bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphorylation events during viral infections provide potential therapeutic targets
Authors: Keating Julie A. , Striker Rob 
Published: November 2011

SUMMARYFor many medically relevant viruses, there is now considerable evidence that both viral and cellular kinases play important roles in viral infection. Ultimately, these kinases, and the cellular signaling pathways that they exploit, may serve as therapeutic targets for treating patients. Currently, small molecule inhibitors of kinases are under investigation as therapy for herpes viral infections. Additionally, a number of cellular or host‐directed tyrosine kinase inhibitors that have been previously FDA approved for cancer treatment are under study in animal models and clinical trials, as they have shown promise for the treatment of various viral infections as well. This review will highlight the wide range of viral proteins phosphorylated by viral and cellular kinases, and the potential for variability of kinase recognition sites within viral substrates to impact phosphorylation and kinase prediction. Research studying kinase‐targeting prophylactic and therapeutic treatments for a number of viral infections will also be discussed. Copyright © 2011 John Wiley & Sons, Ltd.
The defects in cell wall integrity and G2–M transition of the ∆htl1 mutant are interconnected
Authors: Wang Shan‐Li , Cheng Ming‐Yuan 
Published: November 2011

AbstractThe Saccharomyces cerevisiae RSC (remodel the structure of chromatin) complex is involved in functions associated with the transcriptional regulation, cell cycle progression, DNA damage repair and cell wall integrity. Here we investigate the cellular functioning of HTL1, which encodes a non‐essential subunit of the RSC complex. The results show that the ∆htl1 mutant displays a characteristic defect in cell wall integrity, and the phenotype of the ∆htl1 cells, which include the cell wall defect, temperature sensitivity and ploidy increase, are rescued by the osmotic stabilizer sorbitol but not by overexpression of PKC1, the signalling kinase important for the cell wall biogenesis and stress response. In addition, the expression level of Slt2p, the MAP kinase downstream of the cell wall integrity pathway, is upregulated in ∆htl1 cells. Furthermore, the mitotic arrest of the ∆htl1 mutant is moderated by 1 m sorbitol and deletion of SLT2. The present findings suggest that HTL1 may play a role that is different from other RSC components in terms of cell wall integrity and the G2–M transition. The results also suggest that the defects in cell wall integrity and the G2–M transition of the ∆htl1 mutant are interconnected. Copyright © 2011 John Wiley & Sons, Ltd.
Patient safety risk factors in minimally invasive surgery: a validation study
Authors: Rodrigues Sharon P. , ter Kuile Moniek , Dankelman Jenny , Jansen Frank W. 
Published: November 2011

AbstractThis study was conducted to adapt and validate a patient safety (PS) framework for minimally invasive surgery (MIS) as a first step in understanding the clinical relevance of various PS risk factors in MIS. Eight patient safety risk factor domains were identified using frameworks from a systems approach to patient safety. A questionnaire was drafted containing 34 questions. Three experts in the field of patient safety critically reviewed the questionnaire on clinical relevance and completeness. The questionnaire was distributed among known patient safety experts in person and also sent electronically. A total of 41 questionnaires were distributed and the response rate was 71%. The intraclass correlation coefficient was 0.42 representing moderate agreement. For seven of nine risk domains, Cronbach’s alpha was sufficient (α > 0.7). Mean scores of the risk domains showed the following order of influence on patient safety from high to low: surgeon’s experience [6.6, standard deviation (SD) 0.5], technical skills surgeon (6.6, SD 0.7), technology (5.9, SD 1.1), complications (5.9, SD 1.2), social interaction (5.0, SD 1.0), leadership surgeon (5.4, SD 1.2), blood loss (5.0, SD 1.2), length of surgery (5.0, SD 1.3), surgical team (4.9, SD 1.3), fallibility (4.9, SD 1.3), patient (4.5, SD 1.5), safety measures (4.4, SD 1.5), and finally environment(3.9, SD 1.5). This study is an initiative to give insight into clinical relevance of the maze of PS risk factors in MIS. All investigated risk domains were considered to be of noticeable influence on PS. Nevertheless, it is possible to prioritize various risk domains. In fact, experience and technical skills of the surgeon, technology, and complications are rated as the most important risk factors, closely followed by social interaction and leadership of the surgeon. Patient, safety measures, and environment are rated as the least important risk factors.
Oxidative stress in Phenylketonuria: future directions
Authors: Rocha Júlio César , Martins Maria João 
Published: November 2011

AbstractPhenylketonuria represents the most prevalent inborn error of amino acid metabolism. In early diagnosed patients adequate and continued dietary treatment results in a good neurologic outcome. Natural protein and phenylalanine‐restricted diet, even if rich in fruits and vegetables, represents a serious risk for nutritional deficiencies, albeit universally accepted. In the last few years, a growing number of reports have been describing oxidative stress as a concern in phenylketonuric patients. The diet itself includes good sources of dietary antioxidants (phytochemicals, some vitamins and minerals) but also a risk factor for some deficiencies (selenium, zinc, ubiquinone‐10 and L‐carnitine). Additionally, the extreme stringency of the diet may impose a reduced synthesis of endogenous antioxidants (like ubiquinone‐10 and glutathione). Furthermore, increased phenylalanine levels, and its metabolites, may enhance the endogenous synthesis of reactive species and free radicals and/or interfere with the endogenous synthesis of enzymatic antioxidants (like glutathione peroxidase). Therefore, oxidative stress will probably increase, mainly in late diagnosed patients or in those with bad metabolic control. Considering the known association between oxidative stress, obesity and cardiovascular disease, it seems advisable to look further to the impact of oxidative stress on body macromolecules and structures (like lipoprotein oxidation), especially in phenylketonuric patients with late diagnosis or bad metabolic control, in order to prevent future increased risks. Recommendations for PKU patient's clinical follow‐up improvement and educational goals are included.
Middleware for wireless sensor networks: an outlook
Authors: Mottola Luca , Picco Gian Pietro 
Published: November 2011

Abstract
In modern distributed computing, applications are rarely built directly atop operating system facilities, e.g., sockets. Higher-level middleware abstractions and systems are often employed to simplify the programmer’s chore or to achieve interoperability. In contrast, real-world wireless sensor network (WSN) applications are almost always developed by relying directly on the operating system.
Why is this the case? Does it make sense to include a middleware layer in the design of WSNs? And, if so, is it the same kind of software system as in traditional distributed computing? What are the fundamental concepts, reasonable assumptions, and key criteria guiding its design? What are the main open research challenges, and the potential pitfalls? Most importantly, is it worth pursuing research in this field?
This paper provides a (biased) answer to these and other research questions, preceded by a brief account on the state of the art in the field.
Buckling of a thin-layer Couette flow
Authors: Slim Anja C. , Teichman Jeremy , Mahadevan L. 
Published: November 2011

AbstractWe analyse the buckling stability of a thin, viscous sheet when subject to simple shear, providing conditions for the onset of the dominant out-of-plane modes using two models: (i) an asymptotic theory for the dynamics of a viscous plate, and (ii) the full Stokes equations. In either case, the plate is stabilized by a combination of viscous resistance, surface tension and buoyancy relative to an underlying denser fluid. In the limit of vanishing thickness, plates buckle at a shear rate $\gamma / (\ensuremath{\mu} d)$ independent of buoyancy, where $2d$ is the plate thickness, $\gamma $ is the average surface tension between the upper and lower surfaces, and $\ensuremath{\mu} $ is the fluid viscosity. For thicker plates stabilized by an equal surface tension at the upper and lower surfaces, at and above onset, the most unstable mode has moderate wavelength, is stationary in the frame of the centreline, spans the width of the plate with crests and troughs aligned at approximately $4{5}^{\ensuremath{\circ} } $ to the walls, and closely resembles elastic shear modes. The thickest plates that can buckle have an aspect ratio (thickness/width) of approximately 0.6 and are stabilized only by internal viscous resistance. We show that the viscous plate model can only accurately describe the onset of buckling for vanishingly thin plates but provides an excellent description of the most unstable mode above onset. Finally, we show that, by modifying the plate model to incorporate advection and make the model material-frame-invariant, it is possible to extend its predictive power to describe relatively short, travelling waves.
An arabinoxylan-rich fraction from wheat enhances caecal fermentation and protects colonocyte DNA against diet-induced damage in pigs
Authors: Belobrajdic Damien P. , Bird Anthony R. , Conlon Michael A. , Williams Barbara A. , Kang Seungha , McSweeney Christopher S. , Zhang Dagong , Bryden Wayne L. , Gidley Michael J. , Topping David L. 
Published: November 2011

Population studies show that greater red and processed meat consumption increases colorectal cancer risk, whereas dietary fibre is protective. In rats, resistant starches (a dietary fibre component) oppose colonocyte DNA strand breaks induced by high red meat diets, consistent with epidemiological data. Protection appears to be through SCFA, particularly butyrate, produced by large bowel carbohydrate fermentation. Arabinoxylans are important wheat fibre components and stimulate large bowel carbohydrate SCFA production. The present study aimed to determine whether an arabinoxylan-rich fraction (AXRF) from wheat protected colonocytes from DNA damage and changed colonic microbial composition in pigs fed with a diet high (30 %) in cooked red meat for 4 weeks. AXRF was primarily fermented in the caecum, as indicated by higher tissue and digesta weights and higher caecal (but not colonic) acetate, propionate and total SCFA concentrations. Protein fermentation product concentrations (caecalp-cresol and mid- and distal colonic phenol) were lower in pigs fed with AXRF. Colonocyte DNA damage was lower in pigs fed with AXRF. The microbial profiles of mid-colonic mucosa and adjacent digesta showed that bacteria affiliating withPrevotellaspp. and Clostridial cluster IV were more abundant in both the mucosa and digesta fractions of pigs fed with AXRF. These data suggest that, although AXRF was primarily fermented in the caecum, DNA damage was reduced in the large bowel, occurring in conjunction with lower phenol concentrations and altered microbial populations. Further studies to determine the relationships between these changes and the lowering of colonocyte DNA damage are warranted.
Population genetics and abundance of the Endangered grey-headed lemurEulemur cinereicepsin south-east Madagascar: assessing risks for fragmented and continuous populations
Authors: Brenneman Rick A. , Johnson Steig E. , Bailey Carolyn A. , Ingraldi Christina , Delmore Kira E. , Wyman Tracy M. , Andriamaharoa Hubert E. , Ralainasolo Fidimalala B. , Ratsimbazafy Jonah H. , Louis Edward E. 
Published: November 2011

AbstractKnowledge of both population size and genetic diversity is critical for assessing extinction risk but few studies include concurrent estimates of these two components of population biology. We conducted an investigation of population density and size, and genetic variation and past demographic events, of the Endangered grey-headed lemurEulemur cinereicepsin south-east Madagascar. We estimated lemur density using line-transect surveys and used satellite imagery to calculate forest fragment area in three localities. We collected tissue samples from 53 individuals and used 26 polymorphic microsatellite loci to obtain measures of population structure (divergence and diversity) across these localities. We tested the probability of past bottleneck events using three models. Contrary to expectation, there were no significant differences in population density across localities. Genetic diversity decreased, but not significantly, with decreasing habitat area and population size. We found a higher likelihood of past bottleneck events in the fragmented coastal populations. The low population size and prior decline in diversity in coastal patches are consistent with their isolation, anthropogenic disturbance, and exposure to cyclone activity. The similarities in the estimates of density between continuous and fragmented sites may indicate recent population growth in the fragments but these populations nevertheless remain at risk from reduced levels of genetic variation. These patterns should be confirmed with more extensive sampling across the limited range ofE. cinereiceps.
BAAL/CUP Seminars 2010
Authors: Donohue James 
Published: November 2011

The Open University, Milton Keynes, 21 April 2010This seminar, organised by Caroline Coffin and Jim Donohue (both from the Open University, UK), took the form of a day of dialogue between invited experts and other interested parties, including academic writing practitioners, researchers and postgraduate students. The invited speakers were asked to form panels representing either Academic Literacies or Systemic Functional Linguistics.
Probable Alzheimer's Disease Patients Presenting as “Focal Temporal Lobe Dysfunction” Show a Slow Rate of Cognitive Decline
Authors: Marra Camillo , Villa Giampiero , Quaranta Davide , Valenza Alessandro , Vita Maria Gabriella , Gainotti Guido 
Published: November 2011

AbstractSeveral authors have recently shown that anterograde amnesia is often associated with semantic memory impairment in amnesic MCI patients. Similarly, after the MCI condition, some patients who convert to Alzheimer's disease (AD) show the classic onset (cAD) characterized by the impairment of memory and executive functions, whereas other AD patients show isolated defects of episodic and semantic memory without deficits in other cognitive domains. The latter have been considered an AD variant characterized by ‘focal Temporal Lobe Dysfunction’ (TLD). The aim of the present study was to assess the differences in disease progression between cAD and TLD. For this purpose a continuous series of newly diagnosed probable AD patients presenting as cAD (n = 30) and TLD (n = 25), matched for severity, and 65 healthy controls underwent a comprehensive neuropsychological evaluation at baseline; TLD and cAD were re-evaluated at a 24-month follow-up. At follow-up, TLD patients showed no significant worsening of cognitive functions, whereas cAD subjects displayed a significant worsening in all explored cognitive domains. In conclusion, our results confirm that probable AD presenting as TLD represents a specific onset of AD characterized by a slower rate of progression. (JINS, 2012, 18, 144–150)
Antagonistic Interaction of BLADE-ON-PETIOLE1 and 2 with BREVIPEDICELLUS and PENNYWISE Regulates Arabidopsis Inflorescence Architecture
Authors: Khan Madiha , Xu Mingli , Murmu Jhadeswar , Tabb Paul , Liu Yuanyuan , Storey Kathryn , McKim Sarah M. , Douglas Carl J. , Hepworth Shelley R. 
Published: November 2011

AbstractThe transition to flowering in many plant species, including Arabidopsis (Arabidopsis thaliana), is marked by the elongation of internodes to make an inflorescence upon which lateral branches and flowers are arranged in a characteristic pattern. Inflorescence patterning relies in part on the activities of two three-amino-acid loop-extension homeodomain transcription factors: BREVIPEDICELLUS (BP) and PENNYWISE (PNY) whose interacting products also promote meristem function. We examine here the genetic interactions between BP-PNY whose expression is up-regulated in stems at the floral transition, and the lateral organ boundary genes BLADE-ON-PETIOLE1 (BOP1) and BOP2, whose expression is restricted to pedicel axils. Our data show that bp and pny inflorescence defects are caused by BOP1/2 gain of function in stems and pedicels. Compatible with this, inactivation of BOP1/2 rescues these defects. BOP expression domains are differentially enlarged in bp and pny mutants, corresponding to the distinctive patterns of growth restriction in these mutants leading to compacted internodes and clustered or downward-oriented fruits. Our data indicate that BOP1/2 are positive regulators of KNOTTED1-LIKE FROM ARABIDOPSIS THALIANA6 expression and that growth restriction in BOP1/2 gain-of-function plants requires KNOTTED1-LIKE FROM ARABIDOPSIS THALIANA6. Antagonism between BOP1/2 and BP is explained in part by their reciprocal regulation of gene expression, as evidenced by the identification of lignin biosynthetic genes that are repressed by BP and activated by BOP1/2 in stems. These data reveal BOP1/2 gain of function as the basis of bp and pny inflorescence defects and reveal how antagonism between BOP1/2 and BP-PNY contributes to inflorescence patterning in a model plant species.
In-house SAD phasing with surface-bound cerium ions
Authors: Vennila K. Natesan , Velmurugan Devadasan 
Published: November 2011

The anomalous signal of cerium(III) ions present in a derivative of hen egg-white lysozyme (HEWL) crystals obtained by the addition of 0.025 M cerium chloride to the crystallization medium was used for phasing. X-ray intensity data were collected to 2 Å resolution using an in-house Cu Kα radiation data-collection facility. Phasing of a single-wavelength data set purely based on its f′′ led to a clearly interpretable electron-density map. Automated substructure solution by AutoSol in PHENIX resulted in four highest peaks corresponding to cerium(III) ions with data limited to 3 Å resolution, and about 90% of the residues were built automatically by AutoBuild in PHENIX. Cerium(III) ions bound on the surface of the enzyme are found to interact mainly with the main-chain and side-chain carbonyl groups of Asn, Glu, Tyr and Asp and with water molecules. Ce3+ ions were used as potential anomalous scatterers for the in-house single-wavelength anomalous scattering technique, and this is proposed as a tool for macromolecular phasing and for the study of the interactions of trivalent metal ions with proteins and other macromolecules.
Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans
Authors: Suzuki Nobuhiro , Kim Young-Min , Fujimoto Zui , Momma Mitsuru , Kang Hee-Kwon , Funane Kazumi , Okuyama Masayuki , Mori Haruhide , Kimura Atsuo 
Published: November 2011

Streptococcus mutans dextranase hydrolyzes the internal α-1,6-linkages of dextran and belongs to glycoside hydrolase family 66. An N- and C-terminal deletion mutant of S. mutans dextranase was crystallized by the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 1.6 Å and belonged to space group P21, with unit-cell parameters a = 53.2, b = 89.7, c = 63.3 Å, β = 102.3°. Assuming that the asymmetric unit of the crystal contained one molecule, the Matthews coefficient was calculated to be 4.07 Å3 Da−1; assuming the presence of two molecules in the asymmetric unit it was calculated to be 2.03 Å3 Da−1.
Overexpression, crystallization and preliminary X-ray crystallographic analysis of shikimate dehydrogenase from Archaeoglobus fulgidus
Authors: Lee Hyung Ho 
Published: November 2011

Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Previous structural studies have shown that SDH exists in two conformations, an open and a closed form, and it is believed that the conformational state is crucial to understanding its catalytic mechanism. In order to facilitate further structural comparisons among SDHs, including the conformational state, structural analysis of an SDH from Archaeoglobus fulgidus encoded by the Af2327 gene has been initiated. SeMet-labelled SDH from A. fulgidus was overexpressed in Escherichia coli and crystallized at 296 K using ammonium sulfate as a precipitant in order to use the MAD method for structure determination. Crystals of A. fulgidus SDH grown in the presence of NADP+ diffracted to 2.8 Å resolution and belonged to the trigonal space group P3221 (or P3221), with unit-cell parameters a = 111.3, b = 111.3, c = 76.2 Å. Three diffraction data sets were collected. The asymmetric unit contains two monomers, with a corresponding V
M of 2.34 Å3 Da−1 and a solvent content of 47% by volume.
Results of ambulatory pH monitoring do not reliably predict response to therapy in patients with eosinophilic oesophagitis
Authors: Francis D. L. , Foxx‐Orenstein A. , Arora A. S. , Smyrk T. C. , Jensen K. , Nord S. L. , Alexander J. A. , Romero Y. , Katzka D. A. 
Published: November 2011

Aliment Pharmacol Ther 2012; 35: #–#SummaryBackground  The consensus statements for eosinophilic oesophagitis recommend that ambulatory pH monitoring is one means of determining if gastro‐oesophageal reflux is the cause of oesophageal eosinophilia and should guide pharmacological therapy.Aim  To evaluate prospectively the accuracy of pH monitoring as a predictor of endoscopic, histological and symptomatic response in patients with oesophageal eosinophilia.Methods  We conducted a prospective trial in which patients with oesophageal eosinophilic infiltration with ≥15 eos/hpf underwent a 24‐h pH study and were placed in one of two treatment arms for 6 weeks based on positive or negative results. Patients with abnormal acid exposure were treated with esomeprazole 40 mg twice daily and others were treated with oral viscous budesonide 1 g twice daily. Response to treatment was assessed by oesophageal histology (<5 eos/hpf) and symptoms.Results  A total of 51 patients were enrolled in the study. The average patient age was 39 years and 31 patients (61%) were male. The average number of eosinophils per hpf, prior to study enrolment was 41.2 (range 15–140, s.d. 27.7). Nineteen (37%) had positive pH studies and 32 (63%) had negative pH studies. Eighteen patients completed treatment with esomeprazole. Only eleven (61%) had histological response and, of these eleven, five (46%) had symptomatic improvement. A total of 28 patients with normal acid exposure completed treatment with budesonide. Only 16 (57%) had histological and 11 (69%) had symptomatic improvement.Conclusion  In this prospective trial of pH‐guided treatment, neither positive nor negative results of initial pH monitoring accurately predicted response to therapy.