bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knowledge-based gene expression classification via matrix factorization
Authors: Schachtner R. , Lutter D. , Knollmüller P. , Tomé A. M. , Theis F. J. , Schmitz G. , Stetter M. , Vilda P. Gómez , Lang E. W. 
Published: June 2008

AbstractMotivation: Modern machine learning methods based on matrix decomposition techniques, like independent component analysis (ICA) or non-negative matrix factorization (NMF), provide new and efficient analysis tools which are currently explored to analyze gene expression profiles. These exploratory feature extraction techniques yield expression modes (ICA) or metagenes (NMF). These extracted features are considered indicative of underlying regulatory processes. They can as well be applied to the classification of gene expression datasets by grouping samples into different categories for diagnostic purposes or group genes into functional categories for further investigation of related metabolic pathways and regulatory networks.Results: In this study we focus on unsupervised matrix factorization techniques and apply ICA and sparse NMF to microarray datasets. The latter monitor the gene expression levels of human peripheral blood cells during differentiation from monocytes to macrophages. We show that these tools are able to identify relevant signatures in the deduced component matrices and extract informative sets of marker genes from these gene expression profiles. The methods rely on the joint discriminative power of a set of marker genes rather than on single marker genes. With these sets of marker genes, corroborated by leave-one-out or random forest cross-validation, the datasets could easily be classified into related diagnostic categories. The latter correspond to either monocytes versus macrophages or healthy vs Niemann Pick C disease patients.Supplementary information: Supplementary data are available at Bioinformatics online.Contact: elmar.lang@biologie.uni-regensburg.de
Increased formation of sister chromatid exchanges, but not of micronuclei, in anaesthetists exposed to low levels of sevoflurane
Authors: Wiesner G. , Schiewe‐Langgartner F. , Lindner R. , Gruber M. 
Published: June 2008

SummaryWe have assessed, for the first time, genotoxicity (i.e. sister chromatid exchanges and micronuclei) in anaesthetists exposed to a single volatile anaesthetic (sevoflurane) without nitrous oxide. The anaesthetists were exposed to an 8‐h time‐weighted average of 0.2 parts per million sevoflurane. Internists served as non‐exposed controls. Mean (SD) sister chromatid exchanges per cell were significantly higher in anaesthetists compared to internists (6.6 (0.9) vs 5.1 (0.8); p < 0.001) whereas median (IQR [range]) micronuclei per 1000 binucleated cells did not differ (9.5 (6.3–10.8 [2.0–15.5]) vs 8.5 (6.0–10.5 [3.0–25.5]), respectively). Although the anaesthetists were exposed to rather low concentrations of sevoflurane, this 30% increase of sister chromatid exchanges is in agreement with a recently reported 300% increase with a high level exposure to sevoflurane and nitrous oxide. Omitting nitrous oxide does not normalise increased rates of sister chromatid exchanges.
Performance of oxygen delivery devices when the breathing pattern of respiratory failure is simulated*
Authors: Sim M. A. B. , Dean P. , Kinsella J. , Black R. , Carter R. , Hughes M. 
Published: June 2008

SummaryOxygen is the commonest drug prescribed in hospitals. The inhaled concentration is altered by the administered oxygen flow rate, the characteristics of the delivery device and the patient’s respiratory pattern. Using healthy volunteers we measured the inspired oxygen concentration achieved with different devices both at rest and when the breathing pattern of respiratory failure was simulated by binding the subjects' chests until the forced expiratory volume in 1 s was reduced by > 50% and the respiratory rate was > 25 breaths.min−1. With this respiratory pattern, there was a statistically significant fall in FIo2 while administering oxygen via a Hudson mask at 4 l.min−1 (23.8% (95% CI 17.4–30.3%) reduction), 12 l.min−1, humidified (17.8% (95% CI 8.8–26.7%) reduction) and 24 l.min−1, humidified (12.2% (95% CI 5.0–19.3%) reduction). There was no statistically significant change with a nonrebreathing (reservoir) mask at 15 and 110 l.min−1 or with a Vapotherm 2000i™ at 40 l.min−1, humidified, via nasal prongs. We conclude that the FIo2 delivered by high flow devices is unaffected when the breathing pattern of respiratory failure is simulated. The FIo2 achieved at rest by a nonrebreathing mask (0.68) is less than that often quoted in the literature.
Phase 2, single‐arm trial to evaluate the effectiveness of darbepoetin alfa for correcting anaemia in patients with myelodysplastic syndromes
Authors: Gabrilove Janice , Paquette Ronald , Lyons Roger M. , Mushtaq Chaudhry , Sekeres Mikkael A. , Tomita Dianne , Dreiling Lyndah 
Published: June 2008

SummaryPatients with myelodysplastic syndromes (MDS) often develop anaemia resulting in frequent transfusions and fatigue. Darbepoetin alfa is an erythropoiesis‐stimulating agent (ESA) approved for treating chemotherapy‐induced anaemia. This single‐arm, phase 2 study examined the efficacy of darbepoetin alfa 500 μg every 3 weeks (Q3W) for treating anaemia in low‐risk MDS patients (after 6 weeks, poor responders received darbepoetin alfa 500 μg every 2 weeks). The primary end‐point was the incidence of erythroid responses (International Working Group criteria) after 13 weeks of therapy. Secondary end‐points included the incidence of erythroid responses at weeks 28 and 55, [or weeks 27 and 53 for dose escalations to every two weeks (Q2W)], and safety parameters. Analyses were stratified by the patient’s previous ESA therapy status [ESA‐naïve (n = 144) vs. prior ESA‐treated (n = 62)]. After 13 weeks of therapy, 49% of ESA‐naïve patients and 26% of prior ESA‐treated patients achieved a major erythroid response. After 53/55 weeks, 59% of ESA‐naïve patients and 34% of prior ESA‐treated patients achieved a major erythroid response; 82% of ESA‐naïve patients and 55% of prior ESA‐treated patients achieved target haemoglobin of 110 g/l. Thromboembolic or related adverse events occurred in 2% of patients; no pulmonary embolisms were reported. In conclusion, darbepoetin alfa, 500 μg Q3W appeared well tolerated and increased haemoglobin levels in low‐risk MDS patients.
Prevention and management of BK‐virus associated haemorrhagic cystitis in children following haematopoietic stem cell transplantation – a systematic review and evidence‐based guidance for clinical management
Authors: Harkensee Christian , Vasdev Nikhil , Gennery Andrew R. , Willetts Ian E. , Taylor Clive 
Published: June 2008

SummaryHaemorrhagic cystitis (HC) is a common and, in its severe form, potentially life‐threatening complication of Haematopoietic stem cell transplantation (HSCT) in children. Recent data indicate an important role of BK virus reactivation during the time of maximal post‐transplant immune suppression in the pathogenesis of late‐onset HC. Treatment of HC is mainly symptomatic and often frustrating. To give clinicians guidance on prevention and treatment options and their backing by scientific evidence, we have systematically assessed the available literature and devised evidence‐based guidelines. Our comprehensive review demonstrates that evidence for the most commonly used interventions (such as cidofovir, oestrogen, hyperbaric oxygen, bladder instillation with formalin, alum salts or prostaglandin) is very limited. Some of these interventions also carry significant risks. Higher level evidence exists only for 2‐mercaptoethane sodium (MESNA) and hyperhydration as a preventative intervention, and for systemic recombinant Factor VII as a treatment to stop acute haemorrhage. Further high‐quality studies are required to establish effective and safe prevention and treatment options for HC.
Toll‐like receptor signalling on Tregs: to suppress or not to suppress?
Authors: Van Maren Wendy W. C. , Jacobs Joannes F. M. , De Vries I. Jolanda M. , Nierkens Stefan , Adema Gosse J. 
Published: June 2008

SummaryTo balance self‐tolerance and immunity against pathogens or tumours, the immune system depends on both activation mechanisms and down‐regulatory mechanisms. Immunologists have long been focusing on activation mechanisms, and a major breakthrough was the identification of the Toll‐like receptor (TLR) family of proteins. TLRs recognize conserved molecular patterns present on pathogens, including bacteria, viruses, fungi and protozoa. Pathogen recognition via TLRs activates the innate as well as the adaptive immune response. The discovery of a suppressive T‐cell subset that constitutively expresses the interleukin (IL)‐2 receptor α‐chain (CD25) has boosted efforts to investigate the negative regulation of immune responses. It is now well appreciated that these regulatory T cells (Tregs) play a pivotal role in controlling immune function. Interestingly, recent studies revealed that TLR2 signalling affects Treg expansion and function. This review will focus on the presence and influence of different TLRs on T lymphocytes, including Tregs, and their role in cancer.
Enzyme‐assisted hexane extraction of Ricinodendron heudelotii (Bail.) Pierre ex Pax seeds oil
Authors: Dandjouma Almeck K. Aboubakar , Tchiégang Clergé , Kapseu César , Linder Michel , Parmentier Michel 
Published: June 2008

SummaryThe effects of an enzymatic pretreatment with a protease and a cellulase in the Ricinodendron heudelotii seeds oil extraction process were studied. This was done in a factorial experiment involving three enzyme concentrations and three treatment times for each enzyme. Measured variables were oil extraction yield and quality. Enzymatic hydrolysis significantly (P < 0.05) increased the oil extraction yield. The highest improvement was obtained for R. heudelotii seeds treated with Protamex (Protease) which gave 15% (w/w) increase. Notwithstanding the increase in free fatty acids, mono, diglycerides, peroxide and acid values, the quality of the oil was not significantly (P < 0.05) altered by the enzymatic treatments, suggesting the possibility of using enzyme‐assisted oil extraction methods to improve upon R. heudelotii processing.
Effect of microwave heating of wheat grains on the browning of dough and quality of chapattis
Authors: Yadav Deep Narayan , Patki Prakash Eknathrao , Sharma Gopal Kumar , Bawa Amarinder Singh 
Published: June 2008

SummaryStudies were conducted to evaluate the effect of microwave (900 W, 2450 MHz) heating of wheat grains conditioned to different moisture levels on the activity of polyphenol oxidase (PPO) and subsequent colour changes during storage of wheat dough. The results showed that microwave heating of wheat grains for 80 s decreased the PPO activity significantly (P ≤ 0.05) with an increase in moisture level from 12 to 18%. Whole wheat flour milled from microwave treated wheat grains (80 s, 18% MC) had 93.39% less activity of PPO. The dough balls (40 g), pressed and rolled into circular form (150.00 mm diameter and 2.00 mm thickness) and stored at 5–6 °C for 72 h. The colour of flattened circular dough was measured using Hunter Colour Meter and it was found that L‐value (lightness) decreased from 64.21 to 60.23 in treated and from 64.79 to 47.93 in control samples after 72 h of storage. The results showed that the microwave heating effectively controlled the enzymatic browning in dough and improved the consumer acceptability of chapattis prepared from the same during refrigerated (5–6 °C) storage for 72 h.
Convective hot air drying of blanched yam slices
Authors: Sobukola Olajide Philip , Dairo Olawale Usman , Odunewu Adebayo Victor 
Published: June 2008

SummaryIn this study, a laboratory convective hot air dryer was used for the thin layer drying of blanched yam slices and experimental moisture ratio was compared with Newton, Logarithmic, Henderson and Pabis, modified Henderson and Pabis, approximation of diffusion, modified page 1, two‐term exponential, Verma et al. and Wang and Singh models. Among all the models, the approximation of diffusion model was found to satisfactorily describe the kinetics of air‐drying of blanched yam slices. The increase in air temperature significantly reduced the drying time with no constant rate period but drying occurs in falling rate period. The effective diffusivity values varied between 7.62 × 10−8 to 9.06 × 10−8 m2 s−1 and increased with increase in temperature. An Arrhenius relation with an activation energy value of 8.831 kJ mol−1 showed the effect of temperature on moisture diffusivity.
Gluten contamination of cereal foods in Canada
Authors: Gélinas Pierre , McKinnon Carole M. , Mena Mari Carmen , Méndez Enrique 
Published: June 2008

SummaryPersons suffering from celiac disease (CD) must avoid foods containing gluten or those contaminated with wheat, barley, or rye. This study was designed to estimate gluten contamination of cereal‐based foods available in Canada, whether labelled gluten‐free or not. About half of the 148 foods sampled were labelled as gluten‐free. According to R5‐enzyme‐linked immunosorbent assay (ELISA), twenty‐three cereal‐based foods (or 15%) contained more than 20 mg of gluten per kg, including sixteen regular and seven gluten‐free foods, the latter being the least contaminated. When used in combination with R5‐ELISA, AOAC‐ELISA (not detecting barley) was a simple and efficient tool to roughly estimate the nature of the gluten contamination, which was later confirmed by real‐time polymerase chain reaction for barley, and wheat/barley/rice. Rice‐, corn‐ or quinoa‐based foods were the safest for celiac patients. In addition to misleading food labelling for both gluten‐rich and gluten‐free foods, critical issues for persons with CD included foods made with oats or buckwheat (contaminated with wheat and barley gluten) in addition to those, such as breakfast cereals, specifically enriched with barley malt ingredients.
Effect of storage at 0 °C on mantle proteins and functional properties of jumbo squid
Authors: De La Fuente‐Betancourt Gabriela , García‐Carreño Fernando , Toro María de los Ángeles Navarrete del , Pacheco‐Aguilar Ramón , Córdova‐Murueta Julio H. 
Published: June 2008

SummaryEffect of iced storage of jumbo squid mantle with fin on gelling capacity and changes in protein fractions and functional properties of jumbo squid mantle protein during storage at 0 °C were assessed. Most values of texture variables in gels did not significantly change during storage. On average, they were: strength 65.07 ± 4.71 N; elasticity 68.14 ± 5.3%, fracturability 52.97 ± 1.28 N and cohesiveness 36.6 ± 0.1%. Protein solubility increased more than 40%. Whippability increased during storage for 16 days at 0 °C (81–162%), as did foam stability (73–94%). Results suggest that iced squid mantle protein is a suitable ingredient for food products where these functional properties are desirable. Muscle fibres of squid mantle undergo various changes during storage. At 0 °C, they are disrupted, whereas at −20 °C, they aggregate and develop empty spaces in the tissue.
Spoilage potential of ice‐stored whole musky octopus (Eledone moschata)
Authors: Lougovois Vladimiros P. , Kolovou Maria K. , Savvaidis Ioannis N. , Kontominas Michael G. 
Published: June 2008

SummaryThe spoilage potential of fresh musky octopus (Eledone moschata) was determined by evaluating the changes in biochemical and physical properties, microbial growth and sensory quality of the mantle and tentacles, over a period of 18 days. Whole musky octopus, stored in melting ice from the time of harvest, had a storage life of 10 days. Early deterioration in the sensory quality resulted primarily from autolytic reactions. Pseudomonas spp. dominated the spoilage flora, reaching an average count of 108 CFU g−1 at the end of the trial. The bacterial metabolic end products (trimethylamine, total volatile bases) were not useful as objective indicators of freshness, and measurements of pH would only provide an indicator of decomposition. Changes in the dielectric properties of the mantle were reflective of quality deterioration, but could not yield precise information on the storage history of the cephalopod. The common sulphide producer, Shewanella putrefaciens, was not a major spoiler of ice‐stored musky octopus.
Global properties of the rich cluster ABCG 209 at z∼ 0.2. Spectroscopic and photometric catalogue
Authors: Mercurio A. , La Barbera F. , Haines C. P. , Merluzzi P. , Busarello G. , Capaccioli M. 
Published: June 2008

Abstract
This paper is aimed at giving an overview of the global properties of the rich cluster of galaxies ABCG 209. This is achieved by complementing the already available data with new medium-resolution spectroscopy and near-infrared (NIR) photometry which allow us to (i) analyse in detail the cluster dynamics, distinguishing among galaxies belonging to different substructures and deriving their individual velocity distributions, using a total sample of 148 galaxies in the cluster region, of which 134 belonging to the cluster; (ii) derive the cluster NIR luminosity function; (iii) study the Kormendy relation and the photometric plane of cluster early-type galaxies (ETGs). Finally we provide an extensive photometric (optical and NIR) and spectroscopic data set for such a complex system to be used in further analyses investigating the nature, formation and evolution of rich clusters of galaxies.
The present study shows that the cluster is characterized by a very high value of the line-of-sight velocity dispersion: σv= 1268+93−84 km s−1, that results in a virial mass of Mvir= 2.95+0.80−0.78× 1015h−170 M⊙ within Rvir= 3.42 h−170 Mpc. The analysis of the velocity dispersion profile shows that such high value of σv is already reached in the central cluster region. There is evidence of three significant substructures, the primary one having a velocity dispersion of σv= 847+52−49 km s−1, which makes it consistent with mass estimates from weak lensing analyses.
This observational scenario confirms that ABCG 209 is presently undergoing strong dynamical evolution with the merging of two or more subclumps. This interpretation is also supported by the detection of a radio halo suggesting that there is a recent or ongoing merging.
Cluster ETGs follow a Kormendy relation whose slope is consistent with previous studies both at optical and NIR wavelengths. We investigate the origin of the intrinsic scatter of the photometric plane due to trends of stellar populations, using line indices as indicators of age, metallicity and α/Fe enhancement. We find that the chemical evolution of galaxies could be responsible for the intrinsic dispersion of the photometric plane.
Glucan, water dikinase phosphorylates crystalline maltodextrins and thereby initiates solubilization
Authors: Hejazi Mahdi , Fettke Joerg , Haebel Sophie , Edner Christoph , Paris Oskar , Frohberg Claus , Steup Martin , Ritte Gerhard 
Published: June 2008

SummaryStarch phosphorylation by glucan, water dikinase (GWD; EC 2.7.9.4) is an essential step in the breakdown of native starch particles, but the underlying mechanisms have remained obscure. In this paper, the initial reactions of starch degradation were analyzed using crystallized maltodextrins as model carbohydrates. As revealed by X‐ray diffraction analysis, the crystallized maltodextrins represent the B‐type starch allomorph. Recombinant GWD phosphorylated crystalline maltodextrins with a high specific activity (55–60 nmol mg−1 protein min−1), but exhibited very little activity with the same maltodextrins that had been solubilized by heat treatment. Recombinant phosphoglucan, water dikinase (PWD; EC 2.7.9.5) utilized the crystalline maltodextrins only when pre‐phosphorylated by GWD. Phosphorylation of crystalline maltodextrins, as catalyzed by GWD, initiated solubilization of neutral as well as phosphorylated glucans. In both the insoluble and the soluble state, mono‐, di‐ and triphosphorylated α‐glucans were observed, with wide and overlapping ranges of degree of polymerization. Thus, the substrate specificity of the GWD is defined by the physical arrangement of α‐glucans rather than by structural parameters, such as the distribution of branching points or degree of polymerization. Unlike GWD and PWD, recombinant β‐amylase isozyme 3 (BAM3), which has been shown to be essential for plastidial starch degradation, preferentially degraded soluble maltodextrins rather than crystallized glucans. In summary, two conclusions were reached. Firstly, carbohydrate targets of GWD are primarily defined by the molecular order of glucan helices. Secondly, GWD‐catalyzed phosphorylation mediates the phase transition of glucans from a highly ordered to a less ordered and hydrated state.
Hepatitis E virus as an etiology of acute exacerbation of previously unrecognized asymptomatic patients with hepatitis B virus‐related chronic liver disease
Authors: Kumar Manoj , Sharma Barjesh C , Sarin Shiv K 
Published: June 2008

AbstractBackground and Aim:  Hepatitis E virus (HEV) has recently been implicated in episodes of acute decompensation in patients having underlying chronic liver disease (CLD) of varying etiology. However, HEV as a cause of acute exacerbation of previously asymptomatic and unrecognized hepatitis B virus (HBV)‐infected patients is less well described. The aim of the present study was to investigate the etiology of acute exacerbation of previously asymptomatic and unrecognized HBV‐infected patients and to evaluate the relative role of HEV. We also investigated the effect of superinfection on the clinical spectrum of underlying HBV infection.Methods:  Forty‐three patients presented with the following were retrospectively analyzed: (i) clinical features suggestive of acute hepatitis; (ii) with hepatitis B surface antigen (HBsAg) (+); (iii) IgM hepatitis B core antibody (IgM anti‐HBc) (−); (iv) no previous history of liver disease; (v) no features suggestive of CLD at presentation; (vi) HBsAg remaining (+) for at least 12 months on follow up; and (vii) having a follow‐up biopsy during the convalescent phase showing evidence of chronic hepatitis B.Results:  Of the 43 patients, 21 were hepatitis e antigen (HBeAg) (+) (Gr.1) and 22 HBeAg (−) (Gr.2) at presentation. In Gr.1, only two (9.5%) had superinfection (both with hepatitis A virus), whereas in Gr.2, 11 (50%) had superinfection (27.3% hepatitis E, 13.6% hepatitis A and 9.1% both) (P = 0.007). In Gr.1, the remaining 19 (90.5%) patients had spontaneous exacerbation (immune clearance with spontaneous seroconversion) whereas in Gr.2, the remaining 11 (50%) had spontaneous exacerbation (due to reactivation). Overall, HEV superinfection contributed to 20% of acute exacerbation episodes and, in particular, 36% of episodes in initially HBeAg (−) patients. Time to alanine aminotransferase normalization was longer in patients with superinfection (n = 13) as compared to spontaneous exacerbation (n = 30) (median [range] 36 [8–48]vs 16 [6–36] weeks, P = 0.001). During convalescence, there was no significant difference between histological activity index score (median [range] 8 [4–11]vs 8 [4–16] weeks, P = 0.629) and fibrosis scores (median [range] 3.5 [1–4]vs 2 [1–4] weeks, P = 0.099] on liver biopsy after recovery among patients with acute exacerbation due to superinfection and spontaneous exacerbation.Conclusions:  Acute exacerbations in HBeAg (+) patients are most often due to spontaneous viral activation, while in HBeAg (−) patients, superinfection with non‐B hepatitis viruses and spontaneous viral activation are equally common. HEV is an important cause of acute exacerbation in previously asymptomatic and unrecognized patients with HBV‐related CLD.