bluuebunny/crossref_metadata_2025_split huggingface dataset:
The migration ofAscaris suumlarvae, and the associated pulmonary inflammatory response in susceptible C57BL/6j and resistant CBA/Ca mice
Authors: Lewis R. , Behnke J. M. , Cassidy J. P. , Stafford P. , Murray N. , Holland C. V. 
Published: March 2007

SUMMARYAscariasis is an important infection in humans (Ascaris lumbricoides) and pigs (Ascaris suum) and individuals appear to be predisposed to either heavy or light worm burdens. These extremes of susceptibility and resistance are represented in a mouse model by 2 strains of mice, CBA mice showing high resistance to infection and C57BL/6 which are highly susceptible, as reflected in worm burdens in the lungs 6–7 days after infection. In an attempt to identify the point at which the difference between these 2 strains is first manifested, we quantified worm burdens at key stages during infection leading up to the pulmonary stage of development. Thus mice were inoculated with fully embryonatedA. suumeggs and larval burdens were enumerated in the large intestine and rectum, liver and lungs of the 2 strains at 6 h post-inoculation (p.i.) and on each of days 1–8 p.i. inclusively. A higher percentage of the total inoculum was recovered from the intestine/rectum of C57BL/6j mice in contrast to CBA/Ca mice at 6 h p.i. Larvae were recovered from the intestinal contents and also whilst actively migrating through the large intestinal wall. The number of larvae recovered was significantly reduced in CBA/Ca mice in contrast to C57BL/6j mice between the phase of migration from the liver and arrival in the lungs. The combined results of the inoculation of mice with corticosteroids and the examination of the change in profile and number of leukocytes present in bronchoalveolar lavage fluid suggested that the pulmonary inflammatory immune response was not prominently involved in primary protection of mice toA. suuminfection in the latter days of infection in the lungs. The susceptible C57BL/6j mice produced a BAL response almost twice as intense as that of resistant CBA/Ca mice with stronger neutrophil, lymphocyte and eosinophil but not macrophage components, suggesting that the difference in worm burdens between the strains was generated earlier in the course of infection. These results were further corroborated by a histological examination of the lung tissues which showed that the passage of the larval stages ofA. suumthrough the mouse lungs was associated with a marked inflammatory response in both strains. Again, C57BL/6j mice exhibited increased inflammation relative to CBA/Ca mice. Hence some hepatic/post-hepatic factor that varies between the 2 strains, but exerts its effect before the lung phase plays a critical role in determining the success of larvae through the host tissues. The possible sites of this host defence are reviewed.
Dynamic redundancy resolution in a nonholonomic wheeled mobile manipulator
Authors: White Glenn D. , Bhatt Rajankumar M. , Krovi Venkat N. 
Published: March 2007

SUMMARYWheeled Mobile Manipulators (WMM) possess many advantages over fixed-base counterparts in terms of improved workspace, mobility and robustness. However, the combination of the nonholonomic constraints with the inherent redundancy limits effective exploitation of end-effector payload manipulation capabilities. The dynamic-level redundancy-resolution scheme presented in this paper decomposes the system dynamics into decoupled task-space (end-effector motions/forces) and a dynamically consistent null-space (internal motions/forces) component. This simplifies the subsequent development of a prioritized task-space control (of end-effector interactions) and a decoupled but secondary null-space control (of internal motions) in a hierarchical WMM controller. Various aspects of the ensuing novel capabilities are illustrated using a series of simulation results.
Dietary intake of heterocyclic amines in relation to socio-economic, lifestyle and other dietary factors: estimates in a Swedish population
Authors: Ericson U , Wirfält E , Mattisson I , Gullberg B , Skog K 
Published: March 2007

AbstractObjectivesTo estimate the dietary intakes of heterocyclic amines (HCAs), to examine the intakes in relation to socio-economics, lifestyle and other dietary factors and to compare the classification of subjects by intake of HCA versus intake of meat and fish.DesignCross-sectional analysis within the Malmö Diet and Cancer (MDC) cohort. Data were obtained from a modified diet history, a structured questionnaire on socio-economics and lifestyle, anthropometric measurements and chemical analysis of HCAs. HCA intake was cross-classified against meat and fish intake. The likelihood of being a high consumer of HCAs was estimated by logistic regression analysis. Dietary intakes were examined across quintiles of HCA intake using analysis of variance.SettingBaseline examinations conducted in 1991–1994 in Malmö, Sweden.SubjectsA sub-sample of 8599 women and 6575 men of the MDC cohort.ResultsThe mean daily HCA intake was 583 ng for women and 821 ng for men. Subjects were ranked differently with respect to HCA intake compared with intake of fried and baked meat and fish (κ = 0.13). High HCA intake was significantly associated with lower age, overweight, sedentary lifestyle and smoking. Intakes of dietary fibre, fruits and fermented milk products were negatively associated with HCA intake, while intakes of selenium, vegetables, potatoes, alcohol (among men) and non-milk-based margarines (among women) were positively associated with HCA intake.ConclusionsThe estimated daily HCA intake of 690 ng is similar to values obtained elsewhere. The present study suggests that lifestyle factors (e.g. smoking, physical activity, fruit and vegetable intakes, and types of milk products and margarines) may confound associations between HCA intake and disease. The poor correlation between HCA intake and intakes of fried meat and fish facilitates an isolation of the health effects of HCAs.
Diet and cancer risk in Mediterranean countries: open issues
Authors: Vecchia Carlo La , Bosetti Cristina 
Published: March 2007

AbstractObjectiveTo analyse various aspects of the Mediterranean diet in relation to the risk of several common cancers in Italy.DesignData from a series of case-control studies conducted in northern Italy between 1983 and 2004 on over 20 000 cases of several major cancers and 18 000 controls.ResultsFor most digestive tract cancers, the risk decreased with increasing vegetable and fruit consumption, with relative risks between 0.3 and 0.7 for the highest level of intake, and the population-attributable risks for low intake of vegetables and fruit ranged between 15 and 40%. Less strong inverse relations were observed for other (epithelial) cancers, too. A number of micronutrients contained in vegetables and fruit showed an inverse relation with cancer risk. In particular, flavones, flavonols and resveratrol were inversely related to breast cancer risk. Olive oil, which is a typical aspect of the Mediterranean diet, has also been inversely related to cancers of the colorectum and breast, and mainly of the upper digestive and respiratory tract. Consumption of pizza, one of the most typical Italian foods, was related to a reduced risk of digestive tract cancers, although pizza may simply be an aspecific indicator of the Italian diet.ConclusionsAdherence to the Mediterranean diet is a favourable indicator of the risk of several common epithelial cancers in Italy. A score summarising the major characteristics of the Mediterranean diet was related to a priori defined reduced risks of several digestive tract neoplasms by over 50%.
Mediterranean diet and metabolic syndrome: a cross-sectional study in the Canary Islands
Authors: Álvarez León EE , Henríquez P , Serra-Majem L 
Published: March 2007

AbstractObjectiveAssessment of relation between metabolic syndrome (MS) and Mediterranean diet (MD) adherence.DesignCross-sectional study. ATP III definition of MS was used. Adherence to MD was assessed with a Food Frequency Questionnaire. Intakes of cereal, fruit, legumes, vegetables, fish, nuts, monounsaturated to saturated ratio, alcohol from red wine, whole-fat dairy products and red meat were considered.SettingRepresentative sample of population from the Canary Islands (Spain) participating in the Canarian Nutrition Survey (ENCA).Subjects578 adults>18 years.ResultsOf the subjects, 24.4% presented MS. Once adjusted, MD adherence was not related to MS prevalence, but subjects in the third tertile of adherence presented 70% lower prevalence of the blood pressure criteria and 2.5 times more prevalence of the glycaemia criteria with respect to the first tertile. Red meat intake was associated with higher prevalence of blood pressure criteria. Moderate alcohol intake from red wine was associated with lower prevalence of these criteria in women and lower prevalence of HDL cholesterol criteria in men. Fruit intake showed a protective effect on triglyceride criteria, whereas vegetable intake was associated with higher prevalence of this criterion. Cereals' intake showed a protective effect over insulin resistance measured by high insulinaemia level. Fruit intake showed a significative protective effect over high Homeostasis Model Assessment index. Whole-fat dairy products showed a significant protective effect on the glycaemia criteria. High monounsaturated to saturated fatty acid intake showed a protective effect on insulin resistance.ConclusionsSome components of the MD showed a protective effect on the MS and its components.
Evaluating associations between Mediterranean diet adherence indexes and biomarkers of diet and disease
Authors: Bach-Faig A , Geleva D , Carrasco JL , Ribas-Barba L , Serra-Majem L 
Published: March 2007

AbstractObjectiveWe examined associations between two Mediterranean diet (MD) adherence indexes (the MD index, MDI, and the MD score, MDS) and several blood biomarkers of diet and disease.SubjectsWe studied 328 individuals from Catalonia (Northeastern Spain), ages 18–75, who provided fasting blood samples, a subset of the 2346 individuals as part of a larger representative and random sample from the 1992–1993 Catalan Nutritional Survey.Design and methodDiet was measured using 24-h recalls. Biomarkers studied were plasma levels of β-carotene, α-tocopherol, retinol, vitamins B12, C and folates as well as serum total cholesterol, HDL cholesterol, LDL cholesterol and triglycerides. Multivariate linear regression was used to analyse associations of the nutrient biomarkers with the dietary pattern indexes, adjusting for potential confounders.Results and conclusionsSubjects with higher MD adherence, as measured by the two dietary indexes, had significantly higher plasma concentrations of β-carotene, folates, vitamin C, α-tocopherol and HDL cholesterol. The most highly significant relationship was that between folates and the adherence to the MD Pattern, as determined by both indexes.These research findings suggest the potential usefulness of biomarkers as complementary tools for assessing adherence to a dietary pattern. This type of data not only informs the development of robust dietary adherence indexes, but it also provides specific clues about the potential physiological mechanisms that explain the beneficial effects of the MD pattern on chronic disease risk.
Childhood obesity prevention studies: lessons learned and to be learned
Authors: Livingstone MBE , McCaffrey TA , Rennie KL 
Published: March 2007

AbstractObjectiveTo provide an overview of methodological issues in the design, delivery and evaluation of childhood obesity prevention programmes.DesignReview of existing literature.SettingInternational.ResultsInterventions have varied considerably with regard to their design, subject selection criteria, sample size, attrition rates, intervention components and duration of both the intervention and the follow-up phases. However, overall, there is only a limited body of consistent, high-quality evidence on which valid and generalisable conclusions can be drawn about best practices for the prevention of childhood obesity.ConclusionsAlthough the rationale for targeting children and adolescents through primary prevention is now compelling, effective obesity prevention remains elusive. There is increasing consensus that prevention of childhood obesity necessitates multifaceted health promotion interventions based on population health principles. By definition, such interventions should have a range of outcome indicators of effectiveness, generalisability and sustainability, not just the traditional ones focused on individual lifestyle behaviour change. Given the complexity and intricacy of population-based intervention programmes, multiple methods of data collection which combine both qualitative and quantitative approaches will need to be fully exploited in order to move towards evidence-based practice in the future.
Enhancements and modifications of primer design program Primer3
Authors: Koressaar Triinu , Remm Maido 
Published: March 2007

AbstractSummary: The determination of annealing temperature is a critical step in PCR design. This parameter is typically derived from the melting temperature of the PCR primers, so for successful PCR work it is important to determine the melting temperature of primer accurately. We introduced several enhancements in the widely used primer design program Primer3. The improvements include a formula for calculating melting temperature and a salt correction formula. Also, the new version can take into account the effects of divalent cations, which are included in most PCR buffers. Another modification enables using lowercase masked template sequences for primer design.Availability: Features described in this article have been implemented into the development code of Primer3 and will be available in future versions (version 1.1 and newer) of Primer3. Also, a modified version is compiled under the name of mPrimer3 which is distributed independently. The web-based version of mPrimer3 is available at http://bioinfo.ebc.ee/mprimer3/ and the binary code is freely downloadable from the URL http://bioinfo.ebc.ee/download/.Contact: maido.remm@ut.ee
RETRACTED: Analysis and prediction of β-turn types using multinomial logistic regression and artificial neural network
Authors: Mehdi Poursheikhali Asgary , Parviz Abdolmaleki , Anoshirvan Kazemnejad , Samad Jahandidehs 
Published: March 2007

Abstract

Motivation
So far various statistical and machine learning techniques applied for prediction of β-turns. The majority of these techniques have been only focused on the prediction of β-turn location in proteins. We developed a hybrid approach for analysis and prediction of different types of β-turn.

Results
A two-stage hybrid model developed to predict the β-turn types I, II, IV and VIII. Multinomial logistic regression was initially used for the first time to select significant parameters in prediction of β-turn types using a self-consistency test procedure. The extracted parameters were consisted of 80 amino acid positional occurrences and 20 amino acid percentages in β-turn sequence. The most significant parameters were then selected using multinomial logistic regression model. Among these, the occurrences of glutamine, histidine, glutamic acid and arginine, respectively, in positions i, i+1, i+2 and i+3 of β-turn sequence had an overall relationship with 5 β-turn types. A neural network model was then constructed and fed by the parameters selected by multinomial logistic regression to build a hybrid predictor. The networks have been trained and tested on a non-homologous dataset of 565 protein chains by nine fold cross-validation. It has been observed that the hybrid model gives a Matthews correlation coefficient (MCC) of 0.473 and 0.124, respectively, for β-turn types II and VIII which are best among previously reported results. Our model also distinguished the different types of β-turn in the embedded binary logit comparisons which have not carried out so far.

Availability
Available on request from the authors.
iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
Authors: Huang Liang-Tsung , Gromiha M. Michael , Ho Shinn-Ying 
Published: March 2007

AbstractSummary: We have developed a web server, iPTREE-STAB for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes (ΔΔG) upon single amino acid substitutions from amino acid sequence. The discrimination and prediction are mainly based on decision tree coupled with adaptive boosting algorithm, and classification and regression tree, respectively, using three neighboring residues of the mutant site along N- and C-terminals. Our method showed an accuracy of 82% for discriminating the stabilizing and destabilizing mutants, and a correlation of 0.70 for predicting protein stability changes upon mutations.Availability: http://bioinformatics.myweb.hinet.net/iptree.htmContact: michael-gromiha@aist.go.jpSupplementary information: Dataset and other details are given.
Structure of PICK1 and other PDZ domains obtained with the help of self‐binding C‐terminal extensions
Authors: Elkins Jonathan M. , Papagrigoriou Evangelos , Berridge Georgina , Yang Xiaowen , Phillips Claire , Gileadi Carina , Savitsky Pavel , Doyle Declan A. 
Published: March 2007

AbstractPDZ domains are protein–protein interaction modules that generally bind to the C termini of their target proteins. The C‐terminal four amino acids of a prospective binding partner of a PDZ domain are typically the determinants of binding specificity. In an effort to determine the structures of a number of PDZ domains we have included appropriate four residue extensions on the C termini of PDZ domain truncation mutants, designed for self‐binding. Multiple truncations of each PDZ domain were generated. The four residue extensions, which represent known specificity sequences of the target PDZ domains and cover both class I and II motifs, form intermolecular contacts in the expected manner for the interactions of PDZ domains with protein C termini for both classes. We present the structures of eight unique PDZ domains crystallized using this approach and focus on four which provide information on selectivity (PICK1 and the third PDZ domain of DLG2), binding site flexibility (the third PDZ domain of MPDZ), and peptide–domain interactions (MPDZ 12th PDZ domain). Analysis of our results shows a clear improvement in the chances of obtaining PDZ domain crystals by using this approach compared to similar truncations of the PDZ domains without the C‐terminal four residue extensions.
Structure of M11L: A myxoma virus structural homolog of the apoptosis inhibitor, Bcl‐2
Authors: Douglas Andrew E. , Corbett Kevin D. , Berger James M. , McFadden Grant , Handel Tracy M. 
Published: March 2007

AbstractApoptosis of virally infected cells is an innate host mechanism used to prevent viral spread. However, viruses have evolved a number of proteins that function to modulate the apoptotic cascades and thereby favor productive viral replication. One such antiapoptotic protein, myxoma virus M11L, has been shown to inhibit mitochondrial‐dependent apoptosis by binding to and blocking the two executioner proteins Bak and Bax. Since M11L has no obvious sequence homology with Bcl‐2 or Bcl‐xL, the normal cellular inhibitors for Bak and Bax, and the structure of M11L has not been solved, the mode of binding to Bak and Bax is not known. In order to understand how M11L functions, the crystal structure of M11L was solved to 2.91 Å. Despite the lack of sequence similarity, M11L is a structural homolog of Bcl‐2. Studies using a peptide derived from Bak indicate that M11L binds to Bak with a similar affinity (4.9 ± 0.3 μM) to the published binding affinities of Bcl‐2 and Bcl‐xL to the same peptide (12.7 μM and 0.5 μM, respectively), indicating that M11L inhibits apoptosis by mimicking and competing with host proteins for the binding of Bak and Bax. The structure provides important insight into how myxoma virus and other poxviruses facilitate viral dissemination by inhibiting mitochondrial dependent apoptosis.
Low plasma levels of the protein pro‐LL‐37 as an early indication of severe disease in patients with chronic neutropenia
Authors: Karlsson Jenny , Carlsson Göran , Ramme Kim Göransdotter , Hägglund Hans , Fadeel Bengt , Nordenskjöld Magnus , Henter Jan‐Inge , Palmblad Jan , Pütsep Katrin , Andersson Mats 
Published: March 2007

SummaryChronic neutropenia comprises several different diseases that vary in degree of severity and management. We analysed the levels of the neutrophil‐derived protein pro‐LL‐37 in plasma of patients with chronic neutropenia to assess whether it could be used to differentiate different categories of chronic neutropenia. All patients with severe congenital neutropenia were pro‐LL‐37 deficient. This was in contrast to patients with autoimmune or idiopathic neutropenia, who exhibited normal pro‐LL‐37 levels while patients with cyclic neutropenia displayed an oscillation of pro‐LL‐37 in plasma. Plasma levels of pro‐LL‐37 may thus prove useful for differential diagnosis of chronic neutropenia.
Management of acute graft‐versus‐host disease
Authors: Bacigalupo Andrea 
Published: March 2007

SummaryAcute graft‐versus‐host disease (GvHD) is a frequent complication of allogeneic haemopoietic stem cell transplantation (HSCT) and donor lymphocyte infusions (DLI). Its incidence and severity depends on several factors, such as prophylaxis method, donor/recipient matching, intensity of the conditioning regimen and composition of the graft. Significant progress has been made in recent years in understanding the pathogenesis of the disease, and some of these advances have been translated into clinical trials. First‐line treatment of acute GvHD is based on corticosteroids, and produce sustained responses in 50–80% of patients depending on the initial severity. Non‐responders are offered second‐line therapy, with combinations of immunosuppressive agents, but 1‐year survival is 30% in most large trials. New strategies explored include infusion of expanded mesenchymal stem cells (MSC), down regulation of antigen‐presenting cells (APC) and suicide gene transduced T cells. Acute GvHD is complicated by severe immunodeficiency causing life‐threatening infections. To date, GvHD has not been differentiated from the graft‐versus‐leukaemia effect. The present review will discuss some of these aspects.
Protein Z/Z‐dependent protease inhibitor (PZ/ZPI) anticoagulant system and thrombosis
Authors: Corral Javier , González‐Conejero Rocio , Hernández‐Espinosa David , Vicente Vicente 
Published: March 2007

SummaryA new anticoagulant system involving a serpin has been recently characterised. The protein Z/Z‐dependent protease inhibitor (PZ/ZPI) system inhibits activated factors X, XI and IX by different mechanisms. By homology with other anticoagulant systems (antithrombin or the protein C/protein S), deficiency of the serpin (ZPI) or its cofactor (PZ) might imbalance the haemostatic system with thrombotic consequences. Evidence supports the in vivo anticoagulant role of this complex and the thrombotic consequences of its deficiency. Non‐sense variations of the ZPI (W303X and R67X) have been associated with increased risk of venous thrombosis. Moreover, PZ deficient mice carrying the FV Leiden have a thrombotic phenotype. Finally, some reports suggest that PZ deficiency might increase the risk of thrombosis. However, other studies question the thrombotic relevance of both ZPI and PZ deficiencies. This system could play a redundant role in haemostasis that explains the conflicting results on its thrombotic potential, which might be exacerbated in combination with other prothrombotic factors.