bluuebunny/crossref_metadata_2025 huggingface dataset:
Pediatric squamous cell carcinoma arising in an alpha‐fetoprotein‐producing mature cystic teratoma of the mandible
Authors: Cabay Robert J. , Setty Suman , Schwartz Joel L. , Yao Mike , Schmidt Mary Lou , Gordon Sara C.
Published: September 2008

Teratomas, most often diagnosed in younger patients, represent the most frequently identified subtype of pediatric germ cell tumors. It is very uncommon for teratomas to present in the head and neck region and demonstrate malignant transformation. We present a case of squamous cell carcinoma arising in an alpha‐fetoprotein‐producing cystic teratoma of the mandible in a 2‐year‐old female that is, to the best of our knowledge, the first such published report. The patient was treated with surgical excision along with chemotherapy and has remained disease‐free 2 years after the conclusion of therapy. Pediatr Blood Cancer 2009;52:130–132. © 2008 Wiley‐Liss, Inc.
A study of rituximab and ifosfamide, carboplatin, and etoposide chemotherapy in children with recurrent/refractory B‐cell (CD20+) non‐Hodgkin lymphoma and mature B‐cell acute lymphoblastic leukemia: A report from the Children's Oncology Group
Authors: Griffin Timothy C. , Weitzman Sheila , Weinstein Howard , Chang Myron , Cairo Mitchell , Hutchison Robert , Shiramizu Bruce , Wiley Joseph , Woods Deborah , Barnich Margaret , Gross Thomas G.
Published: September 2008

Background

To estimate the response rate and therapy related toxicities of the anti‐CD20 monoclonal antibody rituximab when combined with chemotherapy including ifosfamide, carboplatin, and etoposide (ICE) in patients with relapsed and refractory B‐cell non‐Hodgkin lymphoma and mature B‐cell acute lymphoblastic leukemia (B‐ALL).

Methods

Patients received rituximab and ICE for 1–3 cycles, depending upon response. Rituximab (375 mg/m2) was given on day 1 and 3 of each cycle (day 1 only for cycle 3), with ifosfamide (3,000 mg/m2) and etoposide (100 mg/m2) given on days 3, 4, and 5 and carboplatin (635 mg/m2) given on day 3 only.

Results

Twenty‐one patients were enrolled, of whom 20 were eligible and evaluable. Although hematologic toxicities were common, only one patient was removed from study due to prolonged myelosuppression. Toxicities related to infusions of rituximab were frequent but manageable. Of the six eligible patients with diffuse large B‐cell lymphoma, three achieved complete remission (CR), one had stable disease (SD), and two had progressive disease (PD). Of the 14 eligible patients with Burkitt lymphoma and B‐ALL, there were four complete responses (CR), five partial responses (PR), one SD, and four with PD. Thus, the CR/PR rate for the entire group was 12/20 (60%). Following completion of protocol therapy six patients were able to proceed to consolidation with high‐dose therapy and stem cell rescue.

Conclusions

The combination of rituximab and ICE chemotherapy was associated with an encouraging objective response (OR) rate and an acceptable toxicity profile. Pediatr Blood Cancer 2009;52:177–181. © 2008 Wiley‐Liss, Inc.
Hemophagocytic lymphohistiocytosis in very young infants
Authors: Tanoshima Reo , Takahashi Hiroyuki , Hokosaki Tatsunori , Yamaguchi Kazuko , Goto Shoko , Kai Sumio
Published: September 2008

We report three cases of hemophagocytic lymphohistiocytosis (HLH) in infants within the first 6 weeks of life. Diagnosis of HLH was made early after symptoms started. All three cases were successfully treated with dexamethasone and none relapsed, indicating that not all cases of HLH in very young infants are familial. Pediatr Blood Cancer 2009;52:137–139. © 2008 Wiley‐Liss, Inc.
Management of Wilms tumors in Drash and Frasier syndromes
Authors: Auber F. , Jeanpierre C. , Denamur E. , Jaubert F. , Schleiermacher G. , Patte C. , Cabrol S. , Leverger G. , Nihoul‐Fékété C. , Sarnacki S.
Published: September 2008

Background

Children with WT1 gene‐related disorders such as Denys–Drash syndrome (DDS) and Frasier syndrome (FS) are at increased risk of Wilms tumor and end‐stage renal disease. We investigated whether Wilms tumors in these patients displayed a specific phenotype or behavior and whether nephron‐sparing surgery was beneficial.

Procedure

We retrospectively studied all patients with DDS, FS, or other WT1 mutations treated at our institutions between 1980 and 2007.

Results

We identified 20 patients, of whom 18 had benign or malignant tumors. Wilms tumors occurred in 15 patients, being unilateral in 10 and bilateral in 5 (20 tumors). Median age at Wilms tumor diagnosis was 9 months. No patients had metastases. According to the International Society of Pediatric Oncology Working Classification, there were 19 intermediate‐risk tumors and one high‐risk tumor; no tumor was anaplastic. In patients with nephropathy who underwent unilateral nephrectomy for Wilms tumor or nephron‐sparing surgery for bilateral Wilms tumor, mean time to dialysis was 11 or 9 months, respectively. Other tumors included three gonadoblastomas (in two patients), one retroperitoneal soft‐tissue tumor, and one transitional cell papilloma of the bladder. Two patients, both with stage I Wilms tumor, died from end‐stage renal disease‐related complications. The median follow‐up time for the 18 survivors was 136 months (range, 17–224 months).

Conclusion

Most Wilms tumors in children with WT1‐related disorders were early‐stage and intermediate‐risk tumors, with a young age at diagnosis. In patients without end‐stage renal disease, nephron‐sparing surgery should be considered for delaying the onset of renal failure. Pediatr Blood Cancer 2009;52:55–59. © 2008 Wiley‐Liss, Inc.
Total body bone measurements: A cross‐sectional study in children with acute lymphoblastic leukemia during and following completion of therapy
Authors: Kelly Kara M. , Thornton John C. , Hughes Deborah , Osunkwo Ifeyinwa , Weiner Michael , Wang Jack , Horlick Mary
Published: September 2008

Background

Abnormalities in bone mineral density (BMD) occur in children treated for acute lymphoblastic leukemia (ALL). However, BMD estimates have been performed using varied instruments, reference data, and interpretations. This exploratory cross sectional study to evaluate bone mass in children with ALL, uses an algorithm that serially adjusts for variables known to affect pediatric bone measures by dual energy X‐ray absorptiometry (DXA), based on models developed in 1,218 healthy children and adolescents.

Procedure

Anthropometry, DXA scans, and factors with possible influence on bone mass were evaluated in 21 ALL patients receiving chemotherapy and 20 in the follow‐up phase. Main outcome was treatment group differences in Z‐scores for total body bone mineral content (BMC), bone area (Area), and areal BMD (aBMD).

Results

Mean Z‐scores for the entire study population for BMC, Area, and aBMD were significantly less than zero. Among possible contributing factors, only calcium intake was a significant co‐variate. Comparison between treatment groups showed that least‐square mean Z‐scores for patients on‐therapy for at least 12 months were significantly lower than those off therapy for at least 12 months (P: 0.0008–0.044), except for BMC at last step of the algorithm (adjusted for sex, age, ethnicity, height, weight, and bone area).

Conclusions

Evaluation of total body DXA by this algorithm is consistent with better general bone status in those off‐therapy. However, in this small exploratory study, the lack of significant difference between Z‐scores for fully adjusted BMC in on‐ versus off‐therapy groups suggests possible risk of low peak bone mass. Additional longitudinal evaluation is warranted. Pediatr Blood Cancer 2009;52:33–38. © 2008 Wiley‐Liss, Inc.
Tensile modulus modeling of carbon‐filled liquid crystal polymer composites
Authors: Keith Jason M. , King Julia A. , Miskioglu Ibrahim , Roache Samuel C.
Published: September 2008

Electrically and thermally conductive resins can be produced by adding conductive fillers to insulating polymers. Mechanical properties, such as tensile modulus, are also important. This research focused on performing compounding runs followed by injection molding and tensile testing of carbon‐filled Vectra liquid crystal polymer. The two carbon fillers investigated were Thermocarb synthetic graphite particles and Fortafil carbon fiber at varying filler amounts. The tensile modulus experimental results were compared to results predicted by several different models. It was found that the Halpin Tsai 2D Randomly Oriented fiber model provided the best fit to the experimental data. The degree of filler‐polymer adhesion was also studied with nanoscratch tests for synthetic graphite and carbon fiber fillers in three polymers: Vectra, nylon 6,6, and polycarbonate. The adhesion trends seen in the nanoscratch tests showed qualitative agreement with the tensile modulus, and should be considered in formulating advanced tensile modulus models. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Fabrication and characterization of 100% green composite: Thermoplastic based on wheat flour reinforced by flax fibers
Authors: Saiah R. , Sreekumar P.A. , Gopalakrishnan P. , Leblanc N. , Gattin R. , Saiter J.M.
Published: September 2008

Biocomposites having flax fibers as reinforcement in wheat flour based thermoplastic matrix were prepared by extrusion method. The fiber content of the composites varied from 0% to 20% w/w. The structure and morphology of the fiber and composites prepared were studied using X‐ray diffraction and scanning electron micrograph methods. The mechanical properties such as stress at failure, strain at failure, and tensile modulus were studied as a function of fiber content. The incorporation of fiber to the matrix increased the tensile properties and is maximum for the composite having a fiber loading of 20% w/w. Thermal stability of the fiber and the composite having various fiber content (0, 5, 10, 15, and 20% w/w) was analyzed by thermogravimetric method. There is no significant variation in the thermal stability of the composites. Finally, comparative studies of the mechanical properties were done to evaluate the efficiency of this new system. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Application of polymer gel electrolyte with graphite powder in quasi‐solid‐state dye‐sensitized solar cells
Authors: Li Qinghua , Wu Jihuai , Tang Qunwei , Lan Zhang , Li Pinjiang , Zhang Tingting
Published: September 2008

A polymer gel electrolyte with ionic conductivity of 5.11 mS cm−1 was prepared by using poly (acrylonitrile‐co‐styrene) as polymer matrix, acetonitrile and tetrahydrofuran as binary organic mixture solvent, NaI + I2 as electrolyte, graphite powder and 1‐methylimidazole as additives. The components ratio of the polymer gel electrolyte was optimized, and the influence of the components and temperature on the ionic conductivity of the polymer gel electrolyte and photoelectronic properties of dye sensitized solar cell were investigated. On the basis of the polymer gel electrolyte with the optimized conditions, a quasi‐solid‐state dye‐sensitized solar cell was fabricated and its light‐ to‐electricity energy conversion efficiency of 3.25% was achieved under irradiation of 100 mW cm−2. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Compressive damage in filament‐wound carbon/carbon composites
Authors: Kuo Wen‐Shyong , Ko Tse‐Hao , Wu Shang‐Yi
Published: September 2008

The processing characteristics and the induced compressive damage in filament‐wound carbon/carbon composites were examined. Tubular carbon/phenolic composites were made by the filament winding method. The inside diameter was 25.4 mm and the nominal thickness was 2.5 mm. The cured composites were then carbonized. Three more cycles of matrix densification were repeated. After densification, the composites were graphitized at 2600°C. Compressive tests were then carried out for the cured, carbonized, and graphitized composites. The load was applied directly on the end of the tube. The loading response and the induced damage were studied. Their microscopic fracture behaviors were examined by optical and scanning electron microscopes. With the heating temperature increased, the damage modes shifted from a ductile fracture in the cured composites to a more brittle fracture in the graphitized composites. The resulting strength and stiffness were also decreased significantly with the temperature. Kinking of fibers was the major mode in the cured specimens, while separation of bundles became more prominent in the graphitized specimens. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Flow behavior of unsaturated polyester resin—Microsized 17‐4PH stainless steel powder—Feedstocks
Authors: Hanemann T.
Published: September 2008

For the realization of stainless steel parts carrying either surface relief microstructures or possessing dimensions in submillimeter‐range the different variants of micro injection molding are suitable replication techniques, followed by thermal postprocessing like debinding and sintering. With respect to warpage‐free sintered parts the initial solid load in the feedstock should be as large as possible. A reduction of the binder viscosity enables a reduction of the feedstock viscosity; hence, larger solid loads can be achieved. Using an unsaturated polyester binder, diluted with different amounts of the reactive thinner styrene, feedstocks with a solid content up to 46 vol% were realized. The influence of the filler on the feedstock viscosity, the maximum accessible load and the flow activation energy was investigated intensely. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Immunochromatographic assay for the detection of pseudojujubogenin glycosides
Authors: Imsungnoen Natnapa , Phrompittayarat Watoo , Ingkaninan Kornkanok , Tanaka Hiroyuki , Putalun Waraporn
Published: September 2008

Introduction

Bacopa monnieri contains pseudojujubogenin glycosides as pharmacologically active compounds. In order to screen large numbers of plant samples for the presence of pseudojujubogenin glycosides, a rapid and simple assay system is required for application to small quantities of test materials. Immunoassays using monoclonal antibodies could be useful for the determination of small quantities of pseudojujubogenin glycosides in plant extracts.

Objective

The objective of this work was to develop a simple method for the detection of pseudojujubogenin glycosides by the immunochromatographic strip test using anti‐bacopaside I monoclonal antibody.

Methodology

The qualitative assay was based on a competitive immunoassay in which the detector reagent consisted of a colloidal gold particle coated with the respective anti‐bacopaside I MAb. The capture reagent was a bacopaside I‐human serum albumin conjugate immobilised onto a test strip membrane.

Results

The sample containing pseudojujubogenin glycosides and the detection reagent were incubated with the immobilised capture reagent. The glycosides in the sample competed in binding to the limited amount of antibodies in the detection reagent with the immobilised bacopaside I‐HSA conjugates and, hence, positive samples showed no colour in the capture spot zone. The detection limit for the strip test was 125 ng/mL.

Conclusion

The assay system was found to be useful as a rapid and simple screening method for the detection of pseudojujubogenin glycosides in plants. Copyright © 2008 John Wiley & Sons, Ltd.
NMR, IR, and ESR spectroscopic investigation of reaction of α‐silylamines with carbon tetrachloride
Authors: Lazareva Nataliya F. , Vakul'skaya Tamara I. , Lazarev Igor M.
Published: September 2008

This paper reports about high reactivity of α‐silylamines in the reaction with CCl4. Unlike Et3N, α‐silylamines rapidly react with CCl4 upon irradiation with daylight to form α‐silylamine hydrochloride salts in 92–98% yields. The influence of structure of α‐silylamines and solvent on the degree of conversion was displayed. The interaction of α‐silylamines with CCl4 was studied by NMR, ESR, and IR spectroscopy. C‐centered radicals of α‐silylamines were detected by ESR spectroscopy with spin traps (MNP, ND, and PBN) in reaction mixtures in CH3CN and C6H6 and it show the radical character of this reaction. Both CH3CN and C6H6 serve as solvents as well as reagents for this reaction. A mechanism of an interaction between α‐silylamines and CCl4 is discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Initiation reactivity of anionic polymerization of fluorinated acrylates and methacrylates with diethyl(ethyl cyanoacetato)aluminum
Authors: Umino Youhei , Narita Tadashi , Hamana Hiroshi
Published: September 2008

Pseudo first‐order rate constants of the reaction of diethyl(ethyl cyanoacetato)aluminum [(C2H5)2Al(NCCHCOOC2H5)] with 17 fluorinated acrylates and methacrylates and five hydrocarbon analogs for references were investigated to examine the initiation reactivities of the anionic polymerization of fluorinated vinyl monomers to afford the reactivity order: CH2C(CF3)COOC2H5 > CH2C(CF3)COOCH(CH3)2 > CH2CHCOOCH2C6F5 > CH2C(CF3)COOC(CH3)3 > CH2C(CF3)COOCH2C6F5 > CH2C(CF3)COOCH(CF3)2 ≥ CH2CHCOOCH3 > CH2CHCOOCH2C6H5 ≥ CH2C(CF3)COOCH2CF3 > CH2C(CH3)COOCH2C6F5 > CH2CHCOOCH2CF3 > CH2CHCOOCH2C2F5 > CH2CHCOOCH(CF3)2 > CH2C(CH3)COOCH3 > CH2C(CH3)COOCH2C6H5 ≥ CH2C(CH3)COOCH2CH2C8F17 > CH2C(CH3)COOCH(CH3)2 > CH2C(CH3)COOCH2C2F5 ≥ CH2C(CH3)COOCH2CF3. No rate constants for CH2C(CH3)COOCH(CF3)2, CH2CFCOOC(CH3)3, and CH2CFCOOCH2C2F5 were obtained because of too fast polymerization. The incorporation of a trifluoromethyl group into the vinyl group enhanced the reactivity toward the delocalized carbanion. The reactivity of other fluorinated acrylates and methacrylates was concluded to approximately be controlled by the fluorine contents and the bulkiness of substituents of monomers. The reactivity was generally decreased by increasing fluorine contents of fluoroalkyl substituents in ester groups. © Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 7011–7021, 2008
Synthesis, photopolymerization and adhesive properties of new hydrolytically stable phosphonic acids for dental applications
Authors: Catel Yohann , Degrange Michel , Le Pluart Loïc , Madec Pierre‐Jean , Pham Thi‐Nhàn , Picton Luc
Published: September 2008

Novel monomers 2‐(N‐methylacrylamido)ethylphosphonic acid, 6‐(N‐methylacrylamido)hexylphosphonic acid, 10‐(N‐methylacrylamido)decylphosphonic acid, and 4‐(N‐methylacrylamidomethyl)benzylphosphonic acid have been prepared in good yields for use in dental adhesives. They have been fully characterized by 1H‐NMR, 13C‐NMR, 31P‐NMR, and by HRMS. All monomers are hydrolytically stable in aqueous solution. Free radical homopolymerizations of these monomers have been carried out in solution of ethanol/water (2.5/1:v/v), using 2,2′‐azo(2‐methylpropionamidine) dihydrochloride (AMPAHC) as initiator. They lead to homopolymers in moderate to excellent yields. Structure of the polymers has been confirmed by SEC/MALLS and 1H‐NMR spectra. The photopolymerization behavior of the synthesized monomers with N,N′‐diethyl‐1,3‐bis(acrylamido)propane has been investigated by DSC. New self‐etch primers, based on these acrylamide monomers, have been formulated. Dentin shear bond strength measurements have shown that primers based on (N‐methylacrylamido)alkylphosphonic acids assure a strong bond between the tooth substance and a dental composite. Moreover, the monomer with the longest spacer group provides the highest shear bond strength. © Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 7074–7090, 2008
One‐pot synthesis of star‐block copolymers using double click reactions
Authors: Durmaz Hakan , Dag Aydan , Hizal Alp , Hizal Gurkan , Tunca Umit
Published: September 2008

3‐Arm star‐block copolymers, (polystyrene‐b‐poly(methyl methacrylate))3, (PS‐b‐PMMA)3, and (polystyrene‐b‐poly(ethylene glycol))3, (PS‐b‐PEG)3, are prepared using double‐click reactions: Huisgen and Diels–Alder, with a one‐pot technique. PS and PMMA blocks with α‐anthracene‐ω‐azide‐ and α‐maleimide‐end‐groups, respectively, are achieved using suitable initiators in ATRP of styrene and MMA, respectively. However, PEG obtained from a commercial source is reacted with 3‐acetyl‐N‐(2‐hydroxyethyl)‐7‐oxabicyclo[2.2.1]hept‐5‐ene‐2‐carboxamide (7) to give furan‐protected maleimide‐end‐functionalized PEG. Finally, PS/PMMA and PS/PEG blocks are linked efficiently with trialkyne functional linking agent 1,1,1‐tris[4‐(2‐propynyloxy)phenyl]‐ethane 2 in the presence of CuBr/N,N,N′,N″,N″‐pentamethyldiethylenetriamine (PMDETA) at 120 °C for 48 h to give two samples of 3‐arm star‐block copolymers. The results of the peak splitting using a Gaussian deconvolution of the obtained GPC traces for (PS‐b‐PMMA)3 and (PS‐b‐PEG)3 displayed that the yields of target 3‐arm star‐block copolymers were found to be 88 and 82%, respectively. © Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 7091–7100, 2008
Encapsulated clay particles in polystyrene by RAFT mediated miniemulsion polymerization
Authors: Samakande Austin , Sanderson Ronald D. , Hartmann Patrice C.
Published: September 2008

RAFT grafted montmorillonite (MMT) clays [i.e., N,N‐dimethyl‐N‐(4‐(((phenylcarbonothioyl)thio)methyl)benzyl)ethanammonium‐MMT (PCDBAB‐MMT) and N‐(4‐((((dodecylthio)carbonothioyl)thio)methyl)benzyl)‐N,N‐dimethylethanammo‐nium‐MMT (DCTBAB‐MMT)] of various loadings were dispersed in styrene (S) monomer and the resultant mixtures emulsified and sonicated in the presence of a hydrophobe (hexadecane) into miniemulsions. The stable miniemulsions thus obtained were polymerized to yield encapsulated polystyrene‐clay nanocomposites (PS‐CNs). The molar mass and polydispersity index (PDI) of the PS‐CNs depended on the amount of RAFT agent in the system, in accordance with the features of the RAFT process. The morphology of the PS‐CNs ranged from partially exfoliated to an intercalated morphology, depending on the percentage clay loading. The thermomechanical properties of the PS‐CNs were better than those of the neat PS polymer, and were dependent on the molar mass, PS‐CN morphology and clay loading. The similarities and differences of the PS‐CNs prepared here by miniemulsion polymerization were compared to those prepared using the same RAFT agents and polymer system by bulk polymerization (as reported by us in a previous article). © Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 7114–7126, 2008
Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study
Authors: Ramelot Theresa A. , Raman Srivatsan , Kuzin Alexandre P. , Xiao Rong , Ma Li‐Chung , Acton Thomas B. , Hunt John F. , Montelione Gaetano T. , Baker David , Kennedy Michael A.
Published: September 2008

The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X‐ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacement (MR) performance with the raw X‐ray diffraction data using MOLREP and Phaser. This method has recently been shown to be generally applicable with improved MR performance demonstrated for eight NMR structures refined using Rosetta (Qian et al., Nature 2007;450:259–264). Additionally, NMR structures of HSPC034 calculated by standard methods that include NMR restraints have improvements in the RMSD to the crystal structure and MR performance in the order DYANA, CYANA, XPLOR‐NIH, and CNS with explicit water refinement (CNSw). Further Rosetta refinement of the CNSw structures, perhaps due to more thorough conformational sampling and/or a superior force field, was capable of finding alternative low energy protein conformations that were equally consistent with the NMR data according to the Recall, Precision, and F‐measure (RPF) scores. On further examination, the additional MR‐performance shortfall for NMR refined structures as compared with the X‐ray structure were attributed, in part, to crystal‐packing effects, real structural differences, and inferior hydrogen bonding in the NMR structures. A good correlation between a decrease in the number of buried unsatisfied hydrogen‐bond donors and improved MR performance demonstrates the importance of hydrogen‐bond terms in the force field for improving NMR structures. The superior hydrogen‐bond network in Rosetta‐refined structures demonstrates that correct identification of hydrogen bonds should be a critical goal of NMR structure refinement. Inclusion of nonbivalent hydrogen bonds identified from Rosetta structures as additional restraints in the structure calculation results in NMR structures with improved MR performance. Proteins 2009. © 2008 Wiley‐Liss, Inc.
A case study of a severe winter storm in the Middle East
Authors: Lee Tiros Pei‐Jiun , Silberberg Steven R. , Bosart Lance F.
Published: September 2008

A detailed synoptic and mesoscale analysis is conducted of an intense convective outbreak which struck much of Israel, Jordan, Lebanon and Syria in early March 1980. Severe winter weather caused considerable personal hardship and economic disruption over a wide area.

The planetary‐scale circulation featured a confluent flow pattern across North Africa and southern Europe downstream of a block just west of the Greenwich meridian. A strong subtropical jet stream was maintained across North Africa in the confluent flow regime. Synoptic‐scale disturbances from the Atlantic were diverted northward across Scandinavia from where they plunged south‐eastward toward the Mediterranean to the west of the Black Sea. A series of three disturbances, the last being the most powerful, swept through the eastern Mediterranean as the vortex settled south‐eastward toward the Middle East.

Our analysis of the available evidence has established that three physical mechanisms contributed primarily to the extreme nature of the event. First, the steady south‐eastward movement of mobile short wave troughs resulted in the progressive cooling of the lower and middle troposphere over the eastern Mediterranean Sea and the Middle East. Second, sea surface heat and moisture fluxes contributed to destabilization and the generation of extreme instability where the cold air from higher latitudes had a long overwater fetch. Third, exceptionally heavy precipitation fell where a strong low‐level moist, unstable westerly air stream impinged on the coastal mountains. The strong westerly flow was generated to the south of an intense subsynoptic‐scale vortex that formed in the lower and mid troposphere as the updraught region of a powerful short‐wave‐trough/ jet‐streak system aloft ingested air that had been destabilized below.
Large‐eddy simulation and parametrization of the baroclinic boundary‐layer
Authors: Brown A. R.
Published: September 2008

Large‐eddy simulations of the non‐entraining dry boundary‐layer, in which the geostrophic wind varies with height, are described. Results are presented for various turbulence statistics, and the large‐eddy model results are used to evaluate the performance of two simple closure‐models. It is shown that the performance of these models is not significantly degraded, in either neutral or convective conditions, by the presence of shear in the geostrophic wind.
A parametrization of the ice water content observed in frontal and convective clouds
Authors: Bower Keith N. , Moss S. J. , Johnson D. W. , Choularton T. W. , Latham J. , Brown P. R. A. , Blyth A. M. , Cardwell J.
Published: September 2008

The properties of the ice phase in a number of cloud types are investigated to improve the ice phase parametrization in atmospheric global‐climate models. Frontal clouds over southern England and the sea areas around the British Isles, maritime convective clouds over the North Atlantic, and continental convective clouds over New Mexico and Montana in the USA are studied.

Ice concentrations are seen to be several orders of magnitude higher than those which could be attributed to primary nucleation of ice nuclei at cloud‐top temperatures. Thus secondary ice multiplication processes must be operating in each cloud type. Evidence suggests that the process of ice splinter production during riming, the Hallett–Mossop process which operates at temperatures around −6°C, is the dominant mechanism operating.

The data analysed are parametrized as phase ratios, the fraction of cloud condensed water found in the liquid phase, and the variation of this phase ratio with temperature is examined. The greatest differences are observed between frontal and convective clouds, although smaller differences between continental and maritime clouds of the same type are also seen. In general, frontal clouds possess very high fractions of ice across a wide range of temperature. In contrast, convective clouds exhibit a wide range of phase ratio across the whole temperature range observed. These differences are attributed to the greater vertical wind velocities present in convective clouds.

These parametrizations have been used in the UK Meteorological Office Global Climate Model. They are valid for clouds which span the Hallett‐Mossop splinter‐production temperature range.
A method to determine the amounts of cloud‐top radiative and evaporative cooling in a stratocumulus‐topped boundary layer
Authors: Shao Qingqiu , Randall David A. , Moeng Chin‐Hoh , Dickinson Robert E.
Published: September 2008

The turbulent processes of a stratocumulus‐topped marine boundary layer are not yet fully understood. Among the issues is the relative importance of the effects of cloud‐top radiative and evaporative cooling in driving the stratocumulus‐topped marine boundary layer turbulence, and in producing cloud break‐up. A better way to analyse the relevant observations is needed.

Based on the concepts of mixing fraction and mixing‐line analysis, a new method to quantitatively determine the radiative and evaporative cooling of the entrained air parcels near cloud top is proposed. Quantities δ(Sv,)R, which includes evaporative cooling and entrainment mixing warming, and δ(Sv,)R,which includes both radiative cooling and the condensation warming due to radiative cooling, are defined to measure the relative importance of entrainment and radiation effects on parcel buoyancy. Provided that radiative cooling does not depend on mixing fraction for a solid cloud, slopes of the mixing lines from the linear regression of aircraft data, rather than the jumps from soundings, can be used to determine δ(Sv,)E, and δ(Sv,)R. In this way, the information from an extra level above cloud is not needed to determine δ(Sv,)E and δ(Sv,)R, and thus the ambiguities associated with the jumps are by‐passed.

The applications of the method to a large‐eddy simulation case and an aircraft data set suggest that radiative cooling is the dominant contributor to the negative buoyancy of the entrained parcels for both cases. They also raise the question as to how much a single sounding can be trusted quantitatively to determine the jumps across the inversion.
Mapping surface‐cover parameters using aggregation rules and remotely sensed cover classes
Authors: Arain Altaf M. , James Shuttleworth W. , Yang Z.‐Liang , Michaud Jené , Dolman Johannes
Published: September 2008

A coupled model, which combines the Biosphere—Atmosphere Transfer Scheme (BATS) with an advanced atmospheric boundary‐layer model, is used to validate hypothetical aggregation rules for BATS‐specific surfacecover parameters. the model is initialized and tested with observations from the Anglo—Brazilian Amazonian Climate Observational Study and is used to simulate surface fluxes for rain forest and pasture mixes at a site near Manaus in Brazil. the aggregation rules are shown to estimate parameters which give area‐average surface fluxes similar to those calculated, with explicit representation of forest and pasture patches for a range of meteorological and surface conditions relevant to this site, but the agreement deteriorates somewhat when there are large patchto‐patch differences in soil moisture. the aggregation rules, validated as above, are then applied to a remotely sensed 1 km land‐cover data set to obtain grid‐average values of BATS vegetation parameters for 2.8° x 2.8° and 1° x 1° grids within the conterminous United States. There are significant differences in key vegetation parameters (aerodynamic roughness length, albedo, leaf‐area index, and stomatal resistance) when aggregate parameters are compared with parameters for the single, dominant cover within the grid. However, the surface energy fluxes calculated by stand‐alone BATS with the 2‐year forcing data from the International Satellite Land Surface Climatology Pogramme CD‐ROM are reasonably similar using aggregate‐vegetation parameters and dominant‐cover parameters, but there are some significant differences, particularly in the western USA.
An explicit flux‐form semi‐lagrangian shallow‐water model on the sphere
Authors: Lin Shian‐Jiann , Rood Richard B.
Published: September 2008

A global shallow‐water model based on the flux‐form semi‐lagrangian scheme is described. the mass‐conserving flux‐form semi‐Lagrangian scheme is a multidimensional semi‐Lagrangian extension of the higher order Godunov‐type finite‐volume schemes (e.g., the piece‐wise parabolic method). Unlike the piece‐wise parabolic methodology, neither directional splitting nor a Riemann solver is involved. A reverse engineering procedure is introduced to achieve the goal of consistent transport of the absolute vorticity and the mass, and hence, the potential vorticity. Gravity waves are treated explicitly, in a manner that is consistent with the forward‐in‐time flux‐form semi‐Lagrangian transport scheme. Due to the finite‐volume nature of the flux‐form semi‐lagrangian scheme and the application of the monotonicity constraint, which can be regarded as a subgrid‐scale flux parametrization, essentially noise‐free solutions are obtained without additional diffusion. Two selected shallow‐water test cases proposed by Williamson et al. (1992) and a stratospheric vortex erosion simulation are presented. Discussions on the accuracy and computational efficiency are given based on the comparisons with a Eulerian spectral model and two advective‐form semi‐implicit semi‐Lagrangian models.
Travelling wave ion mobility mass spectrometry studies of protein structure: biological significance and comparison with X‐ray crystallography and nuclear magnetic resonance spectroscopy measurements
Authors: Scarff Charlotte A. , Thalassinos Konstantinos , Hilton Gillian R. , Scrivens James H.
Published: September 2008

The three‐dimensional conformation of a protein is central to its biological function. The characterisation of aspects of three‐dimensional protein structure by mass spectrometry is an area of much interest as the gas‐phase conformation, in many instances, can be related to that of the solution phase. Travelling wave ion mobility mass spectrometry (TWIMS) was used to investigate the biological significance of gas‐phase protein structure. Protein standards were analysed by TWIMS under denaturing and near‐physiological solvent conditions and cross‐sections estimated for the charge states observed. Estimates of collision cross‐sections were obtained with reference to known standards with published cross‐sections. Estimated cross‐sections were compared with values from published X‐ray crystallography and nuclear magnetic resonance (NMR) spectroscopy structures. The cross‐section measured by ion mobility mass spectrometry varies with charge state, allowing the unfolding transition of proteins in the gas phase to be studied. Cross‐sections estimated experimentally for proteins studied, for charge states most indicative of native structure, are in good agreement with measurements calculated from published X‐ray and NMR structures. The relative stability of gas‐phase structures has been investigated, for the proteins studied, based on their change in cross‐section with increase in charge. These results illustrate that the TWIMS approach can provide data on three‐dimensional protein structures of biological relevance. Copyright © 2008 John Wiley & Sons, Ltd.
Hepatitis B and liver transplantation: 2008 update
Authors: Beckebaum Susanne , Sotiropoulos Georgios C. , Gerken Guido , Cicinnati Vito R.
Published: September 2008

The ultimate goal of treatment is suppression of viral replication to undetectable HBV‐DNA levels prior to and after liver transplantation (LT) to prevent infection of the newly transplanted liver. Most published data are available from therapy with lamivudine (LAM) in pre‐ and post‐transplant HBV patients. Add‐on therapy with adefovir dipivoxil (ADV) in pre‐transplant LAM‐resistant patients has been shown to represent an effective antiviral strategy leading to hepatic recompensation in many cases and, eventually, removal from the waiting list. Newer nucleos(t)ide analogues such as entecavir, tenofovir and telbivudine have shown lower resistance rates than LAM and more antiviral potency in studies in the non‐transplant setting. Combined hepatitis B immune globulin (HBIG) and nucleos(t)ide analogue therapy have been widely adopted as the most effective treatment strategy against recurrent HBV disease after LT. Many programs have evaluated lower doses or a shorter duration of HBIG and intramuscular versus intravenous routes of administration. Active immunisation using recombinant HBV vaccines, including the S, pre‐S1 and pre‐S2 regions, and those with immunostimulatory adjuvants, seem to be more immunogenic than the currently available vaccines and have been used in studies to replace HBIG. Furthermore, it has been shown that immune memory against HBV can be adoptively transferred from organ donors to transplant recipients. Nucleos(t)ide analogue combination therapies might provide an alternative to the current treatment paradigm with costly HBIG; however, experience with this new treatment regimen is very limited and controlled clinical studies are urgently warranted to investigate its safety and efficacy and to determine which nucleos(t)ide analogue combinations will be the most promising in the long term after LT. Copyright © 2008 John Wiley & Sons, Ltd.
Multiple choice tries and distributed hash tables
Authors: Devroye Luc , Lugosi Gábor , Park Gahyun , Szpankowski Wojciech
Published: September 2008

In this article we consider tries built fromnstrings such that each string can be chosen from a pool ofkstrings, each of them generated by a discrete i.i.d. source. Three cases are considered:k= 2,kis large but fixed, andk˜clogn. The goal in each case is to obtain tries as balanced as possible. Various parameters such as height and fill‐up level are analyzed. It is shown that for two‐choice tries a 50% reduction in height is achieved when compared with ordinary tries. In a greedy online construction when the string that minimizes the depth of insertion for every pair is inserted, the height is only reduced by 25%. To further reduce the height by another 25%, we design a more refined online algorithm. The total computation time of the algorithm isO(nlogn). Furthermore, when we choose the best amongk≥ 2 strings, then for large but fixedkthe height is asymptotically equal to the typical depth in a trie. Finally, we show that further improvement can be achieved if the number of choices for each string is proportional to logn. In this case highly balanced trees can be constructed by a simple greedy algorithm for which the difference between the height and the fill‐up level is bounded by a constant with high probability. This, in turn, has implications for distributed hash tables, leading to a randomized ID management algorithm in peer‐to‐peer networks such that, with high probability, the ratio between the maximum and the minimum load of a processor is O(1). © 2008 Wiley Periodicals, Inc. Random Struct. Alg., 2009
Network risk management using attacker profiling
Authors: Dantu Ram , Kolan Prakash , Cangussu João
Published: September 2008

Risk management refers to the process of making decisions that minimize the effects of vulnerabilities on the network hosts. This can be a difficult task in the context of high‐exploit probability and the difficult to identify new exploits and vulnerabilities. For many years, security engineers have performed risk analysis using economic models for the design and operation of risk‐prone, technological systems using attack profiles. Based on the type of attacker identified, security administrators can formulate effective risk management policies for a network. We hypothesize that sequence of network actions by an attacker depends on the social behavior (e.g., skill level, tenacity, financial ability). We extended this and formulated a mechanism to estimate the risk level of critical resources that may be compromised based on attacker behavior. This estimation is accomplished using behavior based attack graphs representing all the possible attack paths to all the critical resources. The risk level is computed based on these graphs and are used as a measure of the vulnerability of the resource and forming an effective basis for a system administrator to perform suitable changes to network configuration. Copyright © 2008 John Wiley & Sons, Ltd.
Avoiding infinite estimates of time‐dependent effects in small‐sample survival studies
Authors: Heinze Georg , Dunkler Daniela
Published: September 2008

We address the phenomenon of monotone likelihood in Cox regression with time‐dependent effects. Monotone likelihood occurs in the fitting process of a Cox model if at least one parameter estimate diverges to ± infinity. We show that the probability of monotone likelihood is increased by the inclusion of time‐dependent effects, particularly in small samples with several unbalanced and highly predictive covariates, and with a high percentage of censoring. Firth's bias reduction procedure was shown to provide an ideal solution to monotone likelihood. Here we extend his idea to Cox regression with time‐dependent effects. By penalized maximum likelihood estimation, finite hazard ratio estimates of constant and time‐dependent effects can be obtained. Penalized likelihood ratio tests and profile penalized likelihood confidence intervals are proposed as tools for inference. A Monte Carlo study of Cox regression with time‐dependent effects confirms advantages of Firth‐corrected (FC) over standard Cox analysis in terms of average bias and median absolute deviation. We also compare the FC and standard Cox approaches by means of analyses of two studies with time‐dependent effects. An SAS macro and an R package for FC Cox regression with time‐varying covariates and time‐dependent effects are available at:http://www.muw.ac.at/msi/biometrie/programs. Copyright © 2008 John Wiley & Sons, Ltd.
Curtailed two‐stage designs in Phase II clinical trials
Authors: Chi Yunchan , Chen Chia‐Min
Published: September 2008

When the accrual rate is low and the treatment period is long, a long observational period is required before information concerning the primary end point, such as binary response, becomes available in the study. Simon's two‐stage designs are often employed in Phase II clinical trials to avoid giving patient an ineffective drug. Thus, if the new drug is ineffective then this design would certainly accelerate the process of drug discovery and development. However, for a promising new drug this design may still require a long observational period. Therefore, when drug safety is not a primary concern, this paper proposes curtailed two‐stage designs to shorten the drug development process as soon as the treatment either shows lack of efficacy or is very effective. The proposed design is superior to Simon's two‐stage designs in terms of savings in expected sample size and is much easier to implement in practice than stochastically curtailed Simon's designs. Copyright © 2008 John Wiley & Sons, Ltd.
An R2 statistic for fixed effects in the linear mixed model
Authors: Edwards Lloyd J. , Muller Keith E. , Wolfinger Russell D. , Qaqish Bahjat F. , Schabenberger Oliver
Published: September 2008

Statisticians most often use the linear mixed model to analyze Gaussian longitudinal data. The value and familiarity of the R2 statistic in the linear univariate model naturally creates great interest in extending it to the linear mixed model. We define and describe how to compute a model R2 statistic for the linear mixed model by using only a single model. The proposed R2 statistic measures multivariate association between the repeated outcomes and the fixed effects in the linear mixed model. The R2 statistic arises as a 1–1 function of an appropriate F statistic for testing all fixed effects (except typically the intercept) in a full model. The statistic compares the full model with a null model with all fixed effects deleted (except typically the intercept) while retaining exactly the same covariance structure. Furthermore, the R2 statistic leads immediately to a natural definition of a partial R2 statistic. A mixed model in which ethnicity gives a very small p‐value as a longitudinal predictor of blood pressure (BP) compellingly illustrates the value of the statistic. In sharp contrast to the extreme p‐value, a very small R2 , a measure of statistical and scientific importance, indicates that ethnicity has an almost negligible association with the repeated BP outcomes for the study. Copyright © 2008 John Wiley & Sons, Ltd.
A comparison of three random effects approaches to analyze repeated bounded outcome scores with an application in a stroke revalidation study
Authors: Molas Marek , Lesaffre Emmanuel
Published: September 2008

Discrete bounded outcome scores (BOS), i.e. discrete measurements that are restricted on a finite interval, often occur in practice. Examples are compliance measures, quality of life measures, etc. In this paper we examine three related random effects approaches to analyze longitudinal studies with a BOS as response: (1) a linear mixed effects (LM) model applied to a logistic transformed modified BOS; (2) a model assuming that the discrete BOS is a coarsened version of a latent random variable, which after a logistic‐normal transformation, satisfies an LM model; and (3) a random effects probit model. We consider also the extension whereby the variability of the BOS is allowed to depend on covariates. The methods are contrasted using a simulation study and on a longitudinal project, which documents stroke rehabilitation in four European countries using measures of motor and functional recovery. Copyright © 2008 John Wiley & Sons, Ltd.
Multivariate logit copula model with an application to dental data
Authors: Nikoloulopoulos Aristidis K. , Karlis Dimitris
Published: September 2008

Applications of copulas for multivariate continuous data abound but there are only a few that treat multivariate binary data. In the present paper, we model multivariate binary data based on copulas using mixtures of max‐infinitely divisible copulas, introduced by Joe and Hu (J. Multivar. Anal.1996;57(2): 240–265). When applying copulas to binary data the marginal distributions also contribute to the dependence measures. We propose the use of covariate information in the copula parameters to obtain a direct effect of a covariate on dependence. To deal with model uncertainty due to selecting among several candidate models, we use a model averaging technique. We apply the model to data from the Signal‐Tandmobiel©dental study and, in particular, to four binary responses that refer to caries experience in the mandibular and maxillary left and right molars. We aim to model Kendall's tau associations between them, and examine how covariate information affects these associations. We found that there are systematically larger associations between the two mandibular and the two maxillary molars. Using covariates to model these associations more closely, we found that the systematic fluoride and age of the children affect the associations. Note that such relationships could not have been revealed by methods that focus on the marginal models. Copyright © 2008 John Wiley & Sons, Ltd.