bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and stability of icosahedral particles of a covalent coat protein dimer of bacteriophage MS2
Authors: Plevka Pavel , Tars Kaspars , Liljas Lars 
Published: June 2009

AbstractParticles formed by the bacteriophage MS2 coat protein mutants with insertions in their surface loops induce a strong immune response against the inserted epitopes. The covalent dimers created by fusion of two copies of the coat protein gene are more tolerant to various insertions into the surface loops than the single subunits. We determined a 4.7‐Å resolution crystal structure of an icosahedral particle assembled from covalent dimers and compared its stability with wild‐type virions. The structure resembled the wild‐type virion except for the intersubunit linker regions. The covalent dimer orientation was random with respect to both icosahedral twofold and quasi‐twofold symmetry axes. A fraction of the particles was unstable in phosphate buffer because of assembly defects. Our results provide a structural background for design of modified covalent coat protein dimer subunits for use in immunization.
Two alternative modes for optimizing nylon‐6 byproduct hydrolytic activity from a carboxylesterase with a β‐lactamase fold: X‐ray crystallographic analysis of directly evolved 6‐aminohexanoate‐dimer hydrolase
Authors: Ohki Taku , Shibata Naoki , Higuchi Yoshiki , Kawashima Yasuyuki , Takeo Masahiro , Kato Dai‐ichiro , Negoro Seiji 
Published: June 2009

AbstractPromiscuous 6‐aminohexanoate‐linear dimer (Ald)‐hydrolytic activity originally obtained in a carboxylesterase with a β‐lactamase fold was enhanced about 80‐fold by directed evolution using error‐prone PCR and DNA shuffling. Kinetic studies of the mutant enzyme (Hyb‐S4M94) demonstrated that the enzyme had acquired an increased affinity (Km = 15 mM) and turnover (kcat = 3.1 s−1) for Ald, and that a catalytic center suitable for nylon‐6 byproduct hydrolysis had been generated. Construction of various mutant enzymes revealed that the enhanced activity in the newly evolved enzyme is due to the substitutions R187S/F264C/D370Y. Crystal structures of Hyb‐S4M94 with bound substrate suggested that catalytic function for Ald was improved by hydrogen‐bonding/hydrophobic interactions between the AldCOOH and Tyr370, a hydrogen‐bonding network from Ser187 to AldNH, and interaction between AldNH and Gln27‐Oε derived from another subunit in the homo‐dimeric structure. In wild‐type Ald‐hydrolase (NylB), Ald‐hydrolytic activity is thought to be optimized by the substitutions G181D/H266N, which improve an electrostatic interaction with AldNH (Kawashima et al., FEBS J 2009; 276:2547–2556). We propose here that there exist at least two alternative modes for optimizing the Ald‐hydrolytic activity of a carboxylesterase with a β‐lactamase fold.
Homology modeling of human Toll‐like receptors TLR7, 8, and 9 ligand‐binding domains
Authors: Wei Tiandi , Gong Jing , Jamitzky Ferdinand , Heckl Wolfgang M. , Stark Robert W. , Rössle Shaila C. 
Published: June 2009

AbstractToll‐like receptors (TLRs) play a key role in the innate immune system. The TLR7, 8, and 9 compose a family of intracellularly localized TLRs that signal in response to pathogen‐derived nucleic acids. So far, there are no crystallographic structures for TLR7, 8, and 9. For this reason, their ligand‐binding mechanisms are poorly understood. To enable first predictions of the receptor–ligand interaction sites, we developed three‐dimensional structures for the leucine‐rich repeat ectodomains of human TLR7, 8, and 9 based on homology modeling. To achieve a high sequence similarity between targets and templates, structural segments from all known TLR ectodomain structures (human TLR1/2/3/4 and mouse TLR3/4) were used as candidate templates for the modeling. The resulting models support previously reported essential ligand‐binding residues. They also provide a basis to identify three potential receptor dimerization mechanisms. Additionally, potential ligand‐binding residues are identified using combined procedures. We suggest further investigations of these residues through mutation experiments. Our modeling approach can be extended to other members of the TLR family or other repetitive proteins.
Invertebrate drift and benthic exhaustion during disturbance: Response of mayflies (Ephemeroptera) to increasing shear stress and river‐bed instability
Authors: Gibbins Chris , Batalla Ramon J. , Vericat Damià 
Published: June 2009

AbstractWe manipulated hydraulic conditions over patches of sands and fine gravels in an upland, gravel‐bed river using a portable flume and assessed changes in the drift rates of three mayflies (Baetis, EcdyonurusandCaenis). On average, manipulations doubled water velocity in experimental locations and resulted in shear stresses that exceeded the critical threshold for entrainment of patch sediments. Bedload transport rates were used as an indicator of bed disturbance during the manipulations. Partial Least Squares Regression (PLSR) indicated that between 59 and 81% of the variation in the drift rates of the three taxa could be accounted for by the combined effects of shear stress and bed disturbance. Shear stress was more important than bed disturbance as a cause of drift inEcdyonurusandBaetis, while forCaenisthe two variables were equally important. Drift rates fell markedly (10‐fold) after only 5 mins of increased shear stress and bed disturbance. The experiments indicate that (a) dramatic loss of mayflies can occur rapidly from patches of fine and relatively unstable sediment during periods of increased discharge and (b) for some taxa, losses may cause a depletion of the benthic source‐pool and hence result in the exhaustion of supply. Copyright © 2009 John Wiley & Sons, Ltd.
Synthesis of attack actions using model checking for the verification of security protocols
Authors: Basagiannis Stylianos , Katsaros Panagiotis , Pombortsis Andrew 
Published: June 2009

AbstractModel checking cryptographic protocols have evolved to a valuable method for discovering counterintuitive security flaws, which makes it possible for a hostile agent to subvert the goals of the protocol. Published works and existing security analysis tools are usually based on general intruder models that embody at least some aspects of the seminal work of Dolev–Yao, in an attempt to detect failures of secrecy. In this work, we propose an alternative intruder model, which is based on a thorough analysis of how potential attacks might proceed. We introduce an intruder model that provides an open‐ended base for the integration of multiple basic attack tactics. Those attack tactics have the possibility to be combined, in a way to compose complex attack actions that require a number of procedural steps from the intruder's side, such as a Denial of Service attack. In our model checking approach, protocol correctness is checked by appropriate user‐supplied assertions or reachability of invalid end states. The analyst can express security properties of specific attack actions that are not restricted to safety violations captured by a generic model checker. The described intruder model methodology was implemented within the SPIN model checker for verifying two security protocols, Micromint and PayWord. Copyright © 2009 John Wiley & Sons, Ltd.
An adjustment for patient heterogeneity in the design of two‐stage phase II trials
Authors: Sposto Richard , Gaynon Paul S. 
Published: June 2009

AbstractIn single‐arm, two‐stage phase II clinical trials to evaluate efficacy of cancer treatments using a response endpoint, one typically identifies a single reference response rate to be the null hypothesis benchmark. Patients eligible for the trial are assumed to have this response rate on average under the null hypothesis. When patients arise from subpopulations having different response rates, this single response rate reference may not be appropriate for the particular mix of patients actually enrolled on the trial. As a result, the Type I and Type II error rates conditional on the mix of enrolled patients may differ considerably from the unconditional error rates used to design the trial. We describe a method for designing two‐stage Phase II studies that accounts for patient heterogeneity and effectively stabilizes conditional Type I and Type II error over the range of patient mixes that are likely to arise. Use of the design requires good estimates of the expected response rate within each population stratum as well as the stratum membership probabilities, but its properties are similar to and often preferable to the standard two‐stage design even in situations where the underlying assumptions do not hold absolutely. Copyright © 2009 John Wiley & Sons, Ltd.
Mental health and quality of life among doctors, nurses and other hospital staff
Authors: Su Jian‐An , Weng Hsu‐Huei , Tsang Hin‐Yeung , Wu Jhen‐Long 
Published: June 2009

AbstractNumerous studies have shown that doctors, nurses or other hospital staff may suffer from tremendous stress at work. A high level of work‐related stress might increase vulnerability to mental illness and result in a poor quality of clinical care. This study was conducted in a Taiwanese regional general hospital. Minor psychiatric disorder, depressive disorder and quality of life were assessed for all staff, using self‐rating questionnaires including the Chinese Health Questionnaire 12‐item version, the Center for Epidemiologic Studies Depression Scale and World Health Organization Quality of Life Scale brief version. Nearly half of the staff had either a minor psychiatric disorder or depressive disorder. Nurses and pharmacists had the highest prevalence. The risk factors included single/divorced and being a nurse or pharmacist. Quality of life for hospital staff was poor, as compared with the Taiwanese norms, and was even worse for the nurses and pharmacists. In conclusion, the management teams of hospitals should pay more attention to the mental condition of all hospital staff, especially nurses and pharmacists. Adequate staffing, support, counselling or psychological intervention are required for further management, and may logically result in better mental health on the part of the staff and a better quality of care. Copyright © 2009 John Wiley & Sons, Ltd.
A statewide approach to creating veteran‐friendly campuses
Authors: Lokken Jayne M. , Pfeffer Donald S. , McAuley James , Strong Christopher 
Published: June 2009

AbstractThis chapter discusses a statewide response to the needs of veterans, military members, and their families. Specifically, it addresses the collaboration between Minnesota Department of Veterans Affairs‐Higher Education Veterans Programs, St. Cloud State University, and a student veteran organization.
Gfi-1B Promoter Remains Associated with Active Chromatin Marks Throughout Erythroid Differentiation of Human Primary Progenitor Cells
Authors: Laurent Benoît , Randrianarison-Huetz Voahangy , Kadri Zahra , Roméo Paul-Henri , Porteu Françoise , Duménil Dominique 
Published: June 2009

Abstract
Growth Factor Independent-1B (Gfi-1B) is a transcriptional repressor that plays critical roles in the control of erythropoiesis and megakaryopoiesis. Gfi-1B expression was described to be repressed by an autoregulatory feedback control loop. Here, we show that Gfi-1 transcription is positively regulated early after induction of erythroid differentiation and remains highly active to late erythroblasts. Using chromatin immunoprecipitation assays in CD34+ cells from human cord blood, we found that Gfi-1 and GATA-2 in immature progenitors and then Gfi-1B and GATA-1 in erythroblasts are bound to the Gfi-1B promoter as well as to the promoter of c-myc, a known Gfi-1B target gene. Surprisingly, this Gfi-1/GATA-2–Gfi-1B/GATA-1 switch observed at erythroblast stages is associated to an increase in the Gfi-1B transcription whereas it triggers repression of c-myc transcription. Accordingly, analysis of chromatin modification patterns shows that HDAC, CoREST, and LSD1 are recruited to the c-myc promoter leading to appearance of repressive chromatin marks. In contrast, the Gfi-1B promoter remains associated with a transcriptionally active chromatin configuration as highlighted by an increase in histone H3 acetylation and concomitant release of the LSD1 and CoREST corepressors. The repressive function of Gfi-1B therefore depends on the nature of the proteins recruited to the target gene promoters and on chromatin modifications. We conclude that Gfi-1B behaves as a lineage-affiliated gene with an open chromatin configuration in multipotent progenitors and sustained activation as cells progress throughout erythroid differentiation.
Disclosure of potential conflicts of interest is found at the end of this article.
Prospective validation of first‐trimester combined screening for trisomy 21
Authors: Kagan K. O. , Etchegaray A. , Zhou Y. , Wright D. , Nicolaides K. H. 
Published: June 2009

AbstractObjectiveTo examine the performance of the new algorithm in screening for trisomy 21 by a combination of maternal age, fetal nuchal translucency (NT) and maternal serum free β‐human chorionic gonadotropin (β‐hCG) and pregnancy‐associated plasma protein‐A (PAPP‐A).MethodsThis was a prospective screening study for trisomy 21 in singleton pregnancies at 11 + 0 to 13 + 6 weeks of gestation using an algorithm combining maternal age, fetal NT thickness based on the mixture model for the assessment of NT, and maternal serum free β‐hCG and PAPP‐A based on a multiple regression model for the assessment of serum biochemistry. The NT measurements were performed by 60 operators who had obtained The Fetal Medicine Foundation certificate of competence in the 11–13‐week scan.ResultsThe study population consisted of 19 614 pregnancies with a normal karyotype or delivery of a phenotypically normal baby (euploid group) and 122 cases of trisomy 21. In the euploid fetuses the NT was above the previously defined 50th, 95th and 99th centiles in 10 033 (51.2%), 618 (3.2%) and 123 (0.6%) cases and the respective values for trisomy 21 were 117 (95.9%), 94 (77.0%) and 57 (46.7%). The median fetal NT was within 0.1 mm of the expected in 47 (78.3%) of the 60 sonographers and within 0.2 mm in all. In the euploid fetuses the median free β‐hCG was 1.0 (range, 0.1–29.4) multiples of the median (MoM) and the median PAPP‐A was 1.0 (range, 0.2–3.3) MoM. The median MoM values were 1.0 or close to 1.0 MoM for each subgroup of pregnancy characteristics, including gestations of 11, 12 and 13 weeks, maternal weight of < 60 kg, 60–80 kg and > 80 kg, different ethnic origins, cigarette smokers and non‐smokers, natural conception and @ in vitro fertilization. For a false‐positive rate of 3%, the detection rate of trisomy 21 in screening by maternal age and fetal NT was 81% (95% CI, 73–89%), by maternal age and maternal serum biochemistry it was 63% (95% CI, 56–72%) and by combined screening based on maternal age, fetal NT and maternal serum biochemistry it was 90% (95% CI, 84–96%).ConclusionThis study has validated the new risk algorithm and demonstrated that in combined screening for trisomy 21 based on maternal age, fetal NT and free β‐hCG and PAPP‐A the detection rate is about 90% for a 3% false‐positive rate. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Impact of residual in situ carcinoma on postoperative survival in 125 patients with extrahepatic bile duct carcinoma
Authors: Nakanishi Yoshitsugu , Kondo Satoshi , Zen Yoh , Yonemori Atsuya , Kubota Kanako , Kawakami Hiroshi , Tanaka Eiichi , Hirano Satoshi , Itoh Tomoo , Nakanuma Yasuni 
Published: June 2009

AbstractPurposeThe aim of this study was to determine the impact of the presence of carcinoma in situ at the bile duct stump on postoperative survival in patients who underwent resection of extrahepatic bile duct carcinoma.MethodsThe patients with resected extrahepatic bile duct carcinoma were divided into three groups according to resected margin status: no evidence of residual carcinoma (Negative group,n = 96); carcinoma in situ at the bile duct stump (CIS group,n = 10); and invasive carcinoma at any surgical margin (Invasive group,n = 19). Cause‐specific survival for these groups was compared statistically.ResultsSurgical margin status was identified as a prognostic factor on univariate analysis (p = 0.005) and was an independent prognostic factor on multivariate analysis (p = 0.018). The CIS group displayed significantly better survival than the Invasive group (p = 0.006), and the survival was comparable to that for the Negative group (p = 0.533). Two of three patients in the CIS group with local recurrence died >5 years after surgical resection.ConclusionsPatients with positive ductal margins of carcinoma in situ of the extrahepatic bile duct do not appear to show different survival after resection compared to patients with negative margins, but remnant carcinoma in situ is likely to develop late local recurrence.
The Stabilizing Effects of Polyols and Sugars on Porcine Pancreatic Lipase
Authors: Gangadhara  , Ramesh Kumar Parigi , Prakash Vishweshwaraiah 
Published: June 2009

AbstractPorcine pancreatic lipase (PPL) has been used as a biocatalyst for many years and is one of the most widely used enzymes for biotechnological applications; however, it is a rather complex mixture with various active enzymes. The present study has been undertaken to determine the effects of polyols and sugars (cosolvents) on the thermal stability of PPL preparation. The thermal stability of PPL exposed to 60°C for 10 min was enhanced in the presence of cosolvents in terms of both residual specific activity and conformational stability. Thermal denaturation, changes in circular dichroism, fluorescence spectra, apparent kinetic parameters, activity, and preferential interaction parameter of PPL preparation are discussed in terms of contributions to the mechanism of thermal stability and the activity enhancement. Partial specific volume measurement of PPL in the presence of cosolvents is presented for the first time. The preferential interaction parameter (ξ3) was negative in all cosolvents used, and maximum hydration was observed in the presence of trehalose, where the preferential interaction parameter was −0.076 g/g. The observed increase in the thermal stability of PPL preparation in the presence of cosolvents is due to the preferential hydration of the enzyme.
Rheological Properties of Candelilla Wax and Dotriacontane Organogels Measured with a True‐Gap System
Authors: Morales‐Rueda Juan A. , Dibildox‐Alvarado Elena , Charó‐Alonso Miriam A. , Toro‐Vazquez Jorge F. 
Published: June 2009

AbstractThe rheology of organogels developed by candelilla wax (CW) and a pure n‐alkane (dotriacontane, C32) was evaluated with a rheometer equipped with a true‐gap system and compared with the rheograms obtained with a fixed‐gap system. The two systems used a cone and plate geometry. In contrast to the fixed‐gap system, the true‐gap system makes the corrections in the gap size associated with the expansion/shrinkage of the sample and/or the rheometer geometry when changing temperature conditions are used during measurements. The CW and C32 organogels were prepared using safflower oil high in triolein (SFO) as the liquid phase, and the treatments studied resulted from the factorial combinations of two levels of gelator concentration (1 and 3%) and two gel setting temperatures (Tset; 5 and 25 °C) achieved using a cooling rate of 1 or 10 °C/min. The use of the true‐gap system provided rheological parameters (i.e., G′ profiles) that agreed with the micro structure and the calorimetric (i.e., heat of melting, ΔHM) behavior of both the CW and the C32 organogels. The use of a fixed‐gap system in the rheological characterization of organogels must be treated with caution, specially with time dependent G′ determinations involving the use of fast temperature ramps (i.e., 10 °C/min).
Management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (SARS)
Authors: Maxwell Cynthia , McGeer Alison , Young Tai Kin Fan , Sermer Mathew , Farine Dan , Basso Melanie , Delisle Marie‐France , Hudon Lynda , Menticoglou Savas , Mundle William , Ouellet Annie , Yudin Mark H. , Boucher Marc , Castillo Eliana , Cormier Beatrice , Gruslin Andrée , Money Deborah M. , Murphy Kellie , Paquet Caroline , Steenbeek Audrey , Van Eyk Nancy , van Schalkwyk Julie , Wong Thomas 
Published: June 2009

AbstractObjectiveThis document summarizes the limited experience of SARS in pregnancy and suggests guidelines for management.OutcomesCases reported from Asia suggest that maternal and fetal outcomes are worsened by SARS during pregnancy.EvidenceMedline was searched for relevant articles published in English from 2000 to 2007. Case reports were reviewed and expert opinion sought.ValuesRecommendations were made according to the guidelines developed by the Canadian Task Force on Preventive Health Care.
The interactive effects of duality expertise and coping frames on responses to ambivalent messages
Authors: Kramer Thomas , Lau‐Gesk Loraine , Chiu Chi‐yue 
Published: June 2009

AbstractWe examine the interactive effects of biculturals' duality expertise and externally provided coping resources on attitudinal responses to ambivalence. Three studies reveal that ambivalence is associated with greater discomfort for biculturals more (vs. less) conflicted about their cultural duality and with limited exposure to accessing their two cultural knowledge systems simultaneously. Among biculturals with lower duality expertise, coping frames lower their negative evaluation of messages that elicit ambivalence because coping frames help these biculturals resolve the discomfort associated with ambivalence. Provision of coping frames does not impact attitudes of biculturals with greater levels of duality expertise.
Changes in Posterior Lumbar Disk Contour Abnormality with Flexion‐Extension Movement in Subjects with Low Back Pain and Degenerative Disk Disease
Authors: Lee Shi‐Uk , Lee Jong‐In , Butts Kim , Carragee Eugene , Fredericson Michael 
Published: June 2009

ObjectiveTo determine whether posterior lumbar disk contour dimensions differ in the flexed seated, upright seated, and extended seated positions.DesignTwo subgroups of subjects with degenerative disk disease were compared: those with central posterior disk bulge (at L4‐5 or L5‐S1 levels) and those with a dark nucleus pulposus without posterior disk bulge (L3‐4, L4‐5, and/or L5‐S1 levels).SettingAcademic medical center.ParticipantsEight subjects with a central disk bulge and 9 subjects with a dark nucleus pulposus on magnetic resonance imaging.InterventionsNot applicable.Main Outcome MeasuresQuantitative comparisons of posterior disk contour between neutral, flexed, and extended sitting positions.ResultsOf 8 subjects with central disk bulge, spinal flexion (from the neutral position) produced a decreased disk contour in all subjects, whereas spinal extension (from the neutral position) produced an increased disk contour in 6 subjects, a decreased disk contour in 1 subject, and no measurable change in 1 subject. Changes in posterior disk contour in subjects with a dark nucleus pulposus were variable. Approximately half increased and half decreased, but no relation to position was determined.ConclusionsThe results of this pilot study suggest a consistent pattern of decreased posterior disk contour with spinal flexion and increased posterior disk contour with spinal extension in subjects with central disk bulge, but not in those with a dark nucleus pulposus.