bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of lymph node retrieval rates on the utilization of adjuvant chemotherapy in stage II colon cancer
Authors: Earle C.C. , Weiser M.R. , Ter Veer A. , Skibber J.M. , Wilson J. , Rajput A. , Wong Y.N. , Benson A.B. , Shibata S. , Romanus D. , Niland J. , Schrag D.
Published: August 2009

Background

Failing to meet the benchmark of 12 lymph nodes in resection specimens is an indication for adjuvant chemotherapy in stage II colon cancer.

Methods

Among consecutive eligible patients with pathologic stage II colon cancer treated at eight NCI‐designated comprehensive cancer centers between September 1, 2005 and February 19, 2008, we analyzed receipt of adjuvant chemotherapy, with less than 12 versus 12+ lymph nodes removed and examined the primary explanatory variable of interest.

Results

Among 258 patients, 46% received adjuvant chemotherapy. An oxaliplatin‐containing regimen was used 67% of the time. Younger age (<50 years, P < 0.001), presence of lymphovascular invasion (P = 0.007), and higher T stage (P = 0.007) were independently associated with adjuvant chemotherapy use. There was significant inter‐institutional variability in practice with the proportion receiving treatment ranging from 17% to 64% (P < 0.05). Notably, presence of less than 12 lymph nodes in the surgical specimen was a strong predictor of treatment (P = 0.008).

Conclusions

Adjuvant chemotherapy use after resection of stage II colon cancer is common, but by no means standard practice at National Comprehensive Cancer Network (NCCN) institutions. More attention to achieving the recommended benchmark for lymph node dissection has the potential to decrease exposure to the toxicity of adjuvant treatment. J. Surg. Oncol. 2009;100:525–528. © 2009 Wiley‐Liss, Inc.
Cancers of the ampulla of vater: Demographics, morphology, and survival based on 5,625 cases from the SEER program
Authors: Albores‐Saavedra Jorge , Schwartz Arnold M. , Batich Kristen , Henson Donald E.
Published: August 2009

Background

Cancers of the ampulla are unusual and morphologically heterogeneous. The NCI's SEER Program is now large enough so that unusual cancers can be studied. Based on pathologic and epidemiologic characteristics of cancer of the ampulla available in SEER, important clinicopathological correlations can be made.

Methods

All patients with cancer of the ampulla were identified between 1973 and 2005. Demographic features, distribution of histological types, age‐specific incidence rates, and 5‐year survival rates according to stage and histologic type were compared.

Results

There were 5,625 cases of ampullary cancer. Ampullary cancer has been increasing since 1973. In both African Americans and Caucasians, the disease is more common in men. Adenocarcinomas, NOS comprised 65% of all histological types. Survival depends on stage, grade, and histologic type. Papillary carcinomas had a more favorable survival than other types; carcinomas arising in adenomas had a more favorable survival than adenocarcinomas not associated with adenomas. Logarithmic transformation of age‐related incidence data demonstrates that cancers having differing histopathologic phenotypes represent a single population of tumors.

Conclusions

Prognostic factors include histologic type, grade, stage, and coexisting adenomas. These data should be included in pathology reports. Although certain histologic types exhibit morphologic differences, their pathogenesis appears to be similar. J. Surg. Oncol. 2009;100:598–605. © 2009 Wiley‐Liss, Inc.
Duodenal gastrointestinal stromal tumor: Clinical, pathologic, immunohistochemical characteristics, and surgical prognosis
Authors: Yang Wei‐Li , Yu Ji‐Ren , Wu Yi‐Jun , Zhu Kan‐Kai , Ding Wei , Gao Yuan , Shen Qian‐Yun , Lv Ke‐Zhen , Zhang Qing , Yang Xiao‐Jun
Published: August 2009

Objective

Gastrointestinal stromal tumors (GISTs) occur rarely in the duodenum. The characteristics of duodenal GIST have not been well clarified. The aim of this study is to clarify the characteristics and surgical prognosis of patients with primary duodenal GIST.

Methods

Data of patients with surgically treated primary duodenal GIST were retrospectively analyzed. Immunohistochemical expressions of p53, p16, and Ki‐67 were evaluated to explain the prognosis.

Results

Compared with gastric or small intestinal GISTs in historical studies, duodenal GISTs had a relatively smaller size, lower mitotic count, lower Ki‐67 LI, lower p16 loss, and similar p53 expression. The 1‐ and 3‐year recurrence‐free survival rates of patients with complete resection were 100 and 95.2%.

Conclusion

Patients with completely resected primary duodenal GIST seem to have a more favorable prognosis. This may be related to the different expressions of some immunohistological makers compared with GISTs of other locations. J. Surg. Oncol. 2009;100:606–610. © 2009 Wiley‐Liss, Inc.
Gas chromatographic retention in uncoated fused silica capillaries
Authors: Klee Matthew S.
Published: August 2009

Understanding of retention in uncoated fused‐silica capillaries is of interest due to increased attention on precolumn backflushing in capillary GC. Uncoated capillaries offer several advantages as precolumns compared to coated precolumns. In order to examine the possibility of predicting elution temperatures of alkanes from uncoated capillaries a priori, several sizes of deactivated but uncoated fused‐silica capillaries were evaluated under various operating conditions. Retention was found to depend on dimensionless ramp rate (°C/tM), sample loading (capacity), flow mode, and column dimensions (probably related to surface area).
Confocal microscopy study of uptake kinetics of α‐lactalbumin and β‐lactoglobulin onto the cation‐exchanger SP Sepharose FF
Authors: El‐Sayed Mayyada M. H. , Chase Howard A.
Published: August 2009

Confocal laser scanning microscopy (CLSM) was used to study single‐ and two‐component protein uptake for α‐lactalbumin (ALA) and β‐lactoglobulin (BLG), as models for whey proteins, to SP Sepharose FF at pH 3.7 during batch experiments in a finite bath. By coupling a fluorescent dye with the protein molecule, the penetration into individual adsorbent particles at different times during batch uptake was visualised. In a single‐component system, BLG penetrated fast into the adsorbent beads and gradually filled them in a shell‐wise fashion, while adsorption of ALA was mostly confined to the outer shells of the adsorbent. For the two‐component studies, the results showed that ALA was able to displace BLG despite its lower affinity to the adsorbent under the employed conditions. CLSM results were then compared both qualitatively and quantitatively to their counterparts obtained in traditional experiments by indirect measurements of the protein concentration in the fluid phase. A novel quantitative approach was undertaken by modifying the simple kinetic rate model traditionally used to determine the kinetic rate constant, k1, for batch uptake experiments, in order to describe batch uptake kinetics based on CLSM data. Although BLG results were in good agreement, there was a discrepancy in ALA results.
An evolutionary view: What followers want from their leaders
Authors: Winsborough David , Kaiser Robert B. , Hogan Robert
Published: August 2009

A look into the very distant past of human existence shows that some conditions are more conducive to leadership than others and that followers naturally prefer specific forms of leadership and resist other forms. By understanding and acting on the three fundamental individual needs that result from group living and the three tough problems faced by ancient tribes, leaders can better connect with their followers.
Mechanical properties of friction stir butt‐welded Al‐5086 H32 plate
Authors: Çam G. , Güçlüer S. , Çakan A. , Serindag H.T.
Published: August 2009

Al‐5086 H32 plates with a thickness of 3 mm were friction stir butt‐welded using different welding speeds at a tool rotational speed of 1600 rpm. The effect of welding speed on the weld performance of the joints was investigated by conducting optical microscopy, microhardness measurements and mechanical tests (i.e. tensile and bend tests). The effect of heat input during friction stir welding on the microstructure, and thus mechanical properties, of cold‐rolled Al‐ 5086 plates was also determined.

The experimental results indicated that the maximum tensile strength of the joints, which is about 75 % that of the base plate, was obtained with a traverse speed of 200 mm/min at the tool rotational speed used, e.g. 1600 rpm, and the maximum bending angle of the joints can reach 180o. The maximum ductility performance of the joints was, on the other hand, relatively low, e.g. about 20 %. These results are not unexpected due to the loss of the cold‐work strengthening in the weld region as a result of the heat input during welding, and thus the confined plasticity within the stirred zone owing to strength undermatching. Higher joint performances can also be achieved by increasing the penetration depth of the stirring probe in butt‐friction stir welding of Al‐5086 H32 plates.
Discriminatory input pricing and strategic delegation
Authors: Liao Pei‐Cheng
Published: August 2009

This paper examines how discriminatory input pricing by an upstream monopolist affects the incentives that owners of downstream duopolists offer their managers. Regardless of the mode of competition (quantity or price), owners of downstream firms induce their managers to be more profit‐oriented and to behave less aggressively when the monopolist is allowed to price‐discriminate than when he charges a uniform price. If the monopolist price‐discriminates, managerial downstream firms always earn more than owner‐managed profit‐maximizing firms. However, if the monopolist charges a uniform price, managerial downstream firms earn more than profit‐maximizing counterparts under price competition and earn less under quantity competition. Copyright © 2009 John Wiley & Sons, Ltd.
Onset and spread of dyskinesias and motor symptoms in Parkinson's disease
Authors: Fabbrini Giovanni , Defazio Giovanni , Colosimo Carlo , Suppa Antonio , Bloise Maria , Berardelli Alfredo
Published: August 2009

We retrospectively investigated in consecutive Parkinson's disease (PD) outpatients the relationship between the body region in which LID first appeared and the body region where Parkinsonian motor symptoms started. We also studied the spread of LID and motor symptoms to other body parts during the progression of PD. Of the 307 PD patients investigated, 99 with LID were enrolled in the study. In these 99 patients, LID started unilaterally in the limbs in 44, bilaterally in the limbs in 26, and in craniocervical region in 29, whereas motor symptoms invariably started in the limbs. LID and motor symptoms started in the same body region in less than half of the patients studied. Of the 99 patients studied, 69 had LID spread to at least another body region during the course of their disease. In this group, clinical examination yielded a significantly different distribution of LID and motor symptoms. These findings suggest that the onset and spread of LID and motor symptoms may follow different anatomical patterns. © 2009 Movement Disorder Society
Accumulated thermal time, a key factor in affecting generation initiation and duration of top borer, Scirpophaga excerptalis Walker of sugarcane for its model‐based chemical control
Authors: Srivastava Arun K. , Srivastava D. C. , Sinha O. K. , Kumar Rajesh
Published: August 2009

The seasonal variation in the initiation and duration of the I–III generations of the top borer was observed and analysed during five crop cycles from 2002–2003 to 2006–2007 at Lucknow in central Uttar Pradesh. The durations of the I–III generations were significantly correlated with the accumulated thermal time (Tbase = 10°C). Relatively higher temperature and consequently higher accumulated thermal time shortened the brood duration and early initiation of successive generations and vice versa. Based on these correlations, models were developed for predicting the initiation and duration of these generations. These models were validated for 2007–2008 crop cycle. The differences between observed and predicted duration of the I–III generation of the pest were 3, 1 and 3 days respectively reflecting high precision of the models. As the current management strategy for the chemical control of the pest is based on a calendar week, the shift of III generation initiation due to seasonal fluctuations could lead to escape from insecticide and render the chemical application pointless. The model‐based control strategy is more precise and foretells the time of application of chemical against III generation of top borer which is most damaging to sugarcane crop. Copyright © 2009 Royal Meteorological Society
Reconstruction of cracks of different types from far‐field measurements
Authors: Liu Jijun , Sini Mourad
Published: August 2009

In this paper, we deal with the acoustic inverse scattering problem for reconstructing cracks of possibly different types from the far‐field map. The scattering problem models the diffraction of waves by thin two‐sided cylindrical screens. The cracks are characterized by their shapes, the type of boundary conditions and the boundary coefficients (surface impedance). We give explicit formulas of the indicator function of the probe method, which can be used to reconstruct the shape of the cracks, distinguish their types of boundary conditions, the two faces of each of them and reconstruct the possible material coefficients on them by using the far‐field map. To test the validity of these formulas, we present some numerical implementations for a single crack, which show the efficiency of the proposed method for suitably distributed surface impedances. The difficulties for numerically recovering the properties of the crack in the concave side as well as near the tips are presented and some explanations are given. Copyright © 2009 John Wiley & Sons, Ltd.
Shape optimization for low Neumann and Steklov eigenvalues
Authors: Girouard Alexandre , Polterovich Iosif
Published: August 2009

We give an overview of results on shape optimization for low eigenvalues of the Laplacian on bounded planar domains with Neumann and Steklov boundary conditions. These results share a common feature: they are proved using methods of complex analysis. In particular, we present modernized proofs of the classical inequalities due to Szegö and Weinstock for the first nonzero Neumann and Steklov eigenvalues. We also extend the inequality for the second nonzero Neumann eigenvalue, obtained recently by Nadirashvili and the authors, to nonhomogeneous membranes with log‐subharmonic densities. In the homogeneous case, we show that this inequality is strict, which implies that the maximum of the second nonzero Neumann eigenvalue is not attained in the class of simply connected membranes of a given mass. The same is true for the second nonzero Steklov eigenvalue, as follows from our results
on the Hersch–Payne–Schiffer inequalities. Copyright © 2009 John Wiley & Sons, Ltd.
Synchronization for two coupled oscillators with inhibitory connection
Authors: Xiao Ke , Guo Shangjiang
Published: August 2009

In this paper we present an oscillatory neural network composed of two coupled neural oscillators with inhibitory connections. Each of the oscillators describes the dynamics of average activities of excitatory and inhibitory populations of neurons. Regarding time delays τ as the bifurcation parameter, we not only obtain the existence of Hopf bifurcations but also investigate the bifurcation direction and stability of bifurcated periodic solutions by employing normal form theory and center manifold reduction. Finally, numerical simulations are provided to illustrate the theoretical results. Copyright © 2009 John Wiley & Sons, Ltd.
Permanence in a periodic delay logistic system subject to constant impulsive stocking
Authors: Liu Zhijun , Chen Yiping , He Zerong , Wu Jianhua
Published: August 2009

In this paper, a periodic impulsive delay single population system with hereditary effect is established. The constant impulse is realized at fixed moments of time. By using the comparison principle of impulsive differential equations and analysis techniques, the permanence of the system is obtained. It shows that the constant impulsive stocking plays an important role. Numerical simulations are presented to substantiate our analytical results. Copyright © 2009 John Wiley & Sons, Ltd.
Standard operating procedure for metabonomics studies of blood serum and plasma samples using a 1H‐NMR micro‐flow probe
Authors: Sukumaran Dinesh K. , Garcia Erwin , Hua Jia , Tabaczynski Walter , Odunsi Kunle , Andrews Chris , Szyperski Thomas
Published: August 2009

A standard operating procedure (SOP) is presented for high‐throughput metabonomics studies using a 600 MHz NMR spectrometer equipped with a micro‐flow probe that is connected to an auto‐sampler. The procedure is designed to minimize random and systematic variation of NMR data collection. In addition, a protocol is described to assess the quality of the data acquired by a given NMR spectroscopist to ensure that (i) all researchers involved in the NMR data acquisition of a metabonomics research program perform equally and (ii) operator‐associated variation of NMR data collection is statistically not relevant for the interpretation of results obtained from multivariate data analyses. Copyright © 2009 John Wiley & Sons, Ltd.
1H, 13C, 15N and 195Pt NMR studies of Au(III) and Pt(II) chloride organometallics with 2‐phenylpyridine
Authors: Pazderski Leszek , Pawlak Tomasz , Sitkowski Jerzy , Kozerski Lech , Szłyk Edward
Published: August 2009

1H, 13C, 15N and 195Pt NMR studies of gold(III) and platinum(II) chloride organometallics with N(1),C(2′)‐chelated, deprotonated 2‐phenylpyridine (2ppy*) of the formulae [Au(2ppy*)Cl2], trans(N,N)‐[Pt(2ppy*)(2ppy)Cl] and trans(S,N)‐[Pt(2ppy*)(DMSO‐d6)Cl] (formed in situ upon dissolving [Pt(2ppy*)(µ‐Cl)]2 in DMSO‐d6) were performed. All signals were unambiguously assigned by HMBC/HSQC methods and the respective 1H, 13C and 15N coordination shifts (i.e. differences between chemical shifts of the same atom in the complex and ligand molecules: Δ1Hcoord = δ1Hcomplex − δ1Hligand, Δ13Ccoord = δ13Ccomplex − δ13Cligand, Δ15Ncoord = δ15Ncomplex − δ15Nligand), as well as 195Pt chemical shifts and 1H‐195Pt coupling constants discussed in relation to the known molecular structures. Characteristic deshielding of nitrogen‐adjacent H(6) protons and metallated C(2′) atoms as well as significant shielding of coordinated N(1) nitrogens is discussed in respect to a large set of literature NMR data available for related cyclometallated compounds. Copyright © 2009 John Wiley & Sons, Ltd.
Analysis of mRNA associated factors during bovine oocyte maturation and early embryonic development
Authors: Siemer Corinna , Smiljakovic Tatjana , Bhojwani Monika , Leiding Claus , Kanitz Wilhelm , Kubelka Michal , Tomek Wolfgang
Published: August 2009

Regulation of gene expression at the translational level is particularly essential during developmental periods, when transcription is impaired. According to the closed‐loop model of translational initiation, we have analyzed components of the 5´‐mRNA cap‐binding complex eIF4F (eIF4E, eIF4G, eIF4A), the eIF4E repressor 4E‐BP1, and 3´‐mRNA poly‐(A) tail‐associated proteins (PABP1 and 3, PAIP1 and 2, CPEB1, Maskin) during in vitro maturation of bovine oocytes and early embryonic development up to the 16‐cell stage. Furthermore, we have elucidated the activity of distinct kinases which are potentially involved in their phosphorylation. Major phosphorylation of specific target sequences of PKA, PKB, PKC, CDKs, ATM/ATR, and MAPK were observed in M II stage oocytes. Furthermore, main changes in the abundance and/or phosphorylation of distinct mRNA‐binding factors occur at the transition from M II stage oocytes to 2‐cell embryos. In conclusion, the results indicate that, at the transition from oocyte to embryonic development, translational initiation is regulated by striking differences in the abundance and/or phosphorylation of 5´‐end and 3´‐end mRNA associated factors, mainly the poly‐(A) bindings proteins PABP1 and 3, their repressor PAIP2 and a Maskin‐like protein with distinct eIF4E‐binding properties which prevents eIF4E/cap binding and eIF4F formation in vitro. Nevertheless, from the M II stage to 16‐cell embryos a substantial amount of eIF4E and, to a lesser extent, of eIF4G was precipitated by 7m‐GTP‐Separose indicating eIF4F complex formation. Therefore, it is likely that in general the reduction in PABP1 and 3 abundance represses overall translation during early embryonic development. Mol. Reprod. Dev. 76: 1208–1219, 2009. © 2009 Wiley‐Liss, Inc.
Peripheral nerve size in normals and patients with polyneuropathy: An ultrasound study
Authors: Zaidman Craig M. , Al‐Lozi Mohammed , Pestronk Alan
Published: August 2009

Ultrasound has been used for visualizing peripheral nerve pathology. Our goal was to use ultrasound to quantitate the sizes of upper extremity nerves along their length in control subjects and patients with neuropathy. We measured median and ulnar nerve cross‐sectional areas (NCSA) in the arms of 190 subjects, including 100 with neuropathies and 90 controls. We found that NCSAs in healthy child and adult controls were greater with increasing height, at proximal sites, and at sites of entrapment. Nerves were enlarged in all Charcot–Marie–Tooth 1A (CMT‐1A) (11 of 11; 100%), most chronic inflammatory demyelinating polyneuropathy (CIDP) (31 of 36; 86%), half of Guillain–Barré syndrome (GBS) (8 of 17; 47%), but few axonal neuropathy (7 of 36, 19%) subjects. In GBS, nerve enlargement occurred early and with minimal electrodiagnostic abnormalities in some patients. We conclude that NCSA measured by ultrasound is a quantifiable marker of nerve features that should be corrected for patient characteristics and nerve site. NCSA is generally larger in demyelinating than it is in axonal polyneuropathies. Muscle Nerve, 2009
Rippling muscle disease: Variable phenotype in a family with five afflicted members
Authors: Jacobi Christian , Ruscheweyh Ruth , Vorgerd Matthias , Weber Marc‐André , Storch‐Hagenlocher Brigitte , Meinck Hans Michael
Published: August 2009

We report a family with rippling muscle disease (RMD) who had an autosomal dominant mode of inheritance. The father, mother, and one daughter proved to be heterozygous, and two sons were homozygous for the A92T mutation of the caveolin‐3 gene. The cardinal features of RMD, particularly percussion‐induced rapid contractions, muscle mounding, and muscle rippling, varied considerably among these subjects. Moreover, all examined individuals showed muscle weakness; however, the patterns were inconsistent. Muscle Nerve, 2010
NMR‐based metabolomic analysis of cerebrospinal fluid and serum in neurological diseases – a diagnostic tool?
Authors: Sinclair Alexandra J. , Viant Mark R. , Ball Alexandra K. , Burdon Michael A. , Walker Elizabeth A. , Stewart Paul M. , Rauz Saaeha , Young Stephen P.
Published: August 2009

We sought to evaluate the diagnostic accuracy of metabolomic biomarker profiles in neurological conditions (idiopathic intracranial hypertension (IIH), multiple sclerosis (MS) and cerebrovascular disease (CVD) compared to controls with either no neurological disease or mixed neurological diseases).

Spectra of CSF (n = 87) and serum (n = 72) were acquired using 1H NMR spectroscopy. Multivariate pattern recognition analysis was used to identify disease‐specific metabolite biomarker profiles. The metabolite profiles were then used to predict the diagnosis of a second cohort of patients (n = 25). CSF metabolite profiles were able to predict diagnosis with a sensitivity and specificity of 80% for both IIH and MS. The CVD serum metabolite profile was 75% sensitive and specific. On analysing the second patient cohort, the established metabolite biomarker profiles generated from the first cohort showed moderate ability to segregate patients with IIH and MS (sensitivity:specificity of 63:75% and 67:75%, respectively). These findings suggest that NMR spectroscopic metabolic profiling of CSF and serum can identify differences between IIH, MS, CVD and mixed neurological diseases. Metabolomics may, therefore, have the potential to be developed into a clinically useful diagnostic tool. The identification of disease‐unique metabolites may also impart information on disease pathology. Copyright © 2009 John Wiley & Sons, Ltd.
George gives to geology Jane: The name letter effect and incidental similarity cues in fundraising
Authors: Bekkers René
Published: August 2009

People tend to like others with attributes similar to their own (the similarity principle) and favor products with names similar to their own (the name letter effect).

In the present field experiment, the name letter effect and similarity principle are tested in a phonaton among alumni of Utrecht University, The Netherlands. First name and surname initials, fields of education, and association memberships of alumni were matched to those of students soliciting contributions in the phonaton.

Female alumni with first names and fields of study similar to those of solicitors were more likely to donate, as were male alumni with first names similar to the field of study of solicitors. Both male and female alumni with first names similar to the name of the university donated more often than those with dissimilar names.

Name letter effects are a cheap and effective instrument to increase donations in fundraising campaigns conducted by telephone.

Copyright © 2009 John Wiley & Sons, Ltd.
Current awareness: Pharmacoepidemiology and drug safety
Authors:   John Wiley & Sons, Ltd.
Published: August 2009

In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of pharmacoepidemiology and drug safety. Each bibliography is divided into 23 sections: 1 Reviews; 2 General; 3 Anti‐infective Agents; 4 Cardiovascular System Agents; 5 CNS Depressive Agents; 6 Non‐steroidal Anti‐inflammatory Agents; 7 CNS Agents; 8 Anti‐neoplastic Agents; 9 Haematological Agents; 10 Neuroregulator‐Blocking Agents; 11 Dermatological Agents; 12 Immunosuppressive Agents; 13 Autonomic Agents; 14 Respiratory System Agents; 15 Neuromuscular Agents; 16 Reproductive System Agents; 17 Gastrointestinal System Agents; 18 Anti‐inflammatory Agents ‐ Steroidal; 19 Teratogens/fetal exposure; 20 Antidiabetic Agents; 21 Contrast Agents; 22 Bone Conservation Agents; 23 Others. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted.
Ultrafast time‐resolved studies of the photochemistry of diazo carbonyl compounds
Authors: Burdzinski Gotard , Platz Matthew S.
Published: August 2009

The rich photochemistry of diazo carbonyl compounds in solution has been extensively studied by ultrafast transient absorption spectroscopy with UV–Vis and mid‐IR detection. Both, stepwise (carbene mediated) and concerted Wolff rearrangement (WR) mechanisms have been confirmed for cyclic and acyclic diazo carbonyl precursors. Cyclic diazo‐carbonyl compounds are structurally locked in a syn conformation and mainly follow the concerted mechanism, however, a stepwise pathway does slightly contribute to the overall WR process, contrary to Kaplan's rule. With acyclic diazo ester carbonyl compounds, the WR process is dominated by the stepwise mechanism. A carbene–carbene interconversion process and singlet to triplet carbene intersystem crossing (ISC) processes are discussed in this review. The growth of secondary species (cations, ylides, OH insertion product) emerging from an interaction between a singlet carbene and solvent molecules has been characterized by picosecond time‐resolved UV–Vis transient absorption spectroscopy. Carbene reactivity results in shortening of the singlet carbene lifetime relative to more inert solvents. The quantum yield of diazo decomposition can be deduced from partial ground state bleach recovery using ultrafast time‐resolved IR spectroscopy. Copyright © 2009 John Wiley & Sons, Ltd.
Proteomic analysis of Mrr1p‐ and Tac1p‐associated differential protein expression in azole‐resistant clinical isolates of Candida albicans
Authors: Hoehamer Christopher F. , Cummings Edwin D. , Hilliard George M. , Morschhäuser Joachim , Rogers P. David
Published: August 2009

Azole resistance in Candida albicans is frequently caused by the overexpression of multi‐drug efflux pump genes MDR1, CDR1, and CDR2 due to gain‐of‐function mutations in the zinc cluster transcription factors Mrr1p and Tac1p. In this study, we performed a comparative proteomic analysis to identify proteins whose expression level is influenced by these transcription factors. Both 2‐DE and PMF were used to examine the expression profiles of six pairs of matched C. albicans isolates carrying gain‐of‐function mutations in either MRR1 or TAC1 resulting in the overexpression of either MDR1 or CDR1 and CDR2. Using this approach, 17 differentially expressed proteins were identified in the MDR1‐overexpressing isolates, while 14 were identified in the isolates that overexpress CDR1 and CDR2. Furthermore, we found that the expression of many of these proteins was increased in a wild‐type strain of C. albicans after the introduction of a gain‐of‐function allele of MRR1 or TAC1. Moreover, disruption of MRR1 and TAC1 in isolates carrying gain‐of‐function mutations resulted in decreased expression of these proteins, confirming their regulation by Mrr1p or Tac1p. Several proteins involved in heat shock and carbohydrate metabolism were differentially expressed in all clinical isolate sets, but these proteins were not dependent upon either Tac1p or Mrr1p.
Urine collected from diapers can be used for 2‐D PAGE in infants and young children
Authors: Kennedy Mary Jayne , Griffin Angela , Su Ruifeng , Merchant Michael , Klein Jon
Published: August 2009

Urinary proteomic profiling has potential to identify candidate biomarkers of renal injury in infants provided an adequate urine sample can be obtained. Although diapers are used to obtain urine for clinical evaluation, their use for proteomic analysis has not been investigated. We therefore performed feasibility studies on the use of diaper‐extracted urine for 2‐D PAGE. Pediatric waste urine (2–20 mL) was applied to gel‐containing, non‐gel and cotton‐gauze diapers and then mechanically expressed. Urine volume and total protein were measured pre‐ and post‐extraction. Proteins were separated via 2‐D PAGE following application of urine (20–40 mL) to each matrix. 2‐D PAGE was also performed on clinical specimens collected using each diaper type. Differences in the adsorption and retention of urine volume and protein were noted between matrices. Non‐gel and cotton‐gauze diapers provided the best protein/volume recovery and the lowest interference with the Bradford assay. 2‐D PAGE was also successfully completed using urine samples from both cotton fiber matrices. Conversely, samples from low‐gel diapers demonstrated poor protein separation and reproducibility. Diapers containing cotton–fiber matrices appear adequate for 2‐D PAGE. Qualitative and quantitative analyses of resolved proteins using replicate, high‐resolution gels will be required, however, before diaper‐extracted urine can be applied in proteomic profiling.
Elucidation of the stability and functional regions of the human coronavirus OC43 nucleocapsid protein
Authors: Huang Chun‐Yu , Hsu Yen‐Lan , Chiang Wan‐Ling , Hou Ming‐Hon
Published: August 2009

Human coronavirus OC43 (HCoV‐OC43) is one of the causes of the “common cold” in human during seasons of cold weather. The primary function of the HCoV‐OC43 nucleocapsid protein (N protein) is to recognize viral genomic RNA, which leads to ribonucleocapsid formation. Here, we characterized the stability and identified the functional regions of the recombinant HCoV‐OC43 N protein. Circular dichroism and fluorescence measurements revealed that the HCoV‐OC43 N protein is more highly ordered and stabler than the SARS‐CoV N protein previously studied. Surface plasmon resonance (SPR) experiments showed that the affinity of HCoV‐OC43 N protein for RNA was approximately fivefold higher than that of N protein for DNA. Moreover, we found that the HCoV‐OC43 N protein contains three RNA‐binding regions in its N‐terminal region (residues 1–173) and central‐linker region (residues 174–232 and 233–300). The binding affinities of the truncated N proteins and RNA follow the order: residues 1–173–residues 233–300 > residues 174–232. SPR experiments demonstrated that the C‐terminal region (residues 301–448) of HCoV‐OC43 N protein lacks RNA‐binding activity, while crosslinking and gel filtration analyses revealed that the C‐terminal region is mainly involved in the oligomerization of the HCoV‐OC43 N protein. This study may benefit the understanding of the mechanism of HCoV‐OC43 nucleocapsid formation.
Crystallographic structure of the tetratricopeptide repeat domain of Plasmodium falciparum FKBP35 and its molecular interaction with Hsp90 C‐terminal pentapeptide
Authors: Alag Reema , Bharatham Nagakumar , Dong Aiping , Hills Tanya , Harikishore Amaravadhi , Widjaja Anissa Anindya , Shochat Susana Geifman , Hui Raymond , Yoon Ho Sup
Published: August 2009

Plasmodium falciparum FK506‐binding protein 35 (PfFKBP35) that binds to FK506 contains a conserved tetratricopeptide repeat (TPR) domain. Several known TPR domains such as Hop, PPP5, CHIP, and FKBP52 are structurally conserved and are able to interact with molecular chaperones such as Hsp70/Hsp90. Here, we present the crystal structure of PfFKBP35‐TPR and demonstrate its interaction with Hsp90 C‐terminal pentapeptide (MEEVD) by surface plasmon resonance and nuclear magnetic resonance spectroscopy‐based binding studies. Our sequence and structural analyses reveal that PfFKBP35 is similar to Hop and PPP5 in possessing all the conserved residues which are important for carboxylate clamping with Hsp90. Mutational studies were carried out on positively charged clamp residues that are crucial for binding to carboxylate groups of aspartate, showing that all the mutated residues are important for Hsp90 binding. Molecular docking and electrostatic calculations demonstrated that the MEEVD peptide of Hsp90 can form aspartate clamp unlike FKBP52. Our results provide insightful information and structural basis about the molecular interaction between PfFKBP35‐TPR and Hsp90.
Fabrication of nano‐structured diamond films for SAOS‐2 cell cultivation
Authors: Babchenko Oleg , Kromka Alexander , Hruska Karel , Kalbacova Marie , Broz Antonin , Vanecek Milan
Published: August 2009

The present work reports on application of gold, nickel, and diamond nano‐particles as a masking material for realization of diamond 3D nano‐structures after a low power (100 W) plasma etching process in a gas mixture of CF4/O2. Obtained 3D structures strongly depend on the masking material. Application of the Ni mask results in diamond nano‐rods, whereas the Au mask leads to homogenous “ultra” nano‐cone structures. The diamond powder application results in irregular nano‐cone structures. The present procedure uses a strategy where no lithographic steps are implemented. Prepared samples are tested as the substrates for human osteoblast‐like cells cultivation. Obtained results exhibit a distinctive behavior in cell adhesion on used surface morphologies, as demonstrated by immunofluorescent staining of vinculin (a structural protein of focal adhesion).
Effect of the abnormal electric field induced by the passive layer on imprint failures of ferroelectric capacitors
Authors: Zheng X. J. , Yin W. , Zhang T. , Chen Y. Q. , Tang M. H. , Sun J.
Published: August 2009

The polarization and electric field versus time (P –t and E –t) curves of ferroelectric and passive layers were simulated for different thickness ratios based on the Landau–Khalatnikov theory, and the corresponding hysteresis loops of the ferroelectric capacitor placed in a Sawyer–Tower circuit were obtained via the polarization and electric fields at each time point on the P –t and E –t curves. The results show that the larger the thickness ratio is, the more remarkable the abnormal electric field in the ferroelectric layer and the horizontal shift of hysteresis loops are. The imprint failure may be attributed to the abnormal electric field induced by the passive layer. It is expected to predicate the imprint failure of ferroelectric thin films in a metal–ferroelectric–metal structure. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Advanced tilt correction from flow distortion effects on turbulent CO2 fluxes in complex environments using large eddy simulation
Authors: Griessbaum F. , Schmidt A.
Published: August 2009

Measurement of the turbulent fluxes of gases, momentum and heat can be biased by obstacles such as buildings or instrument platforms distorting the flow of air to the flux instruments. Standard methods have long been used to account for non‐horizontal mean flows. Here we demonstrate a novel approach to correct for the effects of flow distortion which combines numerical flow modelling with eddy covariance measurements of the fluxes. This approach applies a flow distortion correction to the data prior to the application of the standard planar‐fit and double‐rotation methods. This new direction‐dependent flow correction allows the determination of the correct orthogonal wind vector components and hence the vertical turbulent fluxes. We applied the method to a 10 Hz dataset of 3D wind components, temperature, and the concentrations of carbon dioxide and water vapour, as measured on top of a military tower above the city of Münster in northwest Germany during spring and summer 2007. Significant differences appeared between the fluxes that were calculated with the standard rotation methods alone and those that underwent flow distortion correction prior to the application of the rotation methods. The highest deviations of 27% were obtained for the momentum flux. Pronounced differences of 15% and 8% were found for the diurnal net fluxes of carbon dioxide and water vapour, respectively. The flow distortion correction for the carbon dioxide fluxes yielded the same magnitude as the WPL (Webb–Pearman–Leuning) correction for density fluctuations. Copyright © 2009 Royal Meteorological Society
Swarm intelligence based key generation for stream cipher
Authors: Sreelaja N. K. , Vijayalakshmi Pai G. A.
Published: August 2009

Encryption of data traffic in a network is essential since it is vulnerable to eavesdropping. The security of data traffic becomes important since the communications over open network occur frequently. This paper focuses on encryption of plain text using a stream cipher method. However, the keys for encryption are generated using a swarm intelligence approach. Swarm intelligence is the emergent collective intelligence of groups of simple autonomous agents. The Ant Colony Optimization key Generation Algorithm (AKGA) is a novel approach to generate keystream for encrypting the plain text. The advantage of this approach is that it reduces the number of keys to be distributed. Experimental results demonstrating AKGA's encrypting plain text of different lengths and the comparison of its performance with other stream cipher methods are presented. Copyright © 2009 John Wiley & Sons, Ltd.
Estimating regional centile curves from mixed data sources and countries
Authors: van Buuren Stef , Hayes Daniel J. , Stasinopoulos D. Mikis , Rigby Robert A. , ter Kuile Feiko O. , Terlouw Dianne J.
Published: August 2009

Regional or national growth distributions can provide vital information on the health status of populations. In most resource poor countries, however, the required anthropometric data from purpose‐designed growth surveys are not readily available. We propose a practical method for estimating regional (multi‐country) age‐conditional weight distributions based on existing survey data from different countries. We developed a two‐step method by which one is able to model data with widely different age ranges and sample sizes. The method produces references both at the country level and at the regional (multi‐country) level. The first step models country‐specific centile curves by Box–Cox t and Box–Cox power exponential distributions implemented in generalized additive model for location, scale and shape through a common model. Individual countries may vary in location and spread. The second step defines the regional reference from a finite mixture of the country distributions, weighted by population size. To demonstrate the method we fitted the weight‐for‐age distribution of 12 countries in South East Asia and the Western Pacific, based on 273 270 observations. We modeled both the raw body weight and the corresponding Z score, and obtained a good fit between the final models and the original data for both solutions. We briefly discuss an application of the generated regional references to obtain appropriate, region specific, age‐based dosing regimens of drugs used in the tropics. The method is an affordable and efficient strategy to estimate regional growth distributions where the standard costly alternatives are not an option. Copyright © 2009 John Wiley & Sons, Ltd.
Fully specified bootstrap confidence intervals for the difference of two independent binomial proportions based on the median unbiased estimator
Authors: Lin Yan , Newcombe Robert G. , Lipsitz Stuart , Carter Rickey E.
Published: August 2009

In studies in which a binary response for each subject is observed, the success probability and functions of this quantity are of interest. The use of confidence intervals has been increasingly encouraged as complementary to, and indeed preferable to, p‐values as the primary expression of the impact of sampling uncertainty on the findings. The asymptotic confidence interval, based on a normal approximation, is often considered, but this interval can have poor statistical properties when the sample size is small and/or when the success probability is near 0 or 1. In this paper, an estimate of the risk difference based on median unbiased estimates (MUEs) of the two group probabilities is proposed. A corresponding confidence interval is derived using a fully specified bootstrap sample space. The proposed method is compared with Chen's quasi‐exact method, Wald intervals and Agresti and Caffo's method with regard to mean square error and coverage probability. For a variety of settings, the MUE‐based estimate of risk difference has mean square error uniformly smaller than maximum likelihood estimate within a certain range of risk difference. The fully specified bootstrap had better coverage probability in the tail area than Chen's quasi‐exact method, Wald intervals and Agresti and Caffo's intervals. Copyright © 2009 John Wiley & Sons, Ltd.
Efficient experimental design for binary matched pairs data
Authors: Lennox Kristin P. , Sherman Michael
Published: August 2009

The analysis of data from matched pairs binary experiments, often performed with McNemar's test, presents a unique experimental design challenge in dealing with the effect of the discordance probability, p. Most approaches for determining size and power use point estimates or maximization, but this fails to account for the considerable variability across values of the nuisance parameter that occur for all common tests. We recommend viewing the size and power functions across the full range of possible discordance probability values, which gives a complete picture of the behavior of a test for any given sample size. This method also allows us to compare the behavior of different hypothesis tests. We present exact power and size functions for several tests, including the original McNemar's test and its most common variants, and compare their properties. This analysis reveals that, in general, McNemar's test comes closest to the nominal size and has the highest power. We also demonstrate our technique using the transmission/disequilibrium test (TDT) to check for linkage between schizophrenia and a locus related to the D3 dopamine receptor, and on a hypnosis pain management data set. Copyright © 2009 John Wiley & Sons, Ltd.
Efficient interval estimation of a ratio of marginal probabilities in matched‐pair data: Non‐iterative method
Authors: Nam Jun‐Mo
Published: August 2009

Matched‐pair designs have been commonly employed in diagnostic, epidemiologic and laboratory studies. For estimation of a ratio of two marginal probabilities in matched‐pair data, a Wald‐type logarithmic method is computationally simple, but an actual coverage rate is known to be smaller than a nominal one and a length of the confidence interval is shorter than it should be. The Fieller‐type method based on constrained maximum likelihood (CML) estimators possesses asymptotically optimum statistical properties and a coverage rate is close to a nominal one. However, hitherto the limits have been obtained by numerical iterations. In this paper, we derive the efficient confidence limits based on CML as analytical solutions of a quartic equation and present the confidence limits in a closed form. Published in 2009 by John Wiley & Sons, Ltd.
Detecting SNP‐expression associations: A comparison of mutual information and median test with standard statistical approaches
Authors: Szymczak S. , Igl B.‐W. , Ziegler A.
Published: August 2009

Single nucleotide polymorphism‐gene expression associations have received increasing interest. The aim of these studies is discovering a difference in the location parameters of gene expressions given genotype. Because gene expressions often are highly skewed, heavy‐tailed or data of different genotypes vary in dispersion, the median is the most appropriate measure of location. In this case, model assumptions of standard statistical methods for comparing locations such as the analysis of variance (ANOVA) or the Kruskal–Wallis (KW) test are violated. Alternatives that might be more appropriate are the median test (MED) and tests based on mutual information (MI). In simulation studies these approaches and a novel MI test are compared with ANOVA and KW. Location, dispersion and skewness parameters of the gene expression distributions given genotypes are varied as well as genotype frequencies. The MED test and the novel MI‐based method keep the nominal significance levels for comparing medians if gene expression data are non‐normally distributed. ANOVA and KW have substantially inflated type I errors. They are, however, optimal if standard model assumptions are fulfilled. The MED test generally has larger power than MI and is therefore recommended if model assumptions of standard procedures are violated. A 300 kb region on chromosome 9p21.3, which is associated with coronary artery disease, was analyzed using the HapMap data. Only the alternative approaches were able to identify three genes (ADM, FCGR3B and ADORA1) as promising candidates to clarify the molecular mechanism of the genetic association. Copyright © 2009 John Wiley & Sons, Ltd.
Simultaneous confidence intervals using ordinal effect measures for ordered categorical outcomes
Authors: Ryu Euijung
Published: August 2009

When outcomes are ordered categorical, a model using an ordinal effect size measure is a good alternative of the cumulative logit model to compare several independent group differences. We present a method of constructing simultaneous confidence intervals for the ordinal effect size measures, using the studentized range distribution with the score test statistic. A simulation study shows that the proposed method performs well in terms of coverage probability, and it seems better than the method using a Bonferroni correction for Wald‐type statistics and methods that account for the dependencies among pairwise ordinal effect size measures using the multivariate normal distribution (or the multivariate t‐distribution for small samples). Copyright © 2009 John Wiley & Sons, Ltd.