up to their respective MTD for treating HCC.

Trial registration
This study was registered with the University Hospital Medical Information Network Clinical Trials Registry (UMIN-CTR000003541).
The identification of a spontaneous 47, XX, +21/46, XY chimeric fetus with male genitalia
Authors: Lee Kuei-Fang , Hsu Chun-Shuo , Kuo Pao-Lin , Chen Jing-Liang , Jiang Yuan-Hong , Liu Ingrid Y 
Published: September 2012

Abstract

Background
Approximately 30 sex-chromosome discordant chimera cases have been reported to date, of which only four cases carried trisomy 21. Here, we present an additional case, an aborted fetus with a karyotype of 47,XX, +21/46,XY.

Case presentation
Autopsy demonstrated that this fetus was normally developed and had male genitalia. Major characteristics of Down syndrome were not observed except an enlarged gap between the first and second toes. Karyotyping of tissues cultured from the fetus revealed the same chimeric chromosomal composition detected in the amniotic fluid but with a different ratio of [47,XX,+21] to [46,XY]. Further short tandem repeat analysis indicated a double paternal contribution and single maternal contribution to the fetus, with the additional chromosome 21 in the [47,XX,+21] cell lineage originating from the paternal side.

Conclusion
We thus propose that this chimeric fetus was formed via the dispermic fertilization of a parthenogenetic ovum with one (Y) sperm and one (X,+21) sperm.
Anti-infectivity of camel polyclonal antibodies against hepatitis C virus in Huh7.5 hepatoma
Authors: EL-Fakharany Esmail M , Abedelbaky Nawal , Haroun Bakry M , Sánchez Lourdes , Redwan Nezar A , Redwan Elrashdy M 
Published: September 2012

Abstract

Purpose
To extend the study of the camel milk proteins which have antiviral activity against HCV, camel naïve polyclonal IgGs, α-lactalbumin were purified from camel milk and their anti-HCV effect was examined using PBMCs and Huh7.5 cell-lines. They were compared with the activity of human polyclonal IgGs and camel lactoferrin and casein.

Material and methods
Three types of experiments were performed on PBMCs and HuH7.5 cell. HCV was directly incubated with the purified proteins and then mixed with both cell types, or the proteins were incubated with the cells and then exposed to HCV, or the HCV pre-infected cells were treated with the proteins to inhibit intracellular replication. The proteins were added to cells or virus at different concentrations and time intervals.

Results
Pretreated PBMCs and Huh7.5 cells with milk proteins were not protected when exposed to HCV infection. The direct interaction between HCV and camel IgGs and camel lactoferrin (cLf) led to a complete inhibition of HCV entry into cells, while casein, α-lactalbumin and human IgGs failed to inhibit HCV entry at any tested concentration. Camel IgGs showed ability to recognize HCV peptides with a significant titer (12 × 103) in comparison with human IgGs which failed to do it. Camel lactoferrin was capable of inhibiting the intracellular HCV replication at concentrations of 0.25-1.25 mg/ml.

Conclusion
Camel milk naïve polyclonal IgGs isolated from camel milk could inhibit the HCV infectivity and demonstrated strong signal against its synthetic peptides. Lactoferrin inhibit the HCV infectivity started from 0.25 mg/ml. However, α-lactalbumin, human IgGs and casein failed to demonstrate any activity against HCV infectivity.
A randomized controlled trial of qigong for fibromyalgia
Authors: Lynch Mary , Sawynok Jana , Hiew Chok , Marcon Dana 
Published: September 2012

Abstract
Introduction
Fibromyalgia is difficult to treat and requires the use of multiple approaches. This study is a randomized controlled trial of qigong compared with a wait-list control group in fibromyalgia.

Methods
One hundred participants were randomly assigned to immediate or delayed practice groups, with the delayed group receiving training at the end of the control period. Qigong training (level 1 Chaoyi Fanhuan Qigong, CFQ), given over three half-days, was followed by weekly review/practice sessions for eight weeks; participants were also asked to practice at home for 45 to 60 minutes per day for this interval. Outcomes were pain, impact, sleep, physical function and mental function, and these were recorded at baseline, eight weeks, four months and six months. Immediate and delayed practice groups were analyzed individually compared to the control group, and as a combination group.

Results
In both the immediate and delayed treatment groups, CFQ demonstrated significant improvements in pain, impact, sleep, physical function and mental function when compared to the wait-list/usual care control group at eight weeks, with benefits extending beyond this time. Analysis of combined data indicated significant changes for all measures at all times for six months, with only one exception. Post-hoc analysis based on self-reported practice times indicated greater benefit with the per protocol group compared to minimal practice.

Conclusions
This study demonstrates that CFQ, a particular form of qigong, provides long-term benefits in several core domains in fibromyalgia. CFQ may be a useful adjuvant self-care treatment for fibromyalgia.

Trial registration
clinicaltrials.gov NCT00938834.
FGF receptors 1 and 2 are key regulators of keratinocyte migration in vitro and in wounded skin
Authors: Meyer Michael , Müller Anna-Katharina , Yang Jingxuan , Moik Daniel , Ponzio Gilles , Ornitz David M. , Grose Richard , Werner Sabine 
Published: September 2012

Summary
Efficient wound repair is essential for the maintenance of the integrity of the skin. The repair process is controlled by a variety of growth factors and cytokines, and their abnormal expression or activity can cause healing disorders. Here, we show that wound repair is severely delayed in mice lacking fibroblast growth factor receptors (FGFR) 1 and 2 in keratinocytes. As the underlying mechanism, we identified impaired wound contraction and a delay in re-epithelialization that resulted from impaired keratinocyte migration at the wound edge. Scratch wounding and transwell assays demonstrated that FGFR1/2-deficient keratinocytes had a reduced migration velocity and impaired directional persistence owing to inefficient formation and turnover of focal adhesions. Underlying this defect, we identified a significant reduction in the expression of major focal adhesion components in the absence of FGFR signaling, resulting in a general migratory deficiency. These results identify FGFs as key regulators of keratinocyte migration in wounded skin.
Dock mediates Scar- and WASp-dependent actin polymerization through interaction with cell adhesion molecules in founder cells and fusion-competent myoblasts
Authors: Kaipa Balasankara Reddy , Shao Huanjie , Schäfer Gritt , Trinkewitz Tatjana , Groth Verena , Liu Jianqi , Beck Lothar , Bogdan Sven , Abmayr Susan M. , Önel Susanne-Filiz 
Published: September 2012

SummaryThe formation of the larval body wall musculature of Drosophila depends on the asymmetric fusion of two myoblast types, founder cells (FCs) and fusion-competent myoblasts (FCMs). Recent studies have established an essential function of Arp2/3-based actin polymerization during myoblast fusion, formation of a dense actin focus at the site of fusion in FCMs, and a thin sheath of actin in FCs and/or growing muscles. The formation of these actin structures depends on recognition and adhesion of myoblasts that is mediated by cell surface receptors of the immunoglobulin superfamily. However, the connection of the cell surface receptors with Arp2/3-based actin polymerization is poorly understood. To date only the SH2-SH3 adaptor protein Crk has been suggested to link cell adhesion with Arp2/3-based actin polymerization in FCMs. Here, we propose that the SH2-SH3 adaptor protein Dock, like Crk, links cell adhesion with actin polymerization. We show that Dock is expressed in FCs and FCMs and colocalizes with the cell adhesion proteins Sns and Duf at cell–cell contact points. Biochemical data in this study indicate that different domains of Dock are involved in binding the cell adhesion molecules Duf, Rst, Sns and Hbs. We emphasize the importance of these interactions by quantifying the enhanced myoblast fusion defects in duf dock, sns dock and hbs dock double mutants. Additionally, we show that Dock interacts biochemically and genetically with Drosophila Scar, Vrp1 and WASp. Based on these data, we propose that Dock links cell adhesion in FCs and FCMs with either Scar– or Vrp1–WASp-dependent Arp2/3 activation.
The Nramp (Slc11) proteins regulate development, resistance to pathogenic bacteria and iron homeostasis in Dictyostelium discoideum
Authors: Peracino Barbara , Buracco Simona , Bozzaro Salvatore 
Published: September 2012

Summary
The Dictyostelium discoideum genome harbors two genes encoding members of the Nramp superfamily, which is conserved from bacteria (MntH proteins) to humans (Slc11 proteins). Nramps are proton-driven metal ion transporters with a preference for iron and manganese. Acquisition of these metal cations is vital for all cells, as they act as redox cofactors and regulate key cellular processes, such as DNA synthesis, electron transport, energy metabolism and oxidative stress. Dictyostelium Nramp1 (Slc11a1), like its mammalian ortholog, mediates resistance to infection by invasive bacteria. We have extended the analysis to the nramp2 gene, by generating single and double nramp1/nramp2 knockout mutants and cells expressing GFP fusion proteins. In contrast to Nramp1, which is recruited to phagosomes and macropinosomes, the Nramp2 protein is localized exclusively in the membrane of the contractile vacuole, a vesicular tubular network regulating cellular osmolarity. Both proteins colocalize with the V-H+-ATPase, which can provide the electrogenic force for vectorial transport. Like nramp1, nramp2 gene disruption affects resistance to Legionella pneumophila. Disrupting both genes additionally leads to defects in development, with strong delay in cell aggregation, formation of large streams and multi-tipped aggregates. Single and double mutants display differential sensitivity to cell growth under conditions of iron overload or depletion. The data favor the hypothesis that Nramp1 and Nramp2, under control of the V-H+-ATPase, synergistically regulate iron homeostasis, with the contractile vacuole possibly acting as a store for metal cations.
Reviews
Authors: Sladen Simon , Chandler David , Laird Paul R. 
Published: September 2012

CREATING PANTOMIME, JOYCE BRANAGH AND KEITH ORTON (2011) Ramsbury: The Crowood Press, 208 pp., ISBN: 978-1-84797-255-2, p/bk, £16.99
WILLIAM VINCENT WALLACE: COMPOSER, VIRTUOSO AND ADVENTURER, ANDREW LAMB (2012) West Byfleet: Fullers Wood Press, x+237 pp., ISBN: 978-0-9524149-7-1,
p/bk, £25.00
WEST SIDE STORY: CULTURAL PERSPECTIVES ON AN AMERICAN MUSICAL, ELIZABETH A. WELLS (2011) Lanham (Maryland), Toronto, Plymouth (UK): Scarecrow Press, xiii+312 pp., ISBN: 978-0-8108-7666-8, h/bk, $39.95
Trends in US Older Adult Disability: Exploring Age, Period, and Cohort Effects
Authors: Lin Shih-Fan , Beck Audrey N. , Finch Brian K. , Hummer Robert A. , Master Ryan K. 
Published: September 2012

Objectives. We elucidated how US late-life disability prevalence has changed over the past 3 decades. Methods. We examined activities of daily living (ADL) and instrumental activities of daily living (IADL) disability trends by using age–period–cohort (APC) models among older adults aged 70 years or older who responded to the National Health Interview Survey between 1982 and 2009. We fitted logistic regressions for ADL and IADL disabilities and for each of the 3 APC trends with 2 models: unadjusted and fully adjusted for age, period, cohort, and sociodemographic variables. Results. The unadjusted and adjusted period trends showed a substantial decline in IADL disability, and ADL disability remained stable across time. Unadjusted cohort trends for both outcomes also showed continual declines across successive cohorts; however, increasing cohort trends were evident in the adjusted models. Conclusions. More recent cohorts of US older adults are becoming more disabled, net of aging and period effects. The net upward cohort trends in ADL and IADL disabilities remain unexplained. Further studies should explore cohort-specific determinants contributing to the increase of cohort-based disability among US older adults.
New Jersey’s HIV Exposure Law and the HIV-Related Attitudes, Beliefs, and Sexual and Seropositive Status Disclosure Behaviors of Persons Living With HIV
Authors: Galletly Carol L. , Glasman Laura R. , Pinkerton Steven D. , DiFranceisco Wayne 
Published: September 2012

Objectives. We explored associations between awareness of New Jersey’s HIV exposure law and the HIV-related attitudes, beliefs, and sexual and seropositive status disclosure behaviors of HIV-positive persons. Methods. A statewide convenience sample (n = 479) completed anonymous written surveys during 2010. We recruited participants through networks of community-based organizations in the state’s 9 health sectors. The survey assessed participants' awareness of New Jersey's HIV exposure law, their sexual and serostatus disclosure behavior in the past year, and their HIV-related attitudes and beliefs. We compared responses of participants who were and were not aware of the law through univariate analyses. Results. Fifty-one percent of participants knew about the HIV exposure law. This awareness was not associated with increased sexual abstinence, condom use with most recent partner, or seropositive status disclosure. Contrary to hypotheses, persons who were unaware of the law experienced greater stigma and were less comfortable with positive serostatus disclosure. Conclusions. Criminializing nondisclosure of HIV serostatus does not reduce sexual risk behavior. Although the laws do not appear to increase stigma, they are also not likely to reduce HIV transmission.