bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of second malignant neoplasm incidence in a large cohort of long‐term survivors of childhood cancers
Authors: Dinu Irina , Liu Yan , Leisenring Wendy , Mertens Ann C. , Neglia Joseph P. , Hammond Sue , Robison Leslie L. , Yasui Yutaka 
Published: August 2007

AbstractBackgroundThe ability to predict adverse‐event occurrences accurately in long‐term survivors of childhood cancer is of high importance in late effects research, both clinically and methodologically.ProcedureThis article considers a statistical prediction of future events in a cohort, taking second malignant neoplasm (SMN) incidence in a large cohort of long‐term childhood cancer survivors as an example. The method consists of dividing the follow‐up period of the cohort into two non‐overlapping periods, using the first period as “training data,” with which we model the patterns of SMN occurrences in the cohort, and the subsequent period as “testing data,” with which we validate the model based on the training data. Future predictions are also applied beyond the testing‐data period to calculate the SMN incidence of the cohort in the next five years for overall and specific types of SMNs.ResultsThe proposed statistical prediction is shown empirically to perform well with respect to the prediction accuracy. Overall, the models were able to predict the future second cancers rates very well, with exceptions of a few cancer types that had very small observed counts in the testing period.ConclusionsOur proposed statistical method predicts future events in a cohort of long‐term childhood cancer survivors and, as such, is a useful tool for late effects research on childhood cancer survivors. Pediatr Blood Cancer 2008;50:1026–1031. © 2007 Wiley‐Liss, Inc.
Intensive chemotherapy followed by consolidative myeloablative chemotherapy with autologous hematopoietic cell rescue (AuHCR) in young children with newly diagnosed supratentorial primitive neuroectodermal tumors (sPNETs): Report of the Head Start I and II experience
Authors: Fangusaro Jason , Finlay Jonathan , Sposto Richard , Ji Lingyun , Saly Monirath , Zacharoulis Stergios , Asgharzadeh Shahab , Abromowitch Minnie , Olshefski Randal , Halpern Steven , Dubowy Ronald , Comito Melanie , Diez Blanca , Kellie Stewart , Hukin Juliette , Rosenblum Marc , Dunkel Ira , Miller Douglas C. , Allen Jeffrey , Gardner Sharon 
Published: August 2007

AbstractBackgroundChildren with newly diagnosed supratentorial primitive neuroectodermal tumors (sPNET) have poor outcomes compared to medulloblastoma patients, despite similar treatments. In an effort to improve overall survival (OS) and event‐free survival (EFS) and to decrease radiation exposure, the Head Start (HS) protocols treated children with newly diagnosed sPNET utilizing intensified induction chemotherapy (ICHT) followed by consolidation with myeloablative chemotherapy and autologous hematopoietic cell rescue (AuHCR).ProceduresBetween 1991 and 2002, 43 children with sPNET were prospectively treated on two serial studies (HS I and II). After maximal safe surgical resection, patients on HS I and patients with localized disease on HS II were treated with five cycles of ICHT (vincristine, cisplatin, cyclophosphamide, and etoposide). Patients on HS II with disseminated disease received high‐dose methotrexate during ICHT. If the disease remained stable or in response, patients received a single cycle of high‐dose myeloablative chemotherapy followed by AuHCR.ResultsFive‐year EFS and OS were 39% (95%CI: 24%, 53%) and 49 (95%CI: 33%, 62%), respectively. Non‐pineal sPNET patients faired significantly better than those patients with pineal sPNETs. Metastasis at diagnosis, age, and extent of resection were not significant prognostic factors. Sixty percent of survivors (12 of 20) are alive without exposure to radiation therapy.ConclusionsICHT followed by AuHCR in young patients with newly diagnosed sPNET appears to not only provide an improved EFS and OS for patients who typically have a poor prognosis, but also it successfully permitted deferral and elimination of radiation therapy in a significant proportion of patients. Pediatr Blood Cancer 2008;50:312–318. © 2007 Wiley‐Liss, Inc.
Phase 2 study of docetaxel in the treatment of childhood refractory acute leukemias: A Children's Oncology Group report
Authors: Franklin Janet L. , Seibel Nita L. , Krailo Mark , Fu Cecilia , Adamson Peter C. , Reaman Gregory 
Published: August 2007

AbstractBackgroundTo determine the response rate and toxicity of docetaxel when administered as a 60 mg/m2 dose by 1 hr intravenous (IV) infusion weekly × 3 weeks in children with relapsed acute lymphoblastic leukemia (ALL) or acute myeloid leukemia (AML).ProcedurePatients who were under the age of 22‐year‐old at the time of the original ALL or AML diagnosis and in a second relapse were accrued from August 2002 to May 2005 for this Children's Oncology Group (COG) phase 2 study (ADVL0023). Ten patients with ALL and two patients with AML were enrolled.ResultsThere were no complete or partial responses observed. The most common grade 3 or 4 toxicities were hematologic followed by febrile neutropenia. One patient developed a dose limiting elevation in serum bilirubin, but no other significant hepatotoxicity was observed.ConclusionsDocetaxel was not effective therapy for children with relapsed ALL at the dose and schedule tested. Pediatr Blood Cancer 2008;50:533–536. © 2007 Wiley‐Liss, Inc.
Modeling the structure of mAb 14B7 bound to the anthrax protective antigen
Authors: Sivasubramanian Arvind , Maynard Jennifer A. , Gray Jeffrey J. 
Published: August 2007

AbstractThe anthrax protective antigen (PA) is a key component of the tripartite anthrax toxin. Monoclonal antibody (mAb) 14B7 and its engineered, affinity‐matured variants have been shown to be effective in blocking PA binding to cellular receptors and mitigating anthrax toxicity. Here, we perform computational structural modeling of the mAb 14B7‐PA interaction. Our objectives are to determine the structure of the 14B7‐PA complex, to deduce a structural explanation for the affinity maturation from the docking models, and to study the effect of inaccuracies in the antibody homology model on docking. We used the RosettaDock program to dock PA with the mAb 14B7 crystal structure or homology model. Our simulations generate two distinct binding orientations consistent with experimental residue mutations that diminish 14B7‐PA binding. Furthermore, the models suggest new site‐directed mutations to positively identify one of these two solutions as the correct 14B7‐PA docking orientation. The models indicate that PA regions 648–660 and 712–720 may be important for 14B7 binding in addition to the known PA epitope, and the binding interfaces are similar to that seen in the PA complex with cellular receptor CMG2. Antibody residues involved in affinity maturation do not contact the antigen in the docking models, suggesting that affinity maturation in the 14B7 family does not result from direct enhancements of antibody–antigen contacts. Docking the homology model produces low‐resolution representations of the crystal structure docking orientations, but homology model docking is frustrated by antibody H3 loop conformation errors. This work demonstrates the usefulness and limitations of computational structure prediction for the development of antibody therapeutics, and reemphasizes the need for flexible backbone docking algorithms to achieve high‐resolution docking using homology models. Proteins 2008. © 2007 Wiley‐Liss, Inc.
RosettaDock in CAPRI rounds 6–12
Authors: Wang Chu , Schueler‐Furman Ora , Andre Ingemar , London Nir , Fleishman Sarel J. , Bradley Philip , Qian Bin , Baker David 
Published: August 2007

AbstractA challenge in protein–protein docking is to account for the conformational changes in the monomers that occur upon binding. The RosettaDock method, which incorporates sidechain flexibility but keeps the backbone fixed, was found in previous CAPRI rounds (4 and 5) to generate docking models with atomic accuracy, provided that conformational changes were mainly restricted to protein sidechains. In the recent rounds of CAPRI (6–12), large backbone conformational changes occur upon binding for several target complexes. To address these challenges, we explicitly introduced backbone flexibility in our modeling procedures by combining rigid‐body docking with protein structure prediction techniques such as modeling variable loops and building homology models. Encouragingly, using this approach we were able to correctly predict a significant backbone conformational change of an interface loop for Target 20 (12 Å rmsd between those in the unbound monomer and complex structures), but accounting for backbone flexibility in protein–protein docking is still very challenging because of the significantly larger conformational space, which must be surveyed. Motivated by these CAPRI challenges, we have made progress in reformulating RosettaDock using a “fold‐tree” representation, which provides a general framework for treating a wide variety of flexible‐backbone docking problems. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A regularization approach for a vertical‐slice model and semi‐Lagrangian Störmer–Verlet time stepping
Authors: Hundertmark T. , Reich S. 
Published: August 2007

AbstractIn this paper, we provide a systematic derivation of regularized equations for a non‐hydrostatic and compressible vertical‐slice model of the dry atmosphere. The derivation is based on an analysis of a semi‐implicit discretization of the equations of motion and a recent regularized formulation is obtained as a special case. An implementation of the regularized equations, using a recent second‐order, centred‐in‐time, two‐time‐level semi‐Lagrangian Störmer–Verlet method, is discussed and a series of numerical experiments is conducted. Copyright © 2007 Royal Meteorological Society
Effects of habitat fragmentation on the three‐way interaction among ants, aphids and larvae of the giant purple emperor, Sasakia charonda (Hewitson), a near‐threatened butterfly
Authors: Kobayashi Takato , Kitahara Masahiko , Tanaka Eri 
Published: August 2007

AbstractSurvival rates of both early and middle instar larvae of the nymphalid butterfly, Sasakiacharonda, were estimated to be lowest on test trees planted in a meadow (site A), intermediate in a small, narrow secondary deciduous broadleaf forest (small patch, site B) and highest in a large secondary deciduous broadleaf forest (large forest, site C). The larval mortality rates due to predation by tree‐climbing predators from the ground (tree climbing predator) such as ants and the larvae of carabids were estimated to be greater at sites A and B than those at site C. The number of predatory ants climbing test trees was significantly greater at sites A and B than at site C, and the ants harvested honeydew from aphids living on tree leaves at those two sites. Aphid densities were significantly higher on trees at sites A and B than at site C, and aphid densities and numbers of predatory ants were significantly and positively correlated at sites A and B. In an experiment controlling aphid density per branch on test trees, the numbers of ants and the mortality rates of S.charonda larvae were greater on branches with high aphid densities than on those with low aphid densities at both sites A and B. These results suggest that the aphid density per host tree was higher in the meadow and the small patch than in the large forest; at both sites these higher aphid densities attracted higher numbers of predatory ants to test trees, and as a result, mortality rates of S.charonda larvae were increased.
Cloning of Flax Oleic Fatty Acid Desaturase and Its Expression in Yeast
Authors: Krasowska Anna , Dziadkowiec Dorota , Polinceusz Anna , Plonka Aneta , Łukaszewicz Marcin 
Published: August 2007

AbstractFatty acid desaturases dehydrogenate acyl chains, which results in the formation of a double bond. Using PCR on flax genomic DNA, we cloned a putative Δ12 fatty acid desaturase (Fad2) gene encoding a 378 amino acid protein. Heterologous expression of this protein in yeast as an N‐terminal fusion to GFP showed its localization within endoplasmic reticulum. Analysis of membrane lipids revealed the production of dienoic fatty acids, decreased levels of FAD2 substrates and an increased concentration of longer fatty acids. Higher peroxidation of lipids in FAD2‐containing strains is not reflected by any visible phenotype in YPD medium. However, FAD2‐containing strains with deleted superoxide dismutase genes exhibited significant growth reductions under oxidative stress.
Urea‐Modified Soy Globulin Proteins (7S and 11S): Effect of Wettability and Secondary Structure on Adhesion
Authors: Zhang Zhonghui , Hua Yufei 
Published: August 2007

AbstractThis investigation characterized wettability and adhesive properties of the major soy protein components conglycinin (7S) and glycinin (11S) after urea modification. Modified 7S and 11S soy proteins were evaluated for gluing strength with pine, walnut, and cherry plywood and for wettability using a bubble shape analyzer. The results showed that different adhesives had varying degrees of wettability on the wood specimens. The 7S soy protein modified with urea had better wettability on cherry and walnut. The 11S soy protein modified with 1M urea had better wettability on pine. The 1M urea modification gave 11S soy protein the greatest bonding strength in all the wood specimens. The 3M urea modification gave 7S soy protein stronger adhesion on cherry and walnut than did 11S protein; but with pine, 11S soy protein had greater adhesion strength than 7S soy protein. Measurement of protein secondary structures indicated that the β‐sheet played an important role in the adhesion strength of 3M urea‐modified soy protein in cherry and walnut, while random coil was the major factor reducing adhesion strength of 7S soy protein modified with 1M urea.
Depression and survival in chronic heart failure: Does gender play a role?
Authors: Faller Hermann , Störk Stefan , Schowalter Marion , Steinbüchel Thomas , Wollner Verena , Ertl Georg , Angermann Christiane E. 
Published: August 2007

AbstractBackground:Data regarding the influence of depression on outcome in chronic heart failure are conflicting and neglect possible gender differences.Aims:To investigate prevalence and prognostic importance of depression in a cohort of patients with symptomatic heart failure and to compare findings in males and females.Methods:Depression was measured at study entry using a self‐reported 9‐item Patient Health Questionnaire (PHQ‐9) in 231 consecutive outpatients. The median follow‐up time was 986 (IQR=664–1120) days.Results:The prevalence of suspected major depression was 13% (minor depression, 17%) and was not different between the sexes. Major (but not minor) depression was associated with an increased mortality risk (hazard ratio [HR]=3.3, 95% confidence interval=1.8–6.1, p<0.001). This relationship remained significant after adjustment for other prognostically relevant factors as age, sex, heart failure aetiology, degree and type of left ventricular dysfunction, and New York Heart Association functional class. However, testing the effect of the interaction between gender and depression failed to reach significance (p=0.37).Conclusion:Our data confirm a high prevalence of depression in chronic heart failure. Further, they prove an independent prognostic impact of major, but not minor, depression. Possible gender differences regarding the prognostic impact of depression require further investigation in a larger patient cohort.
General practitioner sickness absence certification for low back pain is not directly associated with beliefs about back pain
Authors: Watson Paul J. , Bowey Julia , Purcell‐Jones Gari , Gales Tom 
Published: August 2007

AbstractRecent research has demonstrated a relationship between healthcare practitioner beliefs about low back pain and recommendations about activity, work restrictions and work absence. None of the research to date has looked at the relationship between practitioner beliefs and actual behaviour. This study investigated the internal consistency of the pain attitudes and beliefs scale (PABS) and if general practitioner (GP) beliefs about back pain were more predictive of sickness certification for non‐specific low back pain (NSLBP) than a general predisposition to sick certify patients with other non‐specific conditions (common mental illness and non‐specific upper respiratory disorders). Ninty‐four eligible general practitioners were invited to participate in the study and data from 83 (88.3%) were included in the full analysis. Evaluation of the internal consistency of the PABS found the biomedical subscale was good (α=0.781) but the psychosocial subscale was poor (α=0.396) after item elimination both subscales improved; biomedical α=0.790, psychosocial α=0.602. GP sickness certification behaviour for 1 year was gathered from the Department of Employment and Social Security database. Multiple regression analysis demonstrated that neither the biomedical nor the psychosocial subscale of the PABS predicted the number of sickness certificates issued even after controlling for the time employed as a GP, number of hours worked per week and the number of NSLBP patients seen. Certification for other conditions was predictive of NSLBP certificates issued. These results demonstrate that sickness absences certification for NSLBP is predicted by sickness certification behaviour in general and not by scores on the PABS.
Terminal Cambrian and lowest Ordovician succession of Mexican West Gondwana: biotas and sequence stratigraphy of the Tiñu Formation
Authors: LANDING ED , WESTROP STEPHEN R. , KEPPIE JOHN D. 
Published: August 2007

AbstractThe Tiñu Formation of Oaxaca State is the only fossiliferous lower Palaeozoic unit between the Laurentian platform in northwest Mexico and Gondwanan successions in Andean South America. The Tiñu traditionally has been referred to the Lower Ordovician (Tremadoc) and regarded as having a provincially mixed fauna with Laurentian, Avalonian, and Gondwanan elements. Bio- and lithostratigraphic re-evaluation demonstrates that the Tiñu is a Gondwanan, passive margin succession. It includes a lower, thin (to 16 m), condensed, uppermost Cambrian Yudachica Member (new). The Yudachica nonconformably overlies middle Proterozoic basement as a result of very high late Late Cambrian eustatic levels. The Yudachica changes from storm-dominated, but slightly dysoxic, shelf facies (fossil hash limestone and shale) in the south to an upper slope facies with debris flows 50 km to the north. Three biostratigraphically distinct depositional sequences comprise the Yudachica. The Yudachica has Gondwanan-aspect trilobites with low-diversity conodonts characteristic of unrestricted marine/temperate facies. The upper Tiñu, or Río Salinas Member (new), is a Lower Ordovician (Tremadoc) depositional sequence that records strong early, but not earliest, Tremadoc eustatic rise marked by graptolite- and olenid-bearing dysoxic mudstones. Higher strata shoal upward into shell-hash limestones and proximal tempestite sandstones with upper lower Tremadocian unrestricted marine/temperate conodonts. New taxa includeOrminskia rexroadaeLanding gen. et sp. nov. from theCordylodus andresiZone; this euconodont is related to hyaline coniform genera best known from Ordovician tropical platform successions.Cornuodus?clarkeiLanding sp. nov. resembles the coeval, upper lower Tremadoc tropical speciesScalpellodus longipinnatus(Ji & Barnes).
Potential role of rhizobacteria isolated from Northwestern China for enhancing wheat and oat yield
Authors: YAO T. , YASMIN S. , HAFEEZ F. Y. 
Published: August 2007

SUMMARYThe present investigation was designed to assess the range of growth-promoting activities of various rhizosphere bacteria on wheat and oat growing in Lanzhou, China. Detection of the N-fixing bacteria by the acetylene reduction assay-based most probable number (ARA-based MPN) method indicated the presence of significant numbers of N-fixing rhizobacteria, i.e. 5·8×106bacteria/g dry weight of root in association with Chinese wheat varietyV4. A total of 24 rhizobacteria was isolated from wheat and oat grown in Lanzhou, China. These bacterial isolates were studied for growth characteristics, nitrogen fixation, phosphate solubilization and indole acetic acid (IAA) production. All the isolates were motile and gram negative. Acetylene reduction activity was detected in all isolates ranging from 124·6 to 651·6 nmol C2H2reduced/h/vial while almost all isolates produced IAA ranging from 0·2 to 5·1 μg/ml. Only two isolates, ChW1 and ChW6, formed clear zones on Pikovskaia's medium, showing the ability to solubilize phosphates. ChW1 and ChW6 were used to develop fluorescent antibodies to check the cross reactivity of the isolates. Inoculation of these bacterial isolates resulted in higher plant biomass, root area and total N content on Chinese wheat varietyNingchun 2and Pakistani oat varietySwanunder controlled conditions. Among the wheat isolates, ChW5 was the best in promoting wheat growth by increasing its root length, root area, shoot dry weight and total N content. Among oat isolates, ChO3, ChO5 and ChO6 showed significant effects on different growth parameters of their host plants. Using the15N isotope dilution method, the highest N fixation contribution (0·73 of total plant N) was observed in the wheat plants inoculated with isolate ChW5. Random amplified polymorphic DNA (RAPD) analysis of seven selected isolates showed that the variation within the isolates from different host crops grown in the same soil was quite large and helpful not only in defining the bacterial strains associated with different host crops but also in defining the distances of isolates from standard strains of rhizobacteria used. In conclusion, the present results indicate that the selected bacterial isolates did promote the growth of wheat and oat in ways that could be harnessed to practical benefit for the farmer and consistent with sustainable agricultural practices in China.